Segmentation fault

Question

Segmentation fault

Closed this issue a year ago · 10 comments

Hi, I get Segmentation fault unfortunately:

$ ../v0.10.3/EnTAP/build/EnTAP  --runP -i trinity.faa -d /io/bin/EnTAP/test_data/test_data/bin/swiss_prot_test.dmnd --ini ../entap_config.ini
Segmentation fault

But no core file is dumped.

This is the debug file:

Wed Jul 29 10:43:04 2020: Start - EnTAP
Wed Jul 29 10:43:04 2020: Parsing ini file at: ../entap_config.ini
Wed Jul 29 10:43:04 2020: Success!
Wed Jul 29 10:43:04 2020: Printing user input...
Wed Jul 29 10:43:04 2020: ------------------------------------------------------
EnTAP Run Information - Execution
------------------------------------------------------
Current EnTAP Version: 0.10.3
Start time: Wed Jul 29 10:43:04 2020

Working directory has been set to: /io/bin/EnTAP/test_data/entap_outfiles
User Inputs:
out-dir: /io/bin/EnTAP/test_data/entap_outfiles
config: false
runP: true
runN: false
overwrite: false
ini: ../entap_config.ini
input: trinity.faa
database: /io/bin/EnTAP/test_data/test_data/bin/swiss_prot_test.dmnd,
graph: false
no-trim: false
threads: 1
state: +
no-check: false
output-format: 1,3,4,
entap-db-bin: /io/bin/EnTAP/bin/entap_database.bin
entap-db-sql: /io/bin/EnTAP/databases/entap_database.db
entap-graph: /io/bin/EnTAP/src/entap_graphing.py
data-generate: false
data-type: 0,
fpkm: 0.500000
align:
single-end: false
rsem-calculate-expression: /io/bin/EnTAP/libs/RSEM-1.3.0//rsem-calculate-expression
rsem-sam-validator: /io/bin/EnTAP/libs/RSEM-1.3.0//rsem-sam-validator
rsem-prepare-reference: /io/bin/EnTAP/libs/RSEM-1.3.0//rsem-prepare-reference
convert-sam-for-rsem: /io/bin/EnTAP/libs/RSEM-1.3.0//convert-sam-for-rsem
complete: false
frame-selection: 2
genemarkst-exe: gmst.pl
transdecoder-long-exe: /io/bin/EnTAP/libs/TransDecoder-v5.3.0/TransDecoder.LongOrfs
transdecoder-predict-exe: /io/bin/EnTAP/libs/TransDecoder-v5.3.0/TransDecoder.Predict
transdecoder-m: 100
diamond-exe: diamond
taxon:
qcoverage: 50.000000
tcoverage: 50.000000
contam:
e-value: 0.000010
uninformative:
ontology: 0,
level: 1,
eggnog-sql: /io/bin/EnTAP/databases/eggnog.db
eggnog-dmnd: /io/bin/EnTAP/bin/eggnog_proteins.dmnd
interproscan-exe: interproscan.sh
protein:


Wed Jul 29 10:43:04 2020: User has input a database at: /io/bin/EnTAP/test_data/test_data/bin/swiss_prot_test.dmnd
Wed Jul 29 10:43:04 2020: Verifying EnTAP database...
Wed Jul 29 10:43:04 2020: Reading serialized database from: /io/bin/EnTAP/bin/entap_database.bin
 Of type: 2
Wed Jul 29 10:43:22 2020: Success!
Wed Jul 29 10:43:22 2020: Spawn Object - QueryData
Wed Jul 29 10:43:22 2020: Generating transcriptome mappings...
Wed Jul 29 10:43:22 2020: Transcriptome Lines - START
Wed Jul 29 10:43:22 2020: >TRINITY_DN10010_c0_g1_i1len=1162path=[2421:0-4412422:442-4652423:466-4732436:474-6542435:655-9162431:917-9402432:941-1161][-1,2421,2422,2423,2436,2435,2431,2432,-2]
Wed Jul 29 10:43:22 2020: MATHTTTSCIVKPPATIPHFSHKHKVHSLLHSNCLPKFIPFLQKGWPCHGININISRLNV
Wed Jul 29 10:43:22 2020: RKAGSKLARTGRVISPVAALPEALLFDCDGVLVDTERDGHRVSFNEAFSEKGLNVTWDVD
Wed Jul 29 10:43:22 2020: LYGELLKIGGGKERMTAYFNKTGWPDIAPSTEGERKELIASLHRRKTQLFMALIEKRLLP
Wed Jul 29 10:43:22 2020: LRPGVARLIDEALEKGVKVAICSTSNEKAVSAIVQCLLGPPRADAISIFAGDIVPHKKPD
Wed Jul 29 10:43:22 2020: PAIYLLAATTLGVGTSRCVVIEDSAIGLAAAKAAGMKCIVTKSGYTVEEYFTSADAIFDD
Wed Jul 29 10:43:22 2020: IGDPPNANFDLNFCGNLLEKQYAS
Wed Jul 29 10:43:22 2020: >TRINITY_DN10060_c0_g1_i1len=652path=[1293:0-4071294:408-4381295:439-651][-1,1293,1294,1295,-2]
Wed Jul 29 10:43:22 2020: ERGVAGLYRGIGSNLASSAPISGIYTFTYESVKAALLPHLEKEYHAFAHCVAGGCASIAT
Wed Jul 29 10:43:22 2020: Transcriptome Lines - END
Wed Jul 29 10:43:22 2020: Success!
Wed Jul 29 10:43:22 2020: Verifying input flag fpkm
Wed Jul 29 10:43:22 2020: Verifying input flag qcoverage
Wed Jul 29 10:43:22 2020: Verifying input flag tcoverage
Wed Jul 29 10:43:22 2020: Verifying input flag ontology
Wed Jul 29 10:43:22 2020: Verifying input flag frame-selection
Wed Jul 29 10:43:22 2020: Verifying input flag transdecoder-m
Wed Jul 29 10:43:22 2020: Determining if we want to run expression analysis
Wed Jul 29 10:43:22 2020: NO, no alignment file specified from user
Wed Jul 29 10:43:22 2020: Determining if we want to run frame selection...
Wed Jul 29 10:43:22 2020: NO Protein sequences input AND runP, skipping frame selection
Wed Jul 29 10:43:22 2020: Verifying software...
Wed Jul 29 10:43:22 2020: Executing command:
diamond --version
Wed Jul 29 10:43:22 2020:
Std Err:

Wed Jul 29 10:43:22 2020: Verifying EggNOG inputs...
Wed Jul 29 10:43:22 2020: Executing command:
diamond --version
Wed Jul 29 10:43:22 2020:
Std Err:

Wed Jul 29 10:43:22 2020: Success!
Wed Jul 29 10:43:22 2020: Success!
Wed Jul 29 10:43:22 2020: Success! Input verified
Wed Jul 29 10:43:22 2020: Killing Object - EntapDatabase
Wed Jul 29 10:43:25 2020: Killing Object - QueryData
Wed Jul 29 10:43:25 2020: QuerySequence data freed
Wed Jul 29 10:43:25 2020: EnTAP Executing...
Wed Jul 29 10:43:25 2020: verifying state...
Wed Jul 29 10:43:26 2020: verifying state...
Wed Jul 29 10:43:26 2020: Success!
Wed Jul 29 10:43:26 2020: Spawn Object - QueryData
Wed Jul 29 10:43:26 2020: Generating transcriptome mappings...
Wed Jul 29 10:43:26 2020: Transcriptome Lines - START
Wed Jul 29 10:43:26 2020: >TRINITY_DN10010_c0_g1_i1len=1162path=[2421:0-4412422:442-4652423:466-4732436:474-6542435:655-9162431:917-9402432:941-1161][-1,2421,2422,2423,2436,2435,2431,2432,-2]
Wed Jul 29 10:43:26 2020: MATHTTTSCIVKPPATIPHFSHKHKVHSLLHSNCLPKFIPFLQKGWPCHGININISRLNV
Wed Jul 29 10:43:26 2020: RKAGSKLARTGRVISPVAALPEALLFDCDGVLVDTERDGHRVSFNEAFSEKGLNVTWDVD
Wed Jul 29 10:43:26 2020: LYGELLKIGGGKERMTAYFNKTGWPDIAPSTEGERKELIASLHRRKTQLFMALIEKRLLP
Wed Jul 29 10:43:26 2020: LRPGVARLIDEALEKGVKVAICSTSNEKAVSAIVQCLLGPPRADAISIFAGDIVPHKKPD
Wed Jul 29 10:43:26 2020: PAIYLLAATTLGVGTSRCVVIEDSAIGLAAAKAAGMKCIVTKSGYTVEEYFTSADAIFDD
Wed Jul 29 10:43:26 2020: IGDPPNANFDLNFCGNLLEKQYAS
Wed Jul 29 10:43:26 2020: >TRINITY_DN10060_c0_g1_i1len=652path=[1293:0-4071294:408-4381295:439-651][-1,1293,1294,1295,-2]
Wed Jul 29 10:43:26 2020: ERGVAGLYRGIGSNLASSAPISGIYTFTYESVKAALLPHLEKEYHAFAHCVAGGCASIAT
Wed Jul 29 10:43:26 2020: Transcriptome Lines - END
Wed Jul 29 10:43:26 2020: Success!
Wed Jul 29 10:43:26 2020: Spawn Object - GraphingManager
Wed Jul 29 10:43:26 2020: Executing command:
python /io/bin/EnTAP/src/entap_graphing.py -g -1
Wed Jul 29 10:43:43 2020:
Std Err:
/share/home/yuanqyk/.local/lib/python2.7/site-packages/pkg_resources/__init__.py:1299: UserWarning: /share/home/nature/.cache/Python-Eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
  warnings.warn(msg, UserWarning)

Wed Jul 29 10:43:43 2020: Graphing is supported
Wed Jul 29 10:43:43 2020: Reading serialized database from: /io/bin/EnTAP/bin/entap_database.bin
 Of type: 2
Wed Jul 29 10:44:02 2020: STATE - EXPRESSION FILTERING
Wed Jul 29 10:44:02 2020: Determining if we want to run expression analysis
Wed Jul 29 10:44:02 2020: NO, no alignment file specified from user
Wed Jul 29 10:44:02 2020: No alignment file specified, skipping expression analysis
Wed Jul 29 10:44:02 2020: verifying state...
Wed Jul 29 10:44:02 2020: STATE - FRAME SELECTION
Wed Jul 29 10:44:02 2020: Determining if we want to run frame selection...
Wed Jul 29 10:44:02 2020: NO Protein sequences input AND runP, skipping frame selection
Wed Jul 29 10:44:02 2020: verifying state...
Wed Jul 29 10:44:02 2020: Beginning to copy final transcriptome to be used...
Wed Jul 29 10:44:02 2020: FINAL transcriptome generated to: /io/bin/EnTAP/test_data/entap_outfiles/transcriptomes//trinity_final.fasta
Wed Jul 29 10:44:02 2020: verifying state...
Wed Jul 29 10:44:02 2020: STATE - SIMILARITY SEARCH
Wed Jul 29 10:44:02 2020: Spawn Object - SimilaritySearch
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/best_hits_no_contam_lvl0.faa
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/best_hits_lvl0.tsv
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/no_hits.faa
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/best_hits_no_contam_lvl0.fnn
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/best_hits_lvl0.fnn
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/best_hits_contam_lvl0.faa
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/best_hits_contam_lvl0.fnn
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/best_hits_no_contam_lvl0.tsv
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/no_hits.fnn
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/unselected_lvl0.tsv
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/figures/_summary_bar.txt
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/figures/_species_bar.png
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/figures/_species_bar.txt
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/figures/_summary_bar.png
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/best_hits_lvl0.faa
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/best_hits_contam_lvl0.tsv
Wed Jul 29 10:44:02 2020: Setting working directory to: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND
Wed Jul 29 10:44:02 2020: Success! Working directory set
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/best_hits_no_contam_lvl0.faa
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/best_hits_lvl0.tsv
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/no_hits.faa
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/best_hits_no_contam_lvl0.fnn
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/best_hits_lvl0.fnn
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/best_hits_contam_lvl0.faa
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/best_hits_contam_lvl0.fnn
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/best_hits_no_contam_lvl0.tsv
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/no_hits.fnn
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/unselected_lvl0.tsv
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/figures/_summary_bar.txt
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/figures/_species_bar.png
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/figures/_species_bar.txt
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/figures/_summary_bar.png
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/best_hits_lvl0.faa
Wed Jul 29 10:44:02 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/best_hits_contam_lvl0.tsv
Wed Jul 29 10:44:02 2020: Spawn Object - ModDiamond
Wed Jul 29 10:44:02 2020: Verifying previous execution of database: /io/bin/EnTAP/test_data/test_data/bin/swiss_prot_test.dmnd...
Wed Jul 29 10:44:02 2020: File for database swiss_prot_test does not exist.
/io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_trinity_final_swiss_prot_test.out
Wed Jul 29 10:44:02 2020: Success! Verified files for DIAMOND, continuing...
Wed Jul 29 10:44:02 2020: Executing DIAMOND for necessary files....
Wed Jul 29 10:44:02 2020: File not found, executing against database at: /io/bin/EnTAP/test_data/test_data/bin/swiss_prot_test.dmnd
Wed Jul 29 10:44:02 2020: Executing command:
diamond blastp -f 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp stitle -o /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_trinity_final_swiss_prot_test.out -p 1 --more-sensitive  --evalue 0.000010 -d /io/bin/EnTAP/test_data/test_data/bin/swiss_prot_test.dmnd -q /io/bin/EnTAP/test_data/entap_outfiles/transcriptomes//trinity_final.fasta --top 3 --subject-cover 50.000000 --query-cover 50.000000
Wed Jul 29 10:44:02 2020:
Std Err:
diamond v0.9.24.125 | by Benjamin Buchfink <buchfink@gmail.com>
Licensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>
Check http://github.com/bbuchfink/diamond for updates.

#CPU threads: 1
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND
Opening the database...  [6.9e-05s]
Percentage range of top alignment score to report hits: 3
Opening the input file...  [3.9e-05s]
Opening the output file...  [2.4e-05s]
Loading query sequences...  [5.3e-05s]
Masking queries...  [0.001023s]
Building query seed set...  [0.000178s]
Algorithm: Double-indexed
Building query histograms...  [0.000536s]
Allocating buffers...  [7.8e-05s]
Loading reference sequences...  [3.9e-05s]
Building reference histograms...  [0.001043s]
Allocating buffers...  [6.7e-05s]
Initializing temporary storage...  [0.000518s]
Processing query chunk 0, reference chunk 0, shape 0, index chunk 0.
Building reference index...  [0.000529s]
Building query index...  [0.000329s]
Building seed filter...  [0.000189s]
Searching alignments...  [0.001507s]
Processing query chunk 0, reference chunk 0, shape 0, index chunk 1.
Building reference index...  [0.000431s]
Building query index...  [0.000329s]
Building seed filter...  [0.000168s]
Searching alignments...  [0.001648s]
Processing query chunk 0, reference chunk 0, shape 0, index chunk 2.
Building reference index...  [0.000448s]
Building query index...  [0.000343s]
Building seed filter...  [0.000165s]
Searching alignments...  [0.001628s]
Processing query chunk 0, reference chunk 0, shape 0, index chunk 3.
Building reference index...  [0.000423s]
Building query index...  [0.000315s]
Building seed filter...  [0.000166s]
Searching alignments...  [0.001539s]
Processing query chunk 0, reference chunk 0, shape 1, index chunk 0.
Building reference index...  [0.000415s]
Building query index...  [0.000319s]
Building seed filter...  [0.000165s]
Searching alignments...  [0.001476s]
Processing query chunk 0, reference chunk 0, shape 1, index chunk 1.
Building reference index...  [0.000435s]
Building query index...  [0.000334s]
Building seed filter...  [0.000167s]
Searching alignments...  [0.001494s]
Processing query chunk 0, reference chunk 0, shape 1, index chunk 2.
Building reference index...  [0.000452s]
Building query index...  [0.000341s]
Building seed filter...  [0.000168s]
Searching alignments...  [0.001488s]
Processing query chunk 0, reference chunk 0, shape 1, index chunk 3.
Building reference index...  [0.000411s]
Building query index...  [0.000323s]
Building seed filter...  [0.000165s]
Searching alignments...  [0.00151s]
Processing query chunk 0, reference chunk 0, shape 2, index chunk 0.
Building reference index...  [0.000405s]
Building query index...  [0.000317s]
Building seed filter...  [0.000164s]
Searching alignments...  [0.001451s]
Processing query chunk 0, reference chunk 0, shape 2, index chunk 1.
Building reference index...  [0.000424s]
Building query index...  [0.000325s]
Building seed filter...  [0.00016s]
Searching alignments...  [0.001469s]
Processing query chunk 0, reference chunk 0, shape 2, index chunk 2.
Building reference index...  [0.000415s]
Building query index...  [0.00033s]
Building seed filter...  [0.000161s]
Searching alignments...  [0.001487s]
Processing query chunk 0, reference chunk 0, shape 2, index chunk 3.
Building reference index...  [0.000399s]
Building query index...  [0.000318s]
Building seed filter...  [0.000161s]
Searching alignments...  [0.001504s]
Processing query chunk 0, reference chunk 0, shape 3, index chunk 0.
Building reference index...  [0.000386s]
Building query index...  [0.000316s]
Building seed filter...  [0.000159s]
Searching alignments...  [0.001448s]
Processing query chunk 0, reference chunk 0, shape 3, index chunk 1.
Building reference index...  [0.000406s]
Building query index...  [0.000317s]
Building seed filter...  [0.000161s]
Searching alignments...  [0.001493s]
Processing query chunk 0, reference chunk 0, shape 3, index chunk 2.
Building reference index...  [0.000415s]
Building query index...  [0.000325s]
Building seed filter...  [0.000161s]
Searching alignments...  [0.001487s]
Processing query chunk 0, reference chunk 0, shape 3, index chunk 3.
Building reference index...  [0.000375s]
Building query index...  [0.000316s]
Building seed filter...  [0.000165s]
Searching alignments...  [0.001488s]
Processing query chunk 0, reference chunk 0, shape 4, index chunk 0.
Building reference index...  [0.000383s]
Building query index...  [0.000312s]
Building seed filter...  [0.000162s]
Searching alignments...  [0.001464s]
Processing query chunk 0, reference chunk 0, shape 4, index chunk 1.
Building reference index...  [0.00041s]
Building query index...  [0.000328s]
Building seed filter...  [0.000159s]
Searching alignments...  [0.001488s]
Processing query chunk 0, reference chunk 0, shape 4, index chunk 2.
Building reference index...  [0.000421s]
Building query index...  [0.000318s]
Building seed filter...  [0.000158s]
Searching alignments...  [0.001531s]
Processing query chunk 0, reference chunk 0, shape 4, index chunk 3.
Building reference index...  [0.00038s]
Building query index...  [0.000318s]
Building seed filter...  [0.000161s]
Searching alignments...  [0.001489s]
Processing query chunk 0, reference chunk 0, shape 5, index chunk 0.
Building reference index...  [0.000384s]
Building query index...  [0.000305s]
Building seed filter...  [0.000165s]
Searching alignments...  [0.001488s]
Processing query chunk 0, reference chunk 0, shape 5, index chunk 1.
Building reference index...  [0.000403s]
Building query index...  [0.000328s]
Building seed filter...  [0.000165s]
Searching alignments...  [0.001461s]
Processing query chunk 0, reference chunk 0, shape 5, index chunk 2.
Building reference index...  [0.000415s]
Building query index...  [0.000333s]
Building seed filter...  [0.00016s]
Searching alignments...  [0.001476s]
Processing query chunk 0, reference chunk 0, shape 5, index chunk 3.
Building reference index...  [0.000382s]
Building query index...  [0.000301s]
Building seed filter...  [0.000156s]
Searching alignments...  [0.001475s]
Processing query chunk 0, reference chunk 0, shape 6, index chunk 0.
Building reference index...  [0.00038s]
Building query index...  [0.000313s]
Building seed filter...  [0.00016s]
Searching alignments...  [0.001465s]
Processing query chunk 0, reference chunk 0, shape 6, index chunk 1.
Building reference index...  [0.00041s]
Building query index...  [0.000321s]
Building seed filter...  [0.000162s]
Searching alignments...  [0.001467s]
Processing query chunk 0, reference chunk 0, shape 6, index chunk 2.
Building reference index...  [0.000413s]
Building query index...  [0.000327s]
Building seed filter...  [0.000163s]
Searching alignments...  [0.001459s]
Processing query chunk 0, reference chunk 0, shape 6, index chunk 3.
Building reference index...  [0.000373s]
Building query index...  [0.000323s]
Building seed filter...  [0.000156s]
Searching alignments...  [0.001488s]
Processing query chunk 0, reference chunk 0, shape 7, index chunk 0.
Building reference index...  [0.000384s]
Building query index...  [0.000305s]
Building seed filter...  [0.000156s]
Searching alignments...  [0.001447s]
Processing query chunk 0, reference chunk 0, shape 7, index chunk 1.
Building reference index...  [0.000406s]
Building query index...  [0.000323s]
Building seed filter...  [0.000157s]
Searching alignments...  [0.001453s]
Processing query chunk 0, reference chunk 0, shape 7, index chunk 2.
Building reference index...  [0.000446s]
Building query index...  [0.000325s]
Building seed filter...  [0.000162s]
Searching alignments...  [0.001471s]
Processing query chunk 0, reference chunk 0, shape 7, index chunk 3.
Building reference index...  [0.000374s]
Building query index...  [0.000313s]
Building seed filter...  [0.000162s]
Searching alignments...  [0.001534s]
Processing query chunk 0, reference chunk 0, shape 8, index chunk 0.
Building reference index...  [0.000383s]
Building query index...  [0.000324s]
Building seed filter...  [0.000158s]
Searching alignments...  [0.001451s]
Processing query chunk 0, reference chunk 0, shape 8, index chunk 1.
Building reference index...  [0.000409s]
Building query index...  [0.000318s]
Building seed filter...  [0.000157s]
Searching alignments...  [0.001496s]
Processing query chunk 0, reference chunk 0, shape 8, index chunk 2.
Building reference index...  [0.000418s]
Building query index...  [0.000334s]
Building seed filter...  [0.000156s]
Searching alignments...  [0.001463s]
Processing query chunk 0, reference chunk 0, shape 8, index chunk 3.
Building reference index...  [0.000399s]
Building query index...  [0.000314s]
Building seed filter...  [0.000162s]
Searching alignments...  [0.001489s]
Processing query chunk 0, reference chunk 0, shape 9, index chunk 0.
Building reference index...  [0.000377s]
Building query index...  [0.000311s]
Building seed filter...  [0.000159s]
Searching alignments...  [0.001459s]
Processing query chunk 0, reference chunk 0, shape 9, index chunk 1.
Building reference index...  [0.000406s]
Building query index...  [0.000324s]
Building seed filter...  [0.000157s]
Searching alignments...  [0.00146s]
Processing query chunk 0, reference chunk 0, shape 9, index chunk 2.
Building reference index...  [0.000411s]
Building query index...  [0.000319s]
Building seed filter...  [0.000161s]
Searching alignments...  [0.001513s]
Processing query chunk 0, reference chunk 0, shape 9, index chunk 3.
Building reference index...  [0.000412s]
Building query index...  [0.000333s]
Building seed filter...  [0.000163s]
Searching alignments...  [0.001499s]
Processing query chunk 0, reference chunk 0, shape 10, index chunk 0.
Building reference index...  [0.000425s]
Building query index...  [0.000312s]
Building seed filter...  [0.000165s]
Searching alignments...  [0.001467s]
Processing query chunk 0, reference chunk 0, shape 10, index chunk 1.
Building reference index...  [0.000435s]
Building query index...  [0.000338s]
Building seed filter...  [0.00017s]
Searching alignments...  [0.001484s]
Processing query chunk 0, reference chunk 0, shape 10, index chunk 2.
Building reference index...  [0.000455s]
Building query index...  [0.000341s]
Building seed filter...  [0.000165s]
Searching alignments...  [0.001497s]
Processing query chunk 0, reference chunk 0, shape 10, index chunk 3.
Building reference index...  [0.000381s]
Building query index...  [0.000329s]
Building seed filter...  [0.00016s]
Searching alignments...  [0.001503s]
Processing query chunk 0, reference chunk 0, shape 11, index chunk 0.
Building reference index...  [0.000401s]
Building query index...  [0.00031s]
Building seed filter...  [0.000159s]
Searching alignments...  [0.001466s]
Processing query chunk 0, reference chunk 0, shape 11, index chunk 1.
Building reference index...  [0.0004s]
Building query index...  [0.000319s]
Building seed filter...  [0.000157s]
Searching alignments...  [0.001462s]
Processing query chunk 0, reference chunk 0, shape 11, index chunk 2.
Building reference index...  [0.000416s]
Building query index...  [0.000331s]
Building seed filter...  [0.000162s]
Searching alignments...  [0.001476s]
Processing query chunk 0, reference chunk 0, shape 11, index chunk 3.
Building reference index...  [0.000373s]
Building query index...  [0.000315s]
Building seed filter...  [0.000156s]
Searching alignments...  [0.001469s]
Processing query chunk 0, reference chunk 0, shape 12, index chunk 0.
Building reference index...  [0.000377s]
Building query index...  [0.000316s]
Building seed filter...  [0.000157s]
Searching alignments...  [0.001466s]
Processing query chunk 0, reference chunk 0, shape 12, index chunk 1.
Building reference index...  [0.000412s]
Building query index...  [0.000325s]
Building seed filter...  [0.00016s]
Searching alignments...  [0.001515s]
Processing query chunk 0, reference chunk 0, shape 12, index chunk 2.
Building reference index...  [0.00041s]
Building query index...  [0.00033s]
Building seed filter...  [0.000158s]
Searching alignments...  [0.001468s]
Processing query chunk 0, reference chunk 0, shape 12, index chunk 3.
Building reference index...  [0.00038s]
Building query index...  [0.000308s]
Building seed filter...  [0.000156s]
Searching alignments...  [0.001461s]
Processing query chunk 0, reference chunk 0, shape 13, index chunk 0.
Building reference index...  [0.000378s]
Building query index...  [0.00031s]
Building seed filter...  [0.000163s]
Searching alignments...  [0.001461s]
Processing query chunk 0, reference chunk 0, shape 13, index chunk 1.
Building reference index...  [0.000405s]
Building query index...  [0.000316s]
Building seed filter...  [0.000159s]
Searching alignments...  [0.001464s]
Processing query chunk 0, reference chunk 0, shape 13, index chunk 2.
Building reference index...  [0.00042s]
Building query index...  [0.000327s]
Building seed filter...  [0.00016s]
Searching alignments...  [0.001504s]
Processing query chunk 0, reference chunk 0, shape 13, index chunk 3.
Building reference index...  [0.000373s]
Building query index...  [0.000318s]
Building seed filter...  [0.000161s]
Searching alignments...  [0.001473s]
Processing query chunk 0, reference chunk 0, shape 14, index chunk 0.
Building reference index...  [0.00038s]
Building query index...  [0.000314s]
Building seed filter...  [0.000161s]
Searching alignments...  [0.00149s]
Processing query chunk 0, reference chunk 0, shape 14, index chunk 1.
Building reference index...  [0.000406s]
Building query index...  [0.000326s]
Building seed filter...  [0.000165s]
Searching alignments...  [0.001479s]
Processing query chunk 0, reference chunk 0, shape 14, index chunk 2.
Building reference index...  [0.000421s]
Building query index...  [0.000317s]
Building seed filter...  [0.000154s]
Searching alignments...  [0.001454s]
Processing query chunk 0, reference chunk 0, shape 14, index chunk 3.
Building reference index...  [0.000383s]
Building query index...  [0.000312s]
Building seed filter...  [0.000158s]
Searching alignments...  [0.001477s]
Processing query chunk 0, reference chunk 0, shape 15, index chunk 0.
Building reference index...  [0.000376s]
Building query index...  [0.000339s]
Building seed filter...  [0.000158s]
Searching alignments...  [0.00149s]
Processing query chunk 0, reference chunk 0, shape 15, index chunk 1.
Building reference index...  [0.000406s]
Building query index...  [0.000322s]
Building seed filter...  [0.000159s]
Searching alignments...  [0.001509s]
Processing query chunk 0, reference chunk 0, shape 15, index chunk 2.
Building reference index...  [0.000415s]
Building query index...  [0.000326s]
Building seed filter...  [0.000155s]
Searching alignments...  [0.00146s]
Processing query chunk 0, reference chunk 0, shape 15, index chunk 3.
Building reference index...  [0.000378s]
Building query index...  [0.000302s]
Building seed filter...  [0.000158s]
Searching alignments...  [0.001488s]
Deallocating buffers...  [6e-06s]
Computing alignments...  [0.002119s]
Deallocating reference...  [5e-06s]
Loading reference sequences...  [1.5e-05s]
Deallocating buffers...  [4e-06s]
Deallocating queries...  [6e-06s]
Loading query sequences...  [1.7e-05s]
Closing the input file...  [1.9e-05s]
Closing the output file...  [3.4e-05s]
Closing the database file...  [9e-06s]
Deallocating taxonomy...  [4e-06s]
Total time = 0.162353s
Reported 5 pairwise alignments, 5 HSPs.
5 queries aligned.

Wed Jul 29 10:44:02 2020:
Printing to files:
Std Out: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_trinity_final_swiss_prot_test.out_std.out
Std Err: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_trinity_final_swiss_prot_test.out_std.err
Wed Jul 29 10:44:02 2020: Success! Results written to: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_trinity_final_swiss_prot_test.out
Wed Jul 29 10:44:02 2020: Beginning to filter individual DIAMOND files...
Wed Jul 29 10:44:02 2020: DIAMOND file located at /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_trinity_final_swiss_prot_test.out being parsed
Wed Jul 29 10:44:02 2020: Database file at /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_trinity_final_swiss_prot_test.out
Determined to be UniProt
Wed Jul 29 10:44:02 2020: File parsed, calculating statistics and writing output...
Wed Jul 29 10:44:02 2020: GraphingManager - initializing graphing data at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/figures//_species_bar.txt
Wed Jul 29 10:44:02 2020: GraphingManager - initializing graphing data at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/figures//_summary_bar.txt
Wed Jul 29 10:44:02 2020: Executing command:
python /io/bin/EnTAP/src/entap_graphing.py -o /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/figures//_species_bar.png -t swiss_prot_test_Top_10_Species_Distribution -g 0 -i /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/figures//_species_bar.txt
Wed Jul 29 10:44:17 2020:
Std Err:
/share/home/yuanqyk/.local/lib/python2.7/site-packages/pkg_resources/__init__.py:1299: UserWarning: /share/home/nature/.cache/Python-Eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
  warnings.warn(msg, UserWarning)

Wed Jul 29 10:44:17 2020: GraphingManager - closing graphing file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/figures//_species_bar.txt
Wed Jul 29 10:44:17 2020: GraphingManager - closing graphing file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/figures//_species_bar.txt
Wed Jul 29 10:44:17 2020: Executing command:
python /io/bin/EnTAP/src/entap_graphing.py -o /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/figures//_summary_bar.png -t swiss_prot_test_Summary -g 7 -i /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/figures//_summary_bar.txt
Wed Jul 29 10:44:31 2020:
Std Err:
/share/home/yuanqyk/.local/lib/python2.7/site-packages/pkg_resources/__init__.py:1299: UserWarning: /share/home/nature/.cache/Python-Eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
  warnings.warn(msg, UserWarning)

Wed Jul 29 10:44:31 2020: GraphingManager - closing graphing file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/figures//_summary_bar.txt
Wed Jul 29 10:44:31 2020: GraphingManager - closing graphing file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/processed//swiss_prot_test/figures//_summary_bar.txt
Wed Jul 29 10:44:31 2020: Success!
Wed Jul 29 10:44:31 2020: Calculating overall Similarity Searching statistics...
Wed Jul 29 10:44:31 2020: GraphingManager - initializing graphing data at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/figures//_species_bar.txt
Wed Jul 29 10:44:31 2020: GraphingManager - initializing graphing data at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/figures//_summary_bar.txt
Wed Jul 29 10:44:31 2020: Executing command:
python /io/bin/EnTAP/src/entap_graphing.py -o /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/figures//_species_bar.png -t _Top_10_Species_Distribution -g 0 -i /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/figures//_species_bar.txt
Wed Jul 29 10:44:45 2020:
Std Err:
/share/home/yuanqyk/.local/lib/python2.7/site-packages/pkg_resources/__init__.py:1299: UserWarning: /share/home/nature/.cache/Python-Eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
  warnings.warn(msg, UserWarning)

Wed Jul 29 10:44:45 2020: GraphingManager - closing graphing file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/figures//_species_bar.txt
Wed Jul 29 10:44:45 2020: GraphingManager - closing graphing file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/figures//_species_bar.txt
Wed Jul 29 10:44:45 2020: Executing command:
python /io/bin/EnTAP/src/entap_graphing.py -o /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/figures//_summary_bar.png -t _Summary -g 7 -i /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/figures//_summary_bar.txt
Wed Jul 29 10:45:00 2020:
Std Err:
/share/home/yuanqyk/.local/lib/python2.7/site-packages/pkg_resources/__init__.py:1299: UserWarning: /share/home/nature/.cache/Python-Eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
  warnings.warn(msg, UserWarning)

Wed Jul 29 10:45:00 2020: GraphingManager - closing graphing file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/figures//_summary_bar.txt
Wed Jul 29 10:45:00 2020: GraphingManager - closing graphing file at: /io/bin/EnTAP/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/figures//_summary_bar.txt
Wed Jul 29 10:45:00 2020: Success!
Wed Jul 29 10:45:00 2020: Setting working directory to: /io/bin/EnTAP/test_data/entap_outfiles
Wed Jul 29 10:45:00 2020: Success! Working directory set
Wed Jul 29 10:45:00 2020: verifying state...
Wed Jul 29 10:45:00 2020: STATE - GENE ONTOLOGY
Wed Jul 29 10:45:00 2020: Spawn Object - Ontology
Wed Jul 29 10:45:00 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/ontology//EggNOG_DMND/processed//unannotated_sequences_lvl0.tsv
Wed Jul 29 10:45:00 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/ontology//EggNOG_DMND/processed//unannotated_sequences_lvl0.faa
Wed Jul 29 10:45:00 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/ontology//EggNOG_DMND/processed//annotated_sequences_lvl0.tsv
Wed Jul 29 10:45:00 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/ontology//EggNOG_DMND/processed//annotated_sequences_lvl0.faa
Wed Jul 29 10:45:00 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/ontology//EggNOG_DMND/processed//annotated_sequences_lvl0.fnn
Wed Jul 29 10:45:00 2020: Deleting file at: /io/bin/EnTAP/test_data/entap_outfiles/ontology//EggNOG_DMND/processed//unannotated_sequences_lvl0.fnn
Wed Jul 29 10:45:00 2020: Setting working directory to: /io/bin/EnTAP/test_data/entap_outfiles/ontology//EggNOG_DMND
Wed Jul 29 10:45:00 2020: Success! Working directory set
Wed Jul 29 10:45:00 2020: Spawn Object - ModEggnogDMND
Wed Jul 29 10:45:00 2020: Overwrite was unselected, verifying output files...
Wed Jul 29 10:45:00 2020:
File Status at: /io/bin/EnTAP/test_data/entap_outfiles/ontology//EggNOG_DMND/blastp_trinity_eggnog_proteins.out
    Error: File empty
    Error: File could not be found
    Error: File could not be opened
Wed Jul 29 10:45:00 2020: Errors in opening file, continuing with execution...
Wed Jul 29 10:45:00 2020: Running EggNOG against Diamond database...
Wed Jul 29 10:45:00 2020: Executing command:
diamond blastp -d /io/bin/EnTAP/bin/eggnog_proteins.dmnd --top 1 --more-sensitive -q /io/bin/EnTAP/test_data/entap_outfiles/transcriptomes//trinity_final.fasta -o /io/bin/EnTAP/test_data/entap_outfiles/ontology//EggNOG_DMND/blastp_trinity_eggnog_proteins.out -p 1 -f 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp stitle
Wed Jul 29 10:46:47 2020:
Std Err:
diamond v0.9.24.125 | by Benjamin Buchfink <buchfink@gmail.com>
Licensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>
Check http://github.com/bbuchfink/diamond for updates.

#CPU threads: 1
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: /io/bin/EnTAP/test_data/entap_outfiles/ontology//EggNOG_DMND
Opening the database...  [7.7e-05s]
Percentage range of top alignment score to report hits: 1
Opening the input file...  [3.2e-05s]
Opening the output file...  [2.4e-05s]
Loading query sequences...  [5e-05s]
Masking queries...  [0.001077s]
Building query seed set...  [0.0002s]
Algorithm: Query-indexed
Building query histograms...  [5.5e-05s]
Allocating buffers...  [1.5e-05s]
Loading reference sequences...  [3.33054s]
Building reference histograms...  [5.02621s]
Allocating buffers...  [2.1e-05s]
Initializing temporary storage...  [0.000517s]
Processing query chunk 0, reference chunk 0, shape 0, index chunk 0.
Building reference index...  [12.4737s]
Building query index...  [0.000378s]
Building seed filter...  [0.207188s]
Searching alignments...  [5.84974s]
Deallocating buffers...  [0.07934s]
Opening temporary output file...  [9.5e-05s]
Computing alignments...  [0.015997s]
Deallocating reference...  [0.007271s]
Loading reference sequences...  [2.73108s]
Building reference histograms...  [4.98739s]
Allocating buffers...  [1.8e-05s]
Initializing temporary storage...  [0.000344s]
Processing query chunk 0, reference chunk 1, shape 0, index chunk 0.
Building reference index...  [11.4227s]
Building query index...  [0.000373s]
Building seed filter...  [0.250632s]
Searching alignments...  [5.53865s]
Deallocating buffers...  [0.065763s]
Opening temporary output file...  [8.8e-05s]
Computing alignments...  [0.034929s]
Deallocating reference...  [0.007077s]
Loading reference sequences...  [2.69105s]
Building reference histograms...  [4.99575s]
Allocating buffers...  [1.6e-05s]
Initializing temporary storage...  [0.000345s]
Processing query chunk 0, reference chunk 2, shape 0, index chunk 0.
Building reference index...  [11.5641s]
Building query index...  [0.00023s]
Building seed filter...  [0.204025s]
Searching alignments...  [5.84367s]
Deallocating buffers...  [0.074795s]
Opening temporary output file...  [8.2e-05s]
Computing alignments...  [0.051504s]
Deallocating reference...  [0.004585s]
Loading reference sequences...  [2.67511s]
Building reference histograms...  [4.96111s]
Allocating buffers...  [1.6e-05s]
Initializing temporary storage...  [0.00034s]
Processing query chunk 0, reference chunk 3, shape 0, index chunk 0.
Building reference index...  [11.463s]
Building query index...  [0.000218s]
Building seed filter...  [0.205797s]
Searching alignments...  [6.04628s]
Deallocating buffers...  [0.068174s]
Opening temporary output file...  [8.1e-05s]
Computing alignments...  [0.034202s]
Deallocating reference...  [0.00573s]
Loading reference sequences...  [0.542382s]
Building reference histograms...  [1.00604s]
Allocating buffers...  [1.7e-05s]
Initializing temporary storage...  [0.000475s]
Processing query chunk 0, reference chunk 4, shape 0, index chunk 0.
Building reference index...  [1.78007s]
Building query index...  [0.000238s]
Building seed filter...  [0.040044s]
Searching alignments...  [0.781819s]
Deallocating buffers...  [0.000764s]
Opening temporary output file...  [0.000124s]
Computing alignments...  [0.012633s]
Deallocating reference...  [0.002054s]
Loading reference sequences...  [2.4e-05s]
Deallocating buffers...  [1.1e-05s]
Joining output blocks...  [0.000458s]
Deallocating queries...  [0.002196s]
Loading query sequences...  [3e-05s]
Closing the input file...  [1.8e-05s]
Closing the output file...  [2.9e-05s]
Closing the database file...  [1e-05s]
Deallocating taxonomy...  [5e-06s]
Total time = 107.093s
Reported 7 pairwise alignments, 7 HSPs.
5 queries aligned.

Wed Jul 29 10:46:47 2020:
Printing to files:
Std Out: /io/bin/EnTAP/test_data/entap_outfiles/ontology//EggNOG_DMND/blastp_trinity_eggnog_proteins__std.out
Std Err: /io/bin/EnTAP/test_data/entap_outfiles/ontology//EggNOG_DMND/blastp_trinity_eggnog_proteins__std.err
Wed Jul 29 10:46:47 2020: Parsing EggNOG DMND file located at: /io/bin/EnTAP/test_data/entap_outfiles/ontology//EggNOG_DMND/blastp_trinity_eggnog_proteins.out
Wed Jul 29 10:46:47 2020: Beginning to parse EggNOG results...
Wed Jul 29 10:46:47 2020: Success!
Wed Jul 29 10:46:47 2020: Success! Calculating statistics and accessing database...
Wed Jul 29 10:46:47 2020: Opening SQL database...
Wed Jul 29 10:46:47 2020: Opening SQL database at: /io/bin/EnTAP/databases/eggnog.db
Wed Jul 29 10:46:47 2020: Success!
Wed Jul 29 10:46:47 2020: Getting EggNOG database SQL version...
Wed Jul 29 10:46:47 2020: Executing sql cmd: SELECT version FROM version
Wed Jul 29 10:46:47 2020: WARNING: SQL Version less than 4, setting to 'earlier'
Wed Jul 29 10:46:47 2020: Success!
Wed Jul 29 10:46:47 2020: Setting working directory to: /io/bin/EnTAP/test_data/entap_outfiles
Wed Jul 29 10:46:47 2020: Success! Working directory set
Wed Jul 29 10:46:47 2020: Killing Object - QueryData
Wed Jul 29 10:46:47 2020: QuerySequence data freed

Answer 1 · 2020-07-29T13:31:59.000Z

Hm no issues on my end with the latest build. This one may be tougher to track down. Can you send over your ini file as well?

Answer 2 · 2020-07-30T00:01:30.000Z

Hi, this is the ini file:

#-------------------------------
# [ini_instructions]
#When using this ini file keep the following in mind:
#       1. Do not edit the input keys to the left side of the '=' sign
#       2. Be sure to use the proper value type (either a string, list, or number)
#       3. Do not add unecessary spaces to your input
#       4. When inputting a list, only add a ',' between each entry
#-------------------------------
# [configuration]
#-------------------------------
#Specify which EnTAP database you would like to download/generate.
#    0. Serialized Database (default)
#    1. SQLITE Database
#Either or both can be selected with an additional flag. The serialized database will be faster although requires more memory usage. The SQLITE database may be slightly slower.
#type:list (integer)
data-type=0,
#-------------------------------
# [entap]
#-------------------------------
#Path to the EnTAP binary database
#type:string
entap-db-bin=/io/bin/EnTAP/bin/entap_database.bin
#Path to the EnTAP SQL database (not needed if you are using the binary database)
#type:string
entap-db-sql=/io/bin/EnTAP/databases/entap_database.db
#Path to the EnTAP graphing script (entap_graphing.py)
#type:string
entap-graph=/io/bin/EnTAP/src/entap_graphing.py
#-------------------------------
# [expression_analysis]
#-------------------------------
#Specify the FPKM threshold with expression analysis
#EnTAP will filter out transcripts below this value! (default: 0.5)
#type:decimal
fpkm=0.5
#Specify this flag if your BAM/SAM file was generated through single-end reads
#Note: this is only required in expression analysis
#Default: paired-end
#type:boolean (true/false)
single-end=false
#-------------------------------
# [expression_analysis-rsem]
#-------------------------------
#Execution method of RSEM Calculate Expression.
#Example: rsem-calculate-expression
#type:string
rsem-calculate-expression=/io/bin/EnTAP/libs/RSEM-1.3.0//rsem-calculate-expression
#Execution method of RSEM SAM Validate.
#Example: rsem-sam-validator
#type:string
rsem-sam-validator=/io/bin/EnTAP/libs/RSEM-1.3.0//rsem-sam-validator
#Execution method of RSEM Prep Reference.
#Example: rsem-prepare-reference
#type:string
rsem-prepare-reference=/io/bin/EnTAP/libs/RSEM-1.3.0//rsem-prepare-reference
#Execution method of RSEM Convert SAM
#Example: convert-sam-for-rsem
#type:string
convert-sam-for-rsem=/io/bin/EnTAP/libs/RSEM-1.3.0//convert-sam-for-rsem
#-------------------------------
# [frame_selection]
#-------------------------------
#Select this option if all of your sequences are complete proteins.
#At this point, this option will merely flag the sequences in your output file
#type:boolean (true/false)
complete=false
#Specify the Frame Selection software you would like to use. Only one flag can be specified.
#Specify flags as follows:
#    1. GeneMarkS-T
#    2. Transdecoder (default)
#type:integer
frame-selection=2
#-------------------------------
# [frame_selection-genemarks-t]
#-------------------------------
#Method to execute GeneMarkST. This may be the path to the executable.
#type:string
genemarkst-exe=gmst.pl
#-------------------------------
# [frame_selection-transdecoder]
#-------------------------------
#Method to execute TransDecoder.LongOrfs. This may be the path to the executable or simply TransDecoder.LongOrfs
#type:string
transdecoder-long-exe=/io/bin/EnTAP/libs/TransDecoder-v5.3.0/TransDecoder.LongOrfs
#Method to execute TransDecoder.Predict. This may be the path to the executable or simply TransDecoder.Predict
#type:string
transdecoder-predict-exe=/io/bin/EnTAP/libs/TransDecoder-v5.3.0/TransDecoder.Predict
#Transdecoder only. Specify the minimum protein length
#type:integer
transdecoder-m=100
#-------------------------------
# [general]
#-------------------------------
#Specify the output format for the processed alignments.Multiple flags can be specified.
#    1. TSV Format (default)
#    2. CSV Format
#    3. FASTA Amino Acid (default)
#    4. FASTA Nucleotide (default)
#type:list (integer)
output-format=1,3,4,
#-------------------------------
# [ontology]
#-------------------------------
# Specify the ontology software you would like to use
#Note: it is possible to specify more than one! Just usemultiple --ontology flags
#Specify flags as follows:
#    0. EggNOG (default)
#    1. InterProScan
#type:list (integer)
ontology=0,
#Specify the Gene Ontology levels you would like printed
#Default: 1
#A level of 0 means that every term will be printed! It is possible to specify multiple flags as well with
#multiple --level flags
#Example: --level 0 --level 3 --level 1
#type:list (integer)
level=1,
#-------------------------------
# [ontology-eggnog]
#-------------------------------
#Absolute path to the EggNOG SQL database that was downloaded duirng the Configuration stage.
#type:string
eggnog-sql=/io/bin/EnTAP/databases/eggnog.db
#Path to EggNOG DIAMOND configured database.
#type:string
eggnog-dmnd=/io/bin/EnTAP/bin/eggnog_proteins.dmnd
#-------------------------------
# [ontology-interproscan]
#-------------------------------
#Execution method of InterProScan.
#type:string
interproscan-exe=interproscan.sh
#Select which databases you would like for InterProScan. Databases must be one of the following:
#    -tigrfam
#    -sfld
#    -prodom
#    -hamap
#    -pfam
#    -smart
#    -cdd
#    -prositeprofiles
#    -prositepatterns
#    -superfamily
#    -prints
#    -panther
#    -gene3d
#    -pirsf
#    -coils
#    -morbidblite
#Make sure the database is downloaded, EnTAP will not check!
#--protein tigrfam --protein pfam
#type:list (string)
protein=
#-------------------------------
# [similarity_search]
#-------------------------------
#Method to execute DIAMOND. This can be a path to the executable or simple 'diamond'
#type:string
diamond-exe=diamond
#Specify the type of species/taxon you are analyzing and would like hits closer in taxonomic relevance to be favored (based on NCBI Taxonomic Database)
#Note: replace all spaces with underscores '_'
#type:list (string)
taxon=
#Select the minimum query coverage to be allowed during similarity searching (default: 50.0)
#type:decimal
qcoverage=50
#Select the minimum target coverage to be allowed during similarity searching (default: 50.0)
#type:decimal
tcoverage=50
#Specify the contaminants you would like to filter out from similarity searching
#Note: since hits are based upon a multitide of factors a contaminant might be the best hit for a query!
#Contaminants can be selected by species (homo_sapiens) or through a specific taxon (homo)
#If your taxon is more than one word just replace the spaces with underscores (_)
#type:list (string)
contam=
#Specify the E-Value that will be used as a cutoff during similarity searching
#type:decimal
e-value=1e-05
#Path to a list of keywords that should be used to specify uninformativeness of hits during similarity searching. Generally something along the lines of 'hypothetical' or 'unknown' are used. Each term should be on a new line of the file being linked to. This can be used if you would like to tag certain descriptions.
#Example (defaults):
#    -conserved
#    -predicted
#    -unknown
#    -hypothetical
#    -putative
#    -unidentified
#    -uncultured
#    -uninformative
#Ensure each word is on a separate line in the file. EnTAP will take the each line as a new uninformative word!
#type:string
uninformative=

Answer 3 · 2021-01-24T18:19:55.000Z

@harta55 @zhangrengang

I have the same issue in a CentOS HPC SLURM:

/var/spool/slurm/d/job886557/slurm_script: line 22: 26607 Segmentation fault EnTAP --runP -i $i --ini ${dbpath}entap_config.ini -d ${dbpath}eggnog_proteins.dmnd -d ${dbpath}uniprot_sprot.dmnd -d ${dbpath}refseq.dmnd -d ${dbpath}nr.dmnd

The transdecoder and similarity outputs look ok, though.
Log and Debug are below:

log:

EnTAP Run Information - Execution

Current EnTAP Version: 0.10.7
Start time: Sat Jan 23 12:43:30 2021

Working directory has been set to: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles
User Inputs:
out-dir: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles
config: false
runP: true
runN: false
overwrite: false
ini: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/entap_config.ini
input: swiss_prot_test.fasta
database: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/eggnog_proteins.dmnd,/scratch/global/user.hpc/EnTAP-v0.10.7/databases/uniprot_sprot.dmnd,/scratch/global/user.hpc/EnTAP-v0.10.7/databases/refseq.dmnd,/scratch/global/user.hpc/EnTAP-v0.10.7/databases/nr.dmnd,
graph: false
no-trim: false
threads: 1
state: +
no-check: false
output-format: 1,4,
entap-db-bin: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/entap_database.bin
entap-db-sql: /databases/entap_database.db
entap-graph: /scratch/global/user.hpc/EnTAP-v0.10.7/src/entap_graphing.py
data-generate: false
data-type: 0,
fpkm: 0.500000
align:
single-end: false
rsem-calculate-expression: /libs/RSEM-1.3.0//rsem-calculate-expression
rsem-sam-validator: /libs/RSEM-1.3.0//rsem-sam-validator
rsem-prepare-reference: /libs/RSEM-1.3.0//rsem-prepare-reference
convert-sam-for-rsem: /libs/RSEM-1.3.0//convert-sam-for-rsem
complete: false
frame-selection: 2
genemarkst-exe: gmst.pl
transdecoder-long-exe: /libs/TransDecoder-v5.3.0/TransDecoder.LongOrfs
transdecoder-predict-exe: /libs/TransDecoder-v5.3.0/TransDecoder.Predict
transdecoder-m: 100
transdecoder-no-refine-starts: false
diamond-exe: diamond
taxon:
qcoverage: 50.000000
tcoverage: 50.000000
contam:
e-value: 0.000010
uninformative:
ontology: 0,
level: 0,1,2,3,
eggnog-sql: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/entap_outfiles/databases/eggnog.db
eggnog-dmnd: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/eggnog_proteins.dmnd
interproscan-exe: interproscan.sh
protein:

Transcriptome Statistics

Protein sequences found
Total sequences: 10
Total length of transcriptome(bp): 9894
Average sequence length(bp): 989.00
n50: 1020
n90: 678
Longest sequence(bp): 2229 (sp|Q940Y1|ORP2A_ARATH)
Shortest sequence(bp): 483 (sp|P23831|SAMA_SALTY)

Similarity Search - DIAMOND - eggnog_proteins

Search results:
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_eggnog_proteins.out
Total alignments: 12
Total unselected results: 2
Written to: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//eggnog_proteins/unselected_lvl0
Total unique transcripts with an alignment: 10
Reference transcriptome sequences with an alignment (FASTA):
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//eggnog_proteins/best_hits_lvl0
Search results (TSV):
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//eggnog_proteins/best_hits_lvl0
Total unique transcripts without an alignment: 0
Reference transcriptome sequences without an alignment (FASTA):
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//eggnog_proteins/no_hits.faa
Total unique informative alignments: 10
Total unique uninformative alignments: 0
Top 10 alignments by species:
1): 10(100.00%)

Similarity Search - DIAMOND - uniprot_sprot

Search results:
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_uniprot_sprot.out
Total alignments: 10
Total unselected results: 0
Written to: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//uniprot_sprot/unselected_lvl0
Total unique transcripts with an alignment: 10
Reference transcriptome sequences with an alignment (FASTA):
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//uniprot_sprot/best_hits_lvl0
Search results (TSV):
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//uniprot_sprot/best_hits_lvl0
Total unique transcripts without an alignment: 0
Reference transcriptome sequences without an alignment (FASTA):
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//uniprot_sprot/no_hits.faa
Total unique informative alignments: 10
Total unique uninformative alignments: 0
Top 10 alignments by species:
1)arabidopsis thaliana: 3(30.00%)
2)chaetomium globosum (strain atcc 6205 / cbs 148.51 / dsm 1962 / nbrc 6347 / nrrl 1970): 1(10.00%)
3)candida glabrata (strain atcc 2001 / cbs 138 / jcm 3761 / nbrc 0622 / nrrl y-65): 1(10.00%)
4)salmonella typhimurium (strain lt2 / sgsc1412 / atcc 700720): 1(10.00%)
5)cupriavidus necator (strain atcc 17699 / h16 / dsm 428 / stanier 337): 1(10.00%)
6)debaryomyces hansenii (strain atcc 36239 / cbs 767 / jcm 1990 / nbrc 0083 / igc 2968): 1(10.00%)
7)dictyostelium discoideum: 1(10.00%)
8)salmonella typhimurium: 1(10.00%)

Similarity Search - DIAMOND - refseq

Search results:
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_refseq.out
Total alignments: 109
Total unselected results: 99
Written to: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//refseq/unselected_lvl0
Total unique transcripts with an alignment: 10
Reference transcriptome sequences with an alignment (FASTA):
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//refseq/best_hits_lvl0
Search results (TSV):
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//refseq/best_hits_lvl0
Total unique transcripts without an alignment: 0
Reference transcriptome sequences without an alignment (FASTA):
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//refseq/no_hits.faa
Total unique informative alignments: 7
Total unique uninformative alignments: 3
Top 10 alignments by species:
1)arabidopsis thaliana: 3(30.00%)
2)salmonella enterica subsp. enterica serovar typhimurium: 2(20.00%)
3)chaetomium globosum cbs 148.51: 1(10.00%)
4)debaryomyces hansenii cbs767: 1(10.00%)
5)candida] glabrata: 1(10.00%)
6)dictyostelium discoideum ax4: 1(10.00%)
7)cupriavidus necator: 1(10.00%)

Similarity Search - DIAMOND - nr

Search results:
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_nr.out
Total alignments: 312
Total unselected results: 302
Written to: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//nr/unselected_lvl0
Total unique transcripts with an alignment: 10
Reference transcriptome sequences with an alignment (FASTA):
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//nr/best_hits_lvl0
Search results (TSV):
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//nr/best_hits_lvl0
Total unique transcripts without an alignment: 0
Reference transcriptome sequences without an alignment (FASTA):
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//nr/no_hits.faa
Total unique informative alignments: 7
Total unique uninformative alignments: 3
Top 10 alignments by species:
1)arabidopsis thaliana: 3(30.00%)
2)salmonella enterica: 1(10.00%)
3)chaetomium globosum cbs 148.51: 1(10.00%)
4)debaryomyces hansenii cbs767: 1(10.00%)
5)candida] glabrata: 1(10.00%)
6)dictyostelium discoideum ax4: 1(10.00%)
7)salmonella enterica subsp. enterica serovar typhimurium: 1(10.00%)
8)cupriavidus necator: 1(10.00%)

Compiled Similarity Search - DIAMOND - Best Overall

Total unique transcripts with an alignment: 10
	Reference transcriptome sequences with an alignment (FASTA):
		/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/best_hits_lvl0
	Search results (TSV):
		/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/best_hits_lvl0
Total unique transcripts without an alignment: 0
	Reference transcriptome sequences without an alignment (FASTA):
		/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/no_hits.faa
Total unique informative alignments: 10
Total unique uninformative alignments: 0
Top 10 alignments by species:
		1): 8(80.00%)
		2)salmonella typhimurium (strain lt2 / sgsc1412 / atcc 700720): 1(10.00%)
		3)salmonella typhimurium: 1(10.00%)

debug:

Sat Jan 23 12:43:30 2021: Start - EnTAP
Sat Jan 23 12:43:30 2021: Parsing ini file at: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/entap_config.ini
Sat Jan 23 12:43:30 2021: Success!
Sat Jan 23 12:43:30 2021: Printing user input...
Sat Jan 23 12:43:30 2021: ------------------------------------------------------
EnTAP Run Information - Execution

Current EnTAP Version: 0.10.7
Start time: Sat Jan 23 12:43:30 2021

Working directory has been set to: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles
User Inputs:
out-dir: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles
config: false
runP: true
runN: false
overwrite: false
ini: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/entap_config.ini
input: swiss_prot_test.fasta
database: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/eggnog_proteins.dmnd,/scratch/global/user.hpc/EnTAP-v0.10.7/databases/uniprot_sprot.dmnd,/scratch/global/user.hpc/EnTAP-v0.10.7/databases/refseq.dmnd,/scratch/global/user.hpc/EnTAP-v0.10.7/databases/nr.dmnd,
graph: false
no-trim: false
threads: 1
state: +
no-check: false
output-format: 1,4,
entap-db-bin: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/entap_database.bin
entap-db-sql: /databases/entap_database.db
entap-graph: /scratch/global/user.hpc/EnTAP-v0.10.7/src/entap_graphing.py
data-generate: false
data-type: 0,
fpkm: 0.500000
align:
single-end: false
rsem-calculate-expression: /libs/RSEM-1.3.0//rsem-calculate-expression
rsem-sam-validator: /libs/RSEM-1.3.0//rsem-sam-validator
rsem-prepare-reference: /libs/RSEM-1.3.0//rsem-prepare-reference
convert-sam-for-rsem: /libs/RSEM-1.3.0//convert-sam-for-rsem
complete: false
frame-selection: 2
genemarkst-exe: gmst.pl
transdecoder-long-exe: /libs/TransDecoder-v5.3.0/TransDecoder.LongOrfs
transdecoder-predict-exe: /libs/TransDecoder-v5.3.0/TransDecoder.Predict
transdecoder-m: 100
transdecoder-no-refine-starts: false
diamond-exe: diamond
taxon:
qcoverage: 50.000000
tcoverage: 50.000000
contam:
e-value: 0.000010
uninformative:
ontology: 0,
level: 0,1,2,3,
eggnog-sql: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/entap_outfiles/databases/eggnog.db
eggnog-dmnd: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/eggnog_proteins.dmnd
interproscan-exe: interproscan.sh
protein:

Sat Jan 23 12:43:30 2021: User has input a database at: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/eggnog_proteins.dmnd
Sat Jan 23 12:43:30 2021: User has input a database at: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/uniprot_sprot.dmnd
Sat Jan 23 12:43:30 2021: User has input a database at: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/refseq.dmnd
Sat Jan 23 12:43:30 2021: User has input a database at: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/nr.dmnd
Sat Jan 23 12:43:30 2021: Verifying EnTAP database...
Sat Jan 23 12:43:30 2021: Reading serialized database from: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/entap_database.bin
Of type: 2
Sat Jan 23 12:43:50 2021: Success!
Sat Jan 23 12:43:50 2021: Spawn Object - QueryData
Sat Jan 23 12:43:50 2021: Generating transcriptome mappings...
Sat Jan 23 12:43:50 2021: Transcriptome Lines - START
Sat Jan 23 12:43:50 2021: >sp|P23831|SAMA_SALTY Protein SamA OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=samA PE=3 SV=1
Sat Jan 23 12:43:50 2021: MLLLVAPEQEPVQSTAPLFTERCPAGFPSPAADYTEEELDLNAYCIRRPAATFFVRAIGD
Sat Jan 23 12:43:50 2021: SMKEMGLHSGDLMVVDKAEKPMQGDIVIAETDGEFTVKRLQLKPRIALLPINPAYPTLYP
Sat Jan 23 12:43:50 2021: EELQIFGVVTAFIHKTRSTD
Sat Jan 23 12:43:50 2021: >sp|P23832|SAMB_SALTM Protein SamB OS=Salmonella typhimurium GN=samB PE=3 SV=1
Sat Jan 23 12:43:50 2021: MFALADVNSFYASCEKVFRPDLRDRSVVVLSNNDGCVIPRSAEAKKLGIKMGVPWFQLRS
Sat Jan 23 12:43:50 2021: AKFPEPVIAFSSNYALYASMSNRVMVHLEELAPRVEQYSIDEMFLDIRGIDSCIDFEDFG
Sat Jan 23 12:43:50 2021: RQLREHVRSGTGLTIGVGMGPTKTLAKSAQWASKEWSQFGGVLALTLHNQKRTEKLLSLQ
Sat Jan 23 12:43:50 2021: PVEEIWGVGRRISKKLNTMGITTALQLARANPTFIRKNFNVVLERTVRELNGESCISLEE
Sat Jan 23 12:43:50 2021: Transcriptome Lines - END
Sat Jan 23 12:43:50 2021: Success!
Sat Jan 23 12:43:50 2021: Verifying input flag fpkm
Sat Jan 23 12:43:50 2021: Verifying input flag qcoverage
Sat Jan 23 12:43:50 2021: Verifying input flag tcoverage
Sat Jan 23 12:43:50 2021: Verifying input flag ontology
Sat Jan 23 12:43:50 2021: Verifying input flag frame-selection
Sat Jan 23 12:43:50 2021: Verifying input flag transdecoder-m
Sat Jan 23 12:43:50 2021: Determining if we want to run expression analysis
Sat Jan 23 12:43:50 2021: NO, no alignment file specified from user
Sat Jan 23 12:43:50 2021: Determining if we want to run frame selection...
Sat Jan 23 12:43:50 2021: NO Protein sequences input AND runP, skipping frame selection
Sat Jan 23 12:43:50 2021: Verifying software...
Sat Jan 23 12:43:50 2021: Executing command:
diamond --version
Sat Jan 23 12:43:50 2021:
Std Err:

Sat Jan 23 12:43:50 2021: Verifying EggNOG inputs...
Sat Jan 23 12:43:50 2021: Executing command:
diamond --version
Sat Jan 23 12:43:50 2021:
Std Err:

Sat Jan 23 12:43:50 2021: Success!
Sat Jan 23 12:43:50 2021: Success!
Sat Jan 23 12:43:50 2021: Success! Input verified
Sat Jan 23 12:43:50 2021: Killing Object - EntapDatabase
Sat Jan 23 12:43:57 2021: Killing Object - QueryData
Sat Jan 23 12:43:57 2021: QuerySequence data freed
Sat Jan 23 12:43:57 2021: EnTAP Executing...
Sat Jan 23 12:43:57 2021: verifying state...
Sat Jan 23 12:43:57 2021: verifying state...
Sat Jan 23 12:43:57 2021: Success!
Sat Jan 23 12:43:57 2021: Spawn Object - QueryData
Sat Jan 23 12:43:57 2021: Generating transcriptome mappings...
Sat Jan 23 12:43:57 2021: Transcriptome Lines - START
Sat Jan 23 12:43:57 2021: >sp|P23831|SAMA_SALTY Protein SamA OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=samA PE=3 SV=1
Sat Jan 23 12:43:57 2021: MLLLVAPEQEPVQSTAPLFTERCPAGFPSPAADYTEEELDLNAYCIRRPAATFFVRAIGD
Sat Jan 23 12:43:57 2021: SMKEMGLHSGDLMVVDKAEKPMQGDIVIAETDGEFTVKRLQLKPRIALLPINPAYPTLYP
Sat Jan 23 12:43:57 2021: EELQIFGVVTAFIHKTRSTD
Sat Jan 23 12:43:57 2021: >sp|P23832|SAMB_SALTM Protein SamB OS=Salmonella typhimurium GN=samB PE=3 SV=1
Sat Jan 23 12:43:57 2021: MFALADVNSFYASCEKVFRPDLRDRSVVVLSNNDGCVIPRSAEAKKLGIKMGVPWFQLRS
Sat Jan 23 12:43:57 2021: AKFPEPVIAFSSNYALYASMSNRVMVHLEELAPRVEQYSIDEMFLDIRGIDSCIDFEDFG
Sat Jan 23 12:43:57 2021: RQLREHVRSGTGLTIGVGMGPTKTLAKSAQWASKEWSQFGGVLALTLHNQKRTEKLLSLQ
Sat Jan 23 12:43:57 2021: PVEEIWGVGRRISKKLNTMGITTALQLARANPTFIRKNFNVVLERTVRELNGESCISLEE
Sat Jan 23 12:43:57 2021: Transcriptome Lines - END
Sat Jan 23 12:43:58 2021: Success!
Sat Jan 23 12:43:58 2021: Spawn Object - GraphingManager
Sat Jan 23 12:43:58 2021: Executing command:
python /scratch/global/user.hpc/EnTAP-v0.10.7/src/entap_graphing.py -g -1
Sat Jan 23 12:43:58 2021:
Std Err:

Sat Jan 23 12:43:58 2021: Graphing is NOT supported
Sat Jan 23 12:43:58 2021: Reading serialized database from: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/entap_database.bin
Of type: 2
Sat Jan 23 12:44:15 2021: STATE - EXPRESSION FILTERING
Sat Jan 23 12:44:15 2021: Determining if we want to run expression analysis
Sat Jan 23 12:44:15 2021: NO, no alignment file specified from user
Sat Jan 23 12:44:15 2021: No alignment file specified, skipping expression analysis
Sat Jan 23 12:44:15 2021: verifying state...
Sat Jan 23 12:44:15 2021: STATE - FRAME SELECTION
Sat Jan 23 12:44:15 2021: Determining if we want to run frame selection...
Sat Jan 23 12:44:15 2021: NO Protein sequences input AND runP, skipping frame selection
Sat Jan 23 12:44:15 2021: verifying state...
Sat Jan 23 12:44:15 2021: Beginning to copy final transcriptome to be used...
Sat Jan 23 12:44:15 2021: FINAL transcriptome generated to: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/transcriptomes//swiss_prot_test_final.fasta
Sat Jan 23 12:44:15 2021: verifying state...
Sat Jan 23 12:44:15 2021: STATE - SIMILARITY SEARCH
Sat Jan 23 12:44:15 2021: Spawn Object - SimilaritySearch
Sat Jan 23 12:44:15 2021: opendir: Path could not be read: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/figures/
Sat Jan 23 12:44:15 2021: opendir: Path could not be read: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed/
Sat Jan 23 12:44:15 2021: Setting working directory to: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND
Sat Jan 23 12:44:15 2021: Success! Working directory set
Sat Jan 23 12:44:15 2021: opendir: Path could not be read: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results
Sat Jan 23 12:44:15 2021: Spawn Object - ModDiamond
Sat Jan 23 12:44:15 2021: Verifying previous execution of database: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/eggnog_proteins.dmnd...
Sat Jan 23 12:44:15 2021: File for database eggnog_proteins does not exist.
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_eggnog_proteins.out
Sat Jan 23 12:44:15 2021: Verifying previous execution of database: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/uniprot_sprot.dmnd...
Sat Jan 23 12:44:15 2021: File for database uniprot_sprot does not exist.
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_uniprot_sprot.out
Sat Jan 23 12:44:15 2021: Verifying previous execution of database: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/refseq.dmnd...
Sat Jan 23 12:44:15 2021: File for database refseq does not exist.
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_refseq.out
Sat Jan 23 12:44:15 2021: Verifying previous execution of database: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/nr.dmnd...
Sat Jan 23 12:44:15 2021: File for database nr does not exist.
/scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_nr.out
Sat Jan 23 12:44:15 2021: Success! Verified files for DIAMOND, continuing...
Sat Jan 23 12:44:15 2021: Executing DIAMOND for necessary files....
Sat Jan 23 12:44:15 2021: File not found, executing against database at: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/eggnog_proteins.dmnd
Sat Jan 23 12:44:15 2021: Executing command:
diamond blastp -o /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_eggnog_proteins.out --top 3 -q /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/transcriptomes//swiss_prot_test_final.fasta --query-cover 50.000000 -p 1 --evalue 0.000010 -d /scratch/global/user.hpc/EnTAP-v0.10.7/databases/eggnog_proteins.dmnd --subject-cover 50.000000 -f 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp stitle --more-sensitive
Sat Jan 23 12:46:02 2021:
Std Err:

Sat Jan 23 12:46:02 2021:
Printing to files:
Std Out: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_eggnog_proteins.out_std.out
Std Err: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_eggnog_proteins.out_std.err
Sat Jan 23 12:46:02 2021: Success! Results written to: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_eggnog_proteins.out
Sat Jan 23 12:46:02 2021: File not found, executing against database at: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/uniprot_sprot.dmnd
Sat Jan 23 12:46:02 2021: Executing command:
diamond blastp -o /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_uniprot_sprot.out --top 3 -q /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/transcriptomes//swiss_prot_test_final.fasta --query-cover 50.000000 -p 1 --evalue 0.000010 -d /scratch/global/user.hpc/EnTAP-v0.10.7/databases/uniprot_sprot.dmnd --subject-cover 50.000000 -f 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp stitle --more-sensitive
Sat Jan 23 12:46:10 2021:
Std Err:

Sat Jan 23 12:46:10 2021:
Printing to files:
Std Out: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_uniprot_sprot.out_std.out
Std Err: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_uniprot_sprot.out_std.err
Sat Jan 23 12:46:10 2021: Success! Results written to: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_uniprot_sprot.out
Sat Jan 23 12:46:10 2021: File not found, executing against database at: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/refseq.dmnd
Sat Jan 23 12:46:10 2021: Executing command:
diamond blastp -o /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_refseq.out --top 3 -q /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/transcriptomes//swiss_prot_test_final.fasta --query-cover 50.000000 -p 1 --evalue 0.000010 -d /scratch/global/user.hpc/EnTAP-v0.10.7/databases/refseq.dmnd --subject-cover 50.000000 -f 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp stitle --more-sensitive
Sat Jan 23 13:29:24 2021:
Std Err:

Sat Jan 23 13:29:24 2021:
Printing to files:
Std Out: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_refseq.out_std.out
Std Err: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_refseq.out_std.err
Sat Jan 23 13:29:24 2021: Success! Results written to: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_refseq.out
Sat Jan 23 13:29:24 2021: File not found, executing against database at: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/nr.dmnd
Sat Jan 23 13:29:24 2021: Executing command:
diamond blastp -o /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_nr.out --top 3 -q /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/transcriptomes//swiss_prot_test_final.fasta --query-cover 50.000000 -p 1 --evalue 0.000010 -d /scratch/global/user.hpc/EnTAP-v0.10.7/databases/nr.dmnd --subject-cover 50.000000 -f 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp stitle --more-sensitive
Sat Jan 23 14:41:48 2021:
Std Err:

Sat Jan 23 14:41:48 2021:
Printing to files:
Std Out: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_nr.out_std.out
Std Err: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_nr.out_std.err
Sat Jan 23 14:41:48 2021: Success! Results written to: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_nr.out
Sat Jan 23 14:41:48 2021: Beginning to filter individual DIAMOND files...
Sat Jan 23 14:41:48 2021: DIAMOND file located at /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_eggnog_proteins.out being parsed
Sat Jan 23 14:41:48 2021: File parsed, calculating statistics and writing output...
Sat Jan 23 14:41:48 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//eggnog_proteins/best_hits_contam_lvl0
Sat Jan 23 14:41:48 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//eggnog_proteins/best_hits_lvl0
Sat Jan 23 14:41:48 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//eggnog_proteins/best_hits_no_contam_lvl0
Sat Jan 23 14:41:48 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//eggnog_proteins/unselected_lvl0
Sat Jan 23 14:41:48 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//eggnog_proteins/best_hits_contam_lvl0
Sat Jan 23 14:41:48 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//eggnog_proteins/best_hits_lvl0
Sat Jan 23 14:41:48 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//eggnog_proteins/best_hits_no_contam_lvl0
Sat Jan 23 14:41:48 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//eggnog_proteins/unselected_lvl0
Sat Jan 23 14:41:48 2021: GraphingManager - initializing graphing data at: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//eggnog_proteins/figures//_species_bar.txt
Sat Jan 23 14:41:48 2021: GraphingManager - initializing graphing data at: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//eggnog_proteins/figures//_summary_bar.txt
Sat Jan 23 14:41:48 2021: Success!
Sat Jan 23 14:41:48 2021: DIAMOND file located at /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_uniprot_sprot.out being parsed
Sat Jan 23 14:41:48 2021: Database file at /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_uniprot_sprot.out
Determined to be UniProt
Sat Jan 23 14:41:48 2021: File parsed, calculating statistics and writing output...
Sat Jan 23 14:41:48 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//uniprot_sprot/best_hits_contam_lvl0
Sat Jan 23 14:41:48 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//uniprot_sprot/best_hits_lvl0
Sat Jan 23 14:41:48 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//uniprot_sprot/best_hits_no_contam_lvl0
Sat Jan 23 14:41:48 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//uniprot_sprot/unselected_lvl0
Sat Jan 23 14:41:48 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//uniprot_sprot/best_hits_contam_lvl0
Sat Jan 23 14:41:48 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//uniprot_sprot/best_hits_lvl0
Sat Jan 23 14:41:48 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//uniprot_sprot/best_hits_no_contam_lvl0
Sat Jan 23 14:41:48 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//uniprot_sprot/unselected_lvl0
Sat Jan 23 14:41:48 2021: GraphingManager - initializing graphing data at: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//uniprot_sprot/figures//_species_bar.txt
Sat Jan 23 14:41:48 2021: GraphingManager - initializing graphing data at: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//uniprot_sprot/figures//_summary_bar.txt
Sat Jan 23 14:41:48 2021: Success!
Sat Jan 23 14:41:48 2021: DIAMOND file located at /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_refseq.out being parsed
Sat Jan 23 14:41:49 2021: File parsed, calculating statistics and writing output...
Sat Jan 23 14:41:49 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//refseq/best_hits_contam_lvl0
Sat Jan 23 14:41:49 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//refseq/best_hits_lvl0
Sat Jan 23 14:41:49 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//refseq/best_hits_no_contam_lvl0
Sat Jan 23 14:41:49 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//refseq/unselected_lvl0
Sat Jan 23 14:41:49 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//refseq/best_hits_contam_lvl0
Sat Jan 23 14:41:49 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//refseq/best_hits_lvl0
Sat Jan 23 14:41:49 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//refseq/best_hits_no_contam_lvl0
Sat Jan 23 14:41:49 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//refseq/unselected_lvl0
Sat Jan 23 14:41:49 2021: GraphingManager - initializing graphing data at: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//refseq/figures//_species_bar.txt
Sat Jan 23 14:41:49 2021: GraphingManager - initializing graphing data at: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//refseq/figures//_summary_bar.txt
Sat Jan 23 14:41:49 2021: Success!
Sat Jan 23 14:41:49 2021: DIAMOND file located at /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/blastp_swiss_prot_test_final_nr.out being parsed
Sat Jan 23 14:41:50 2021: File parsed, calculating statistics and writing output...
Sat Jan 23 14:41:50 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//nr/best_hits_contam_lvl0
Sat Jan 23 14:41:50 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//nr/best_hits_lvl0
Sat Jan 23 14:41:50 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//nr/best_hits_no_contam_lvl0
Sat Jan 23 14:41:50 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//nr/unselected_lvl0
Sat Jan 23 14:41:50 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//nr/best_hits_contam_lvl0
Sat Jan 23 14:41:50 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//nr/best_hits_lvl0
Sat Jan 23 14:41:50 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//nr/best_hits_no_contam_lvl0
Sat Jan 23 14:41:50 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//nr/unselected_lvl0
Sat Jan 23 14:41:50 2021: GraphingManager - initializing graphing data at: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//nr/figures//_species_bar.txt
Sat Jan 23 14:41:50 2021: GraphingManager - initializing graphing data at: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/processed//nr/figures//_summary_bar.txt
Sat Jan 23 14:41:50 2021: Success!
Sat Jan 23 14:41:50 2021: Calculating overall Similarity Searching statistics...
Sat Jan 23 14:41:50 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/best_hits_contam_lvl0
Sat Jan 23 14:41:50 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/best_hits_lvl0
Sat Jan 23 14:41:50 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/best_hits_no_contam_lvl0
Sat Jan 23 14:41:50 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/unselected_lvl0
Sat Jan 23 14:41:50 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/best_hits_contam_lvl0
Sat Jan 23 14:41:50 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/best_hits_lvl0
Sat Jan 23 14:41:50 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/best_hits_no_contam_lvl0
Sat Jan 23 14:41:50 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/unselected_lvl0
Sat Jan 23 14:41:50 2021: GraphingManager - initializing graphing data at: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/figures//_species_bar.txt
Sat Jan 23 14:41:50 2021: GraphingManager - initializing graphing data at: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/similarity_search/DIAMOND/overall_results/figures//_summary_bar.txt
Sat Jan 23 14:41:50 2021: Success!
Sat Jan 23 14:41:50 2021: Setting working directory to: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles
Sat Jan 23 14:41:50 2021: Success! Working directory set
Sat Jan 23 14:41:50 2021: verifying state...
Sat Jan 23 14:41:50 2021: STATE - GENE ONTOLOGY
Sat Jan 23 14:41:50 2021: Spawn Object - Ontology
Sat Jan 23 14:41:50 2021: opendir: Path could not be read: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/ontology//EggNOG_DMND/figures/
Sat Jan 23 14:41:50 2021: opendir: Path could not be read: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/ontology//EggNOG_DMND/processed/
Sat Jan 23 14:41:50 2021: Setting working directory to: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/ontology//EggNOG_DMND
Sat Jan 23 14:41:50 2021: Success! Working directory set
Sat Jan 23 14:41:50 2021: Spawn Object - ModEggnogDMND
Sat Jan 23 14:41:50 2021: Overwrite was unselected, verifying output files...
Sat Jan 23 14:41:50 2021:
File Status at: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/ontology//EggNOG_DMND/blastp_swiss_prot_test_eggnog_proteins.out
Error: File empty
Error: File could not be found
Error: File could not be opened
Sat Jan 23 14:41:50 2021: Errors in opening file, continuing with execution...
Sat Jan 23 14:41:50 2021: Running EggNOG against Diamond database...
Sat Jan 23 14:41:50 2021: Executing command:
diamond blastp -d /scratch/global/user.hpc/EnTAP-v0.10.7/databases/eggnog_proteins.dmnd --top 1 --more-sensitive -q /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/transcriptomes//swiss_prot_test_final.fasta -o /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/ontology//EggNOG_DMND/blastp_swiss_prot_test_eggnog_proteins.out -p 1 -f 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp stitle
Sat Jan 23 14:43:38 2021:
Std Err:

Sat Jan 23 14:43:38 2021:
Printing to files:
Std Out: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/ontology//EggNOG_DMND/blastp_swiss_prot_test_eggnog_proteins__std.out
Std Err: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/ontology//EggNOG_DMND/blastp_swiss_prot_test_eggnog_proteins__std.err
Sat Jan 23 14:43:38 2021: Parsing EggNOG DMND file located at: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/ontology//EggNOG_DMND/blastp_swiss_prot_test_eggnog_proteins.out
Sat Jan 23 14:43:38 2021: Beginning to parse EggNOG results...
Sat Jan 23 14:43:38 2021: Success!
Sat Jan 23 14:43:38 2021: Success! Calculating statistics and accessing database...
Sat Jan 23 14:43:38 2021: Opening SQL database...
Sat Jan 23 14:43:38 2021: Opening SQL database at: /scratch/global/user.hpc/EnTAP-v0.10.7/databases/entap_outfiles/databases/eggnog.db
Sat Jan 23 14:43:51 2021: Success!
Sat Jan 23 14:43:51 2021: Getting EggNOG database SQL version...
Sat Jan 23 14:43:51 2021: Executing sql cmd: SELECT version FROM version
Sat Jan 23 14:43:57 2021: WARNING: couldn't get SQL version.Setting to earlier version by default
Sat Jan 23 14:43:57 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/ontology//EggNOG_DMND/processed//unannotated_sequences_lvl0
Sat Jan 23 14:43:57 2021: Alignment file started: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/ontology//EggNOG_DMND/processed//annotated_sequences_lvl0
Sat Jan 23 14:44:03 2021: Setting working directory to: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles
Sat Jan 23 14:44:03 2021: Success! Working directory set
Sat Jan 23 14:44:03 2021: Killing Object - QueryData
Sat Jan 23 14:44:03 2021: QuerySequence data freed
Sat Jan 23 14:44:03 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/ontology//EggNOG_DMND/processed//annotated_sequences_lvl0
Sat Jan 23 14:44:03 2021: Alignment file ended: /scratch/global/user.hpc/EnTAP-v0.10.7/test_data/entap_outfiles/ontology//EggNOG_DMND/processed//unannotated_sequences_lvl0

Answer 4 · 2021-02-23T23:52:38.000Z

@harta55 @zhangrengang @Aciole-David

I also encountered the same Segmentation fault without a core dump on a SLURM HPC (Scientific Linux 7.8). Ran into it trying to verify the installation using the test data you'd provided with the tool. I encountered the error via an interactive session (srun).

(I can also share my INI file and debug data if necessary. I don't want to make this thread unreadable.)

EDIT: I figured out what was happening in my case. Looks like EnTAP struggles with relative paths (in my case Diamond was not getting the correct paths). I used full paths (using realpath to be extra safe), and everything worked fine (at the test stage anyway). I'll run a full transcriptome now and report back.

EDIT: I was unable to test the expression-based filtering step since but everything else seems to work fine otherwise (insofar EnTAP completes execution and the output files are there).

Answer 5 · 2021-02-26T19:40:12.000Z

@vragh thanks for checking into it further. Will update next release

Answer 6 · 2021-02-26T20:51:23.000Z

@harta55 @zhangrengang @Aciole-David

I also encountered the same Segmentation fault without a core dump on a SLURM HPC (Scientific Linux 7.8). Ran into it trying to verify the installation using the test data you'd provided with the tool. I encountered the error via an interactive session (srun).

(I can also share my INI file and debug data if necessary. I don't want to make this thread unreadable.)

EDIT: I figured out what was happening in my case. Looks like EnTAP struggles with relative paths (in my case Diamond was not getting the correct paths). I used full paths (using realpath to be extra safe), and everything worked fine (at the test stage anyway). I'll run a full transcriptome now and report back.

EDIT: I was unable to test the expression-based filtering step since but everything else seems to work fine otherwise (insofar EnTAP completes execution and the output files are there).

@vragh , thank you. I'm not sure if I got it right; how do you corrected the paths?
I actually put complete paths in both ini file and the custom scripts that call EnTAP execution, even though the paths are passed with variables like:

dbpath="actual working path"

for i in ls -Sr *.fasta; do
EnTAP --runN -i $i
--ini ${path}entap_config.ini
--threads 7
-d ${dbpath}eggnog_proteins.dmnd
-d ${dbpath}uniprot_sprot.dmnd
-d ${dbpath}refseq.dmnd
-d ${dbpath}nr.dmnd

mv entap_outfiles ${i}_entap_out;

done

I don't remember precisely but I think the segmentation fault started when we updated EnTAP.
I'm running a test without the variables in the calling script to see if it works.
Thanks again

Answer 7 · 2021-02-27T10:09:49.000Z

@Aciole-David I'd probably do something like this:

dbpath=$(realpath /path/to/whatever);

for i in ls -Sr *.fasta; do
EnTAP --runN -i $(realpath $i)
--ini $(realpath ${path}/entap_config.ini)
--threads 7
-d ${dbpath}/eggnog_proteins.dmnd
-d ${dbpath}/uniprot_sprot.dmnd
-d ${dbpath}/refseq.dmnd
-d ${dbpath}/nr.dmnd

mv entap_outfiles ${i}_entap_out;
done

Answer 8 · 2021-04-26T13:06:41.000Z

Guys, just a feedback,

Along with the other suggestions, I switched diamond installation (in the ini file) between inside/outside conda environment and it worked.
Hope you all are doing fine.

Thanks

Answer 9 · 2022-03-10T22:01:53.000Z

I have struggled with this problem. At first, I thought it was due to graphing but seems not to be. I am using the test data.
Funny enough is that I have run my data and it completed successfully before. When I tried with a new dataset, Bam! core dumped. Now all I get is this.

terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Aborted (core dumped)

the debug looks like this.

Thu Mar 10 15:57:54 2022: Beginning to parse EggNOG results...
Thu Mar 10 15:57:54 2022: Success!
Thu Mar 10 15:57:54 2022: Success! Calculating statistics and accessing EggNOG database...
Thu Mar 10 15:57:54 2022: Opening SQL database...
Thu Mar 10 15:57:54 2022: Opening SQL database at: /data1/IxoSca/database/databases/eggnog.db
Thu Mar 10 15:57:54 2022: Success!
Thu Mar 10 15:57:54 2022: Getting EggNOG database SQL version...
Thu Mar 10 15:57:54 2022: Executing sql cmd: SELECT version FROM version
Thu Mar 10 15:57:54 2022: Success!
Thu Mar 10 15:57:54 2022: Alignment file started: /data1/IxoSca/EnTAP-0.10.8-beta/test_data/entap_outfiles/ontology//EggNOG_DMND/processed//unannotated_sequences
Thu Mar 10 15:57:54 2022: Alignment file started: /data1/IxoSca/EnTAP-0.10.8-beta/test_data/entap_outfiles/ontology//EggNOG_DMND/processed//annotated_sequences
Thu Mar 10 15:57:54 2022: Setting working directory to: /data1/IxoSca/EnTAP-0.10.8-beta/test_data
Thu Mar 10 15:57:54 2022: Success! Working directory set
Thu Mar 10 15:57:54 2022: Killing Object - QueryData
Thu Mar 10 15:57:54 2022: QuerySequence data freed
Thu Mar 10 15:57:54 2022: Alignment file ended: /data1/IxoSca/EnTAP-0.10.8-beta/test_data/entap_outfiles/ontology//EggNOG_DMND/processed//annotated_sequences

Answer 10 · 2023-11-08T19:59:35.000Z

Issue has not come up since, closing for now