weng-lab/TEMP2

Installation problem

Closed this issue · 3 comments

Psula23 commented

Hi,
I would like to use your tool, unfortunately I have some problems.
When I run the program on test data, I see the following problems:

/mnt/655a20f4-6ab2-4a63-84cc-be645d22970d/temp22/TEMP2/bin/TEMP2 insertion -l test.1.fastq.gz -r test.2.fastq.gz -I bwa_index/chr2L -g chr2L.fa -R transposon.fa -t rmsk.bed -o test_output -c 2

Testing required softwares:
bwa: /home/pgr/miniconda3/envs/temp22/bin/bwa
samtools: /home/pgr/miniconda3/envs/temp22/bin/samtools
bedtools: /home/pgr/miniconda3/envs/temp22/bin/bedtools
------ Start pipeline ------
bam file not specified, map raw reads tp genome via bwa mem	nie, 16 kwi 2023, 12:53:27 CEST
transform sam to sorted bam and index it	nie, 16 kwi 2023, 12:53:35 CEST
[bam_sort_core] merging from 0 files and 2 in-memory blocks...
get concordant-uniq-split reads	nie, 16 kwi 2023, 12:53:40 CEST
awk: line 2: function and never defined
awk: line 2: function and never defined
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 0 reads
check fragment length	nie, 16 kwi 2023, 12:53:41 CEST
awk: line 2: function and never defined
Błąd w poleceniu 'read.table(Args[6], header = F, row.names = NULL)':
  nie ma dostępnych linii na wejściu
Wykonywanie wstrzymane
insert size set to 95 quantile: 
/mnt/655a20f4-6ab2-4a63-84cc-be645d22970d/temp22/TEMP2/bin/TEMP2_insertion.sh: wiersz 172: [: -gt: oczekiwano operatora jednoargumentowego
get mate seq of the uniq-unpaired	nie, 16 kwi 2023, 12:53:41 CEST
awk: line 2: function and never defined
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 0 reads
map paired split uniqMappers and unpaired uniqMappers to transposons	nie, 16 kwi 2023, 12:53:41 CEST
merge fragments in genome and transposon	nie, 16 kwi 2023, 12:53:41 CEST
awk: line 40: function and never defined
awk: line 40: function and never defined
awk: line 78: function and never defined
awk: line 78: function and never defined
awk: line 78: function and never defined
test.t is empty
merge support reads in the same direction within - 	nie, 16 kwi 2023, 12:53:42 CEST
mkdir: nie można utworzyć katalogu „test.supportReads”: Plik istnieje
/mnt/655a20f4-6ab2-4a63-84cc-be645d22970d/temp22/TEMP2/bin/TEMP2_insertion.sh: wiersz 208: [: -: oczekiwano wyrażenia całkowitego

*****
***** ERROR: Requested column 4, but database file - only has fields 1 - 0.

*****
***** ERROR: Requested column 4, but database file - only has fields 1 - 0.
Traceback (most recent call last):
  File "/mnt/655a20f4-6ab2-4a63-84cc-be645d22970d/temp22/TEMP2/bin/processMergedBed.py", line 108, in <module>
    main()
  File "/mnt/655a20f4-6ab2-4a63-84cc-be645d22970d/temp22/TEMP2/bin/processMergedBed.py", line 10, in main
    tel = int(sys.argv[2])
ValueError: invalid literal for int() with base 10: 'test.supportReads/*.merged.merged.bed'
Traceback (most recent call last):
  File "/mnt/655a20f4-6ab2-4a63-84cc-be645d22970d/temp22/TEMP2/bin/processMergedBed.py", line 108, in <module>
    main()
  File "/mnt/655a20f4-6ab2-4a63-84cc-be645d22970d/temp22/TEMP2/bin/processMergedBed.py", line 10, in main
    tel = int(sys.argv[2])
IndexError: list index out of range
Traceback (most recent call last):
  File "/mnt/655a20f4-6ab2-4a63-84cc-be645d22970d/temp22/TEMP2/bin/processMergedBed.py", line 108, in <module>
    main()
  File "/mnt/655a20f4-6ab2-4a63-84cc-be645d22970d/temp22/TEMP2/bin/processMergedBed.py", line 10, in main
    tel = int(sys.argv[2])
IndexError: list index out of range
merge support reads in different direction within 2 X - 	nie, 16 kwi 2023, 12:53:42 CEST
/mnt/655a20f4-6ab2-4a63-84cc-be645d22970d/temp22/TEMP2/bin/mergeProcessedBed.sh in.processed.bed insert_size read_length out.prefix
/mnt/655a20f4-6ab2-4a63-84cc-be645d22970d/temp22/TEMP2/bin/mergeProcessedBed.sh in.processed.bed insert_size read_length out.prefix
filter candidate insertions which overlap with the same transposon insertion or in high depth region	nie, 16 kwi 2023, 12:53:42 CEST
filter candidate insertions in high depth region	nie, 16 kwi 2023, 12:53:42 CEST
average read number for 200bp bins is 0, set read number cutoff to 0
Filtered insertion number: 0 - 0 (overlap rmsk) 0 (short insertion) - 0 (high depth) = 0
generate the overall distribution of transposon mapping reads, first map all reads to transposon	nie, 16 kwi 2023, 12:53:48 CEST
sam to bed and bedGraph, multiple mappers are divided by their map times	nie, 16 kwi 2023, 12:53:54 CEST
[bam_sort_core] merging from 0 files and 2 in-memory blocks...
mkdir: nie można utworzyć katalogu „test.transposonMapping”: Plik istnieje
estimate de novo insertion number for each transposon using singleton reads	nie, 16 kwi 2023, 12:53:58 CEST
Error: unable to open file or unable to determine types for file test.TPregion.bed

- Please ensure that your file is TAB delimited (e.g., cat -t FILE).
- Also ensure that your file has integer chromosome coordinates in the 
  expected columns (e.g., cols 2 and 3 for BED).
Error: unable to open file or unable to determine types for file test.TPregion.bed

- Please ensure that your file is TAB delimited (e.g., cat -t FILE).
- Also ensure that your file has integer chromosome coordinates in the 
  expected columns (e.g., cols 2 and 3 for BED).
Błąd w poleceniu '`[.data.frame`(soma, , 4)':nie wybrano kolumn
Wywołania: [ -> [.data.frame
Wykonywanie wstrzymane
generate distribution figures for singleton supporting reads	nie, 16 kwi 2023, 12:53:58 CEST
Błąd w poleceniu 'read.table(Args[6], header = F, row.names = NULL)':
  nie ma dostępnych linii na wejściu
Wykonywanie wstrzymane
filter unreliable singleton insertions, also filter 2p insertions overlapped with similar reference transposon copies	nie, 16 kwi 2023, 12:53:59 CEST
Error: unable to open file or unable to determine types for file test.tmp

- Please ensure that your file is TAB delimited (e.g., cat -t FILE).
- Also ensure that your file has integer chromosome coordinates in the 
  expected columns (e.g., cols 2 and 3 for BED).
Error: unable to open file or unable to determine types for file test.tmp

- Please ensure that your file is TAB delimited (e.g., cat -t FILE).
- Also ensure that your file has integer chromosome coordinates in the 
  expected columns (e.g., cols 2 and 3 for BED).
Calculate frequency of each transposon insertion	nie, 16 kwi 2023, 12:53:59 CEST
[main_samview] region "chr2L:0-0" could not be parsed. Continue anyway.
Error: unable to open file or unable to determine types for file test.tmp

- Please ensure that your file is TAB delimited (e.g., cat -t FILE).
- Also ensure that your file has integer chromosome coordinates in the 
  expected columns (e.g., cols 2 and 3 for BED).
get TSD, remove redundant insertions and recalculate de novo insertion rate	nie, 16 kwi 2023, 12:53:59 CEST
awk: line 6: regular expression compile failed (missing operand)
|

*****
***** ERROR: Requested column 2, but database file - only has fields 1 - 0.
Error: unable to open file or unable to determine types for file test.TPregion.bed

- Please ensure that your file is TAB delimited (e.g., cat -t FILE).
- Also ensure that your file has integer chromosome coordinates in the 
  expected columns (e.g., cols 2 and 3 for BED).
Expecting number field 3 line 2 of test.t, got ;;
calculate de novo insertion rate per genome	nie, 16 kwi 2023, 12:53:59 CEST
clean tmp files	nie, 16 kwi 2023, 12:53:59 CEST
Done, Congras!!!🍺🍺🍺

I have the environment installed in miniconda with:

perl                      5.32.1          2_h7f98852_perl5    conda-forge
perl-algorithm-diff       1.1903          pl5321hdfd78af_3    bioconda
perl-base                 2.23            pl5321hdfd78af_2    bioconda
perl-bio-asn1-entrezgene  1.73            pl5321hdfd78af_3    bioconda
perl-bio-coordinate       1.007001        pl5321hdfd78af_3    bioconda
perl-bio-featureio        1.6.905         pl5321hdfd78af_4    bioconda
perl-bio-samtools         1.43            pl5321h7132678_3    bioconda
perl-bio-searchio-hmmer   1.7.3           pl5321hdfd78af_0    bioconda
perl-bio-tools-phylo-paml 1.7.3           pl5321hdfd78af_3    bioconda
perl-bio-tools-run-alignment-clustalw 1.7.4           pl5321hdfd78af_3    bioconda
perl-bio-tools-run-alignment-tcoffee 1.7.4           pl5321hdfd78af_4    bioconda
perl-bioperl              1.7.8                hdfd78af_1    bioconda
perl-bioperl-core         1.7.8           pl5321hdfd78af_1    bioconda
perl-bioperl-run          1.007003        pl5321hdfd78af_0    bioconda
perl-business-isbn        3.007           pl5321hdfd78af_0    bioconda
perl-business-isbn-data   20210112.006    pl5321hdfd78af_0    bioconda
perl-capture-tiny         0.48            pl5321hdfd78af_2    bioconda
perl-carp                 1.38            pl5321hdfd78af_4    bioconda
perl-class-data-inheritable 0.09            pl5321hdfd78af_0    bioconda
perl-compress-raw-zlib    2.105           pl5321h87f3376_0    bioconda
perl-constant             1.33            pl5321hdfd78af_2    bioconda
perl-data-dumper          2.183           pl5321hec16e2b_1    bioconda
perl-db_file              1.858           pl5321h166bdaf_0    conda-forge
perl-devel-stacktrace     2.04            pl5321hdfd78af_1    bioconda
perl-digest-hmac          1.04            pl5321hdfd78af_0    bioconda
perl-digest-md5           2.58            pl5321hec16e2b_1    bioconda
perl-encode               3.19            pl5321hec16e2b_1    bioconda
perl-encode-locale        1.05            pl5321hdfd78af_7    bioconda
perl-exception-class      1.45            pl5321hdfd78af_0    bioconda
perl-exporter             5.72            pl5321hdfd78af_2    bioconda
perl-extutils-makemaker   7.70            pl5321hd8ed1ab_0    conda-forge
perl-file-listing         6.15            pl5321hdfd78af_0    bioconda
perl-file-slurp-tiny      0.004           pl5321hdfd78af_2    bioconda
perl-file-sort            1.01            pl5321hdfd78af_3    bioconda
perl-file-spec            3.48_01         pl5321hdfd78af_2    bioconda
perl-getopt-long          2.54            pl5321hdfd78af_0    bioconda
perl-html-parser          3.81            pl5321h9f5acd7_0    bioconda
perl-html-tagset          3.20            pl5321hdfd78af_4    bioconda
perl-http-cookies         6.10            pl5321hdfd78af_0    bioconda
perl-http-daemon          6.16            pl5321hdfd78af_0    bioconda
perl-http-date            6.05            pl5321hdfd78af_0    bioconda
perl-http-message         6.36            pl5321hdfd78af_0    bioconda
perl-http-negotiate       6.01            pl5321hdfd78af_4    bioconda
perl-io-html              1.004           pl5321hdfd78af_0    bioconda
perl-io-socket-ssl        2.074           pl5321hdfd78af_0    bioconda
perl-io-string            1.08            pl5321hdfd78af_4    bioconda
perl-io-tty               1.16            pl5321hec16e2b_1    bioconda
perl-ipc-run              20200505.0      pl5321hdfd78af_0    bioconda
perl-libwww-perl          6.67            pl5321hdfd78af_0    bioconda
perl-libxml-perl          0.08            pl5321hdfd78af_3    bioconda
perl-lwp-mediatypes       6.04            pl5321hdfd78af_1    bioconda
perl-mime-base64          3.16            pl5321hec16e2b_2    bioconda
perl-net-http             6.22            pl5321hdfd78af_0    bioconda
perl-net-ssleay           1.92            pl5321h0e0aaa8_1    bioconda
perl-ntlm                 1.09            pl5321hdfd78af_5    bioconda
perl-parent               0.236           pl5321hdfd78af_2    bioconda
perl-socket               2.027           pl5321hec16e2b_3    bioconda
perl-sub-uplevel          0.2800          pl5321hec16e2b_4    bioconda
perl-test-deep            1.130           pl5321hdfd78af_0    bioconda
perl-test-differences     0.69            pl5321hdfd78af_0    bioconda
perl-test-exception       0.43            pl5321hdfd78af_3    bioconda
perl-test-most            0.38            pl5321hdfd78af_0    bioconda
perl-test-warn            0.36            pl5321hdfd78af_2    bioconda
perl-text-diff            1.45            pl5321hdfd78af_1    bioconda
perl-time-local           1.30            pl5321hdfd78af_0    bioconda
perl-timedate             2.33            pl5321hdfd78af_2    bioconda
perl-tree-dag_node        1.32            pl5321hdfd78af_0    bioconda
perl-try-tiny             0.31            pl5321hdfd78af_1    bioconda
perl-uri                  5.12            pl5321hdfd78af_0    bioconda
perl-url-encode           0.03            pl5321h9ee0642_0    bioconda
perl-www-robotrules       6.02            pl5321hdfd78af_4    bioconda
perl-xml-dom              1.46            pl5321hdfd78af_1    bioconda
perl-xml-dom-xpath        0.14            pl5321hdfd78af_2    bioconda
perl-xml-parser           2.44_01         pl5321hc3e0081_1003    conda-forge
perl-xml-regexp           0.04            pl5321hdfd78af_3    bioconda
perl-xml-xpathengine      0.14            pl5321hdfd78af_3    bioconda
pip                       20.1.1             pyh9f0ad1d_0    conda-forge
pixman                    0.38.0            h516909a_1003    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
python                    2.7.18               h42bf7aa_3  
python_abi                2.7                    1_cp27mu    conda-forge
r                         4.2             r42hd8ed1ab_1006    conda-forge
r-base                    4.2.0                h1ae530e_0  
r-boot                    1.3_28.1          r42hc72bb7e_0    conda-forge
r-class                   7.3_21            r42h133d619_0    conda-forge
r-cluster                 2.1.4             r42h8da6f51_0    conda-forge
r-codetools               0.2_19            r42hc72bb7e_0    conda-forge
r-foreign                 0.8_84            r42h133d619_0    conda-forge
r-kernsmooth              2.23_20           r42hd009a43_1    conda-forge
r-lattice                 0.21_8            r42h133d619_0    conda-forge
r-mass                    7.3_58.3          r42h133d619_0    conda-forge
r-matrix                  1.5_4             r42he1ae0d6_0    conda-forge
r-mgcv                    1.8_42            r42he1ae0d6_0    conda-forge
r-nlme                    3.1_157           r42h640688f_0  
r-nnet                    7.3_18            r42h06615bd_1    conda-forge
r-recommended             4.2             r42hd8ed1ab_1005    conda-forge
r-rpart                   4.1.19            r42h06615bd_0    conda-forge
r-spatial                 7.3_16            r42h133d619_0    conda-forge
r-survival

Same errors for Python version 3.8 and 2.7.

I hope you can help me get this problem solved. Sorry that some messages are in Polish, but I think the most important message is in English.
Best,
Paulina

tianxiongbb commented
tianxiongbb commented
Psula23 commented

Thank you for your answer. It turned out to be helpful and meaningful to my errors. In addition, I had to install Python version 2.7 and Bedtools outside of Miniconda (error: unrecognized command: intersectBed). And now everything works fine.

Best,
Paulina