stopped at step 14
Closed this issue · 6 comments
the run is showing this error
"wc: /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/: Is a directory
wc: /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/: Is a directory
wc: /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/metabat2/: Is a directory
Error running command: jgi_summarize_bam_contig_depths /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL1.bam /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL2.bam /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL3.bam --outputDepth /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/metabat2/contigs.depth.txt.PROV >> /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/syslog 2>&1 at /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/lib/SqueezeMeta/bin_metabat2.pl line 62.
wc: /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/metabat2/: Is a directory
wc: /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/bins/: Is a directory"
and bin is not generated
kindly help me.
syslog:
Run started Wed Aug 21 16:14:32 2024 in coassembly mode
SqueezeMeta v1.6.3, September 2023 - (c) J. Tamames, F. Puente-Sánchez CNB-CSIC, Madrid, SPAIN
Please cite: Tamames & Puente-Sanchez, Frontiers in Microbiology 10.3389 (2019). doi: https://doi.org/10.3389/fmicb.2018.03349
Run started for DS_Squeezmeta_Results, Wed Aug 21 16:14:32 2024
Project: DS_Squeezmeta_Results
Map file: test.samples
Fastq directory: /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/RawData
Command: /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/scripts/SqueezeMeta.pl -t 12 -m coassembly -p DS_Squeezmeta_Results -s test.samples -f /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/RawData
[0 seconds]: STEP0 -> SqueezeMeta.pl
COGS; KEGG; PFAM;
[0 seconds]: STEP1 -> 01.run_all_assemblies.pl (megahit)
Preparing files for pair1: cat /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/RawData/D1_R1.fastq /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/RawData/D2_R1.fastq /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/RawData/D3_R1.fastq > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/raw_fastq/par1.fastq
Preparing files for pair2: cat /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/RawData/D1_R2.fastq /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/RawData/D2_R2.fastq /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/RawData/D3_R2.fastq > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/raw_fastq/par2.fastq
Running assembly with megahit: perl /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/lib/SqueezeMeta/assembly_megahit.pl /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results DS_Squeezmeta_Results /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/raw_fastq/par1.fastq /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/raw_fastq/par2.fastq
2024-08-21 16:22:05 - MEGAHIT v1.2.9
2024-08-21 16:22:05 - Using megahit_core with POPCNT and BMI2 support
2024-08-21 16:22:05 - Convert reads to binary library
2024-08-21 16:38:36 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 0 (/media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/raw_fastq/par1.fastq,/media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/raw_fastq/par2.fastq): pe, 104440926 reads, 151 max length'
2024-08-21 16:38:36 - b'INFO utils/utils.h : 152 - Real: 991.0421\tuser: 239.3704\tsys: 72.3044\tmaxrss: 246312'
2024-08-21 16:38:36 - k-max reset to: 141
2024-08-21 16:38:36 - Start assembly. Number of CPU threads 12
2024-08-21 16:38:36 - k list: 21,29,39,59,79,99,119,141
2024-08-21 16:38:36 - Memory used: 60456565555
2024-08-21 16:38:36 - Extract solid (k+1)-mers for k = 21
2024-08-21 16:51:49 - Build graph for k = 21
2024-08-21 17:22:21 - Assemble contigs from SdBG for k = 21
2024-08-21 20:03:51 - Local assembly for k = 21
2024-08-21 20:07:53 - Extract iterative edges from k = 21 to 29
2024-08-21 20:21:40 - Build graph for k = 29
2024-08-21 20:34:49 - Assemble contigs from SdBG for k = 29
2024-08-21 21:37:29 - Local assembly for k = 29
2024-08-21 21:44:46 - Extract iterative edges from k = 29 to 39
2024-08-21 21:48:18 - Build graph for k = 39
2024-08-21 21:55:58 - Assemble contigs from SdBG for k = 39
2024-08-21 22:48:41 - Local assembly for k = 39
2024-08-21 22:58:33 - Extract iterative edges from k = 39 to 59
2024-08-21 23:00:29 - Build graph for k = 59
2024-08-21 23:05:46 - Assemble contigs from SdBG for k = 59
2024-08-21 23:32:32 - Local assembly for k = 59
2024-08-21 23:42:11 - Extract iterative edges from k = 59 to 79
2024-08-21 23:43:27 - Build graph for k = 79
2024-08-21 23:46:06 - Assemble contigs from SdBG for k = 79
2024-08-21 23:59:19 - Local assembly for k = 79
2024-08-22 00:07:39 - Extract iterative edges from k = 79 to 99
2024-08-22 00:08:39 - Build graph for k = 99
2024-08-22 00:10:26 - Assemble contigs from SdBG for k = 99
2024-08-22 00:19:36 - Local assembly for k = 99
2024-08-22 00:26:16 - Extract iterative edges from k = 99 to 119
2024-08-22 00:26:59 - Build graph for k = 119
2024-08-22 00:28:18 - Assemble contigs from SdBG for k = 119
2024-08-22 00:35:23 - Local assembly for k = 119
2024-08-22 00:41:10 - Extract iterative edges from k = 119 to 141
2024-08-22 00:41:39 - Build graph for k = 141
2024-08-22 00:42:42 - Assemble contigs from SdBG for k = 141
2024-08-22 00:48:44 - Merging to output final contigs
2024-08-22 00:48:55 - 1118299 contigs, total 659201744 bp, min 200 bp, max 98624 bp, avg 589 bp, N50 571 bp
2024-08-22 00:48:56 - ALL DONE. Time elapsed: 30411.015075 seconds
Running prinseq for selecting contigs longer than 200: /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/prinseq-lite.pl -fasta /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/01.DS_Squeezmeta_Results.fasta -min_len 200 -out_good /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/prinseq; mv /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/prinseq.fasta /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/01.DS_Squeezmeta_Results.fasta > /dev/null 2>&1
Running prinseq for contig statistics: /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/prinseq-lite.pl -fasta /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/01.DS_Squeezmeta_Results.fasta -stats_len -stats_info -stats_assembly > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/01.DS_Squeezmeta_Results.stats
[8 hours, 35 minutes, 26 seconds]: STEP2 -> 02.rnas.pl
Running barrnap for Bacteria: /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/barrnap --quiet --threads 12 --kingdom bac --reject 0.1 /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/02.DS_Squeezmeta_Results.maskedrna.fasta --dbdir /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/database/db > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/bac.gff
Running barrnap for Archaea: /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/barrnap --quiet --threads 12 --kingdom arc --reject 0.1 /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/02.DS_Squeezmeta_Results.maskedrna.fasta --dbdir /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/database/db > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/arc.gff
Running barrnap for Eukaryote: /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/barrnap --quiet --threads 12 --kingdom euk --reject 0.1 /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/02.DS_Squeezmeta_Results.maskedrna.fasta --dbdir /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/database/db > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/euk.gff
Running barrnap for Mitochondrial: /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/barrnap --quiet --threads 12 --kingdom mito --reject 0.1 /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/02.DS_Squeezmeta_Results.maskedrna.fasta --dbdir /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/database/db > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/mito.gff
Running RDP classifier: java -jar /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/lib/classifier/classifier.jar classify /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/16S.fasta -o /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/16S.out -f filterbyconf
Running Aragorn: /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/aragorn -w /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/02.DS_Squeezmeta_Results.maskedrna.fasta -o /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/trnas.aragorn
Creating new gff file: cat /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/*gff.mod > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/02.DS_Squeezmeta_Results.rna.gff
[8 hours, 46 minutes, 2 seconds]: STEP3 -> 03.run_prodigal.pl
Running prodigal for predicting ORFs: /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/prodigal -q -m -p meta -i /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/02.DS_Squeezmeta_Results.maskedrna.fasta -a /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/03.DS_Squeezmeta_Results.faa -d /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/03.DS_Squeezmeta_Results.fna -f gff -o /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/02.DS_Squeezmeta_Results.cds.gff.temp
[9 hours, 40 minutes, 27 seconds]: STEP4 -> 04.rundiamond.pl
Diamond block size set to 7.3 (Free Mem 58.41 Gb)
Working with taxonomy database in /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/database/db/nr.dmnd
Running Diamond for taxa: /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/diamond blastp -q /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/03.DS_Squeezmeta_Results.faa -p 12 -d /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/database/db/nr.dmnd -e 0.001 --id 40 -f tab -b 7.3 -o /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/04.DS_Squeezmeta_Results.nr.diamond > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/diamond.nr.log 2>&1
Running Diamond for COGs: /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/diamond blastp -q /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/03.DS_Squeezmeta_Results.faa -p 12 -d /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/database/db/eggnog -e 0.001 --id 30 --quiet -b 7.3 -f 6 qseqid qlen sseqid slen pident length evalue bitscore qstart qend sstart send -o /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/04.DS_Squeezmeta_Results.eggnog.diamond
Running Diamond for KEGG: /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/diamond blastp -q /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/03.DS_Squeezmeta_Results.faa -p 12 -d /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/database/db/keggdb -e 0.001 --id 30 --quiet -b 7.3 -f 6 qseqid qlen sseqid slen pident length evalue bitscore qstart qend sstart send -o /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/04.DS_Squeezmeta_Results.kegg.diamond
[1 days, 9 hours, 47 minutes, 21 seconds]: STEP5 -> 05.run_hmmer.pl
Running HMMER3 for Pfam: /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/hmmer/hmmsearch --domtblout /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/05.DS_Squeezmeta_Results.pfam.hmm -E 1e-10 --cpu 12 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/database/db/Pfam-A.hmm /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/03.DS_Squeezmeta_Results.faa > /dev/null 2>&1
[1 days, 21 hours, 19 minutes, 35 seconds]: STEP6 -> 06.lca.pl
Splitting Diamond file
Total lines in Diamond: 31726499; Allocating 2643874 in 12 threads
Opening file 1 in line (estimated in 2643874)
Opening file 2 in line 2643895 (estimated in 2643874)
Opening file 3 in line 5287758 (estimated in 5287748)
Opening file 4 in line 7931643 (estimated in 7931622)
Opening file 5 in line 10575506 (estimated in 10575496)
Opening file 6 in line 13219384 (estimated in 13219370)
Opening file 7 in line 15863257 (estimated in 15863244)
Opening file 8 in line 18507135 (estimated in 18507118)
Opening file 9 in line 21151015 (estimated in 21150992)
Opening file 10 in line 23794870 (estimated in 23794866)
Opening file 11 in line 26438754 (estimated in 26438740)
Opening file 12 in line 29082637 (estimated in 29082614)
Starting multithread LCA in 12 threads
Starting thread 2
Starting thread 5
Starting thread 10
Starting thread 11
Starting thread 1
Starting thread 3
Starting thread 4
Starting thread 12
Starting thread 6
Starting thread 7
Starting thread 9
Starting thread 8
Creating /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/06.DS_Squeezmeta_Results.fun3.tax.wranks file: cat /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_1.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_2.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_3.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_4.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_5.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_6.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_7.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_8.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_9.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_10.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_11.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_12.wranks > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/06.DS_Squeezmeta_Results.fun3.tax.wranks
Creating /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/06.DS_Squeezmeta_Results.fun3.tax.noidfilter.wranks file: cat /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_1.noidfilter.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_2.noidfilter.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_3.noidfilter.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_4.noidfilter.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_5.noidfilter.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_6.noidfilter.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_7.noidfilter.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_8.noidfilter.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_9.noidfilter.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_10.noidfilter.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_11.noidfilter.wranks /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/fun3tax_12.noidfilter.wranks > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/06.DS_Squeezmeta_Results.fun3.tax.noidfilter.wranks
Removing temporaty diamond files in /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp
[1 days, 21 hours, 27 minutes, 50 seconds]: STEP7 -> 07.fun3assign.pl
Reading COGs hits from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/04.DS_Squeezmeta_Results.eggnog.diamond
Output in /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/07.DS_Squeezmeta_Results.fun3.cog
Reading KEGG hits from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/04.DS_Squeezmeta_Results.kegg.diamond
Output in /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/07.DS_Squeezmeta_Results.fun3.kegg
Reading pfam hits from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/05.DS_Squeezmeta_Results.pfam.hmm
Output in /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/07.DS_Squeezmeta_Results.fun3.pfam
[1 days, 21 hours, 30 minutes, 5 seconds]: STEP9 -> 09.summarycontigs3.pl
Reading taxa for genes from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/06.DS_Squeezmeta_Results.fun3.tax.wranks
Writing output to /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/09.DS_Squeezmeta_Results.allorfs and /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/09.DS_Squeezmeta_Results.contiglog
Reading taxa for genes from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/06.DS_Squeezmeta_Results.fun3.tax.noidfilter.wranks
Writing output to /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/09.DS_Squeezmeta_Results.allorfs.noidfilter and /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/09.DS_Squeezmeta_Results.contiglog.noidfilter
[1 days, 21 hours, 35 minutes, 9 seconds]: STEP10 -> 10.mapsamples.pl
Creating Bowtie reference: python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/bowtie2/bowtie2-build --quiet /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/01.DS_Squeezmeta_Results.fasta /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/DS_Squeezmeta_Results.bowtie
Getting raw reads for DL1: cp /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/RawData/D1_R1.fastq /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.DL1.current_1; cp /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/RawData/D1_R2.fastq /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.DL1.current_2;
Aligning with bowtie: /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/bowtie2/bowtie2 -x /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/DS_Squeezmeta_Results.bowtie -1 /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.DL1.current_1 -2 /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.DL1.current_2 --quiet -p 12 -S /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL1.sam --very-sensitive-local
Calling sqm_counter: Sample DL1, BAM /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL1.bam, Number of reads 25527322
Getting raw reads for DL2: cp /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/RawData/D2_R1.fastq /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.DL2.current_1; cp /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/RawData/D2_R2.fastq /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.DL2.current_2;
Aligning with bowtie: /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/bowtie2/bowtie2 -x /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/DS_Squeezmeta_Results.bowtie -1 /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.DL2.current_1 -2 /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.DL2.current_2 --quiet -p 12 -S /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL2.sam --very-sensitive-local
Calling sqm_counter: Sample DL2, BAM /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL2.bam, Number of reads 35921832
Getting raw reads for DL3: cp /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/RawData/D3_R1.fastq /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.DL3.current_1; cp /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/RawData/D3_R2.fastq /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.DL3.current_2;
Aligning with bowtie: /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/bowtie2/bowtie2 -x /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/DS_Squeezmeta_Results.bowtie -1 /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.DL3.current_1 -2 /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.DL3.current_2 --quiet -p 12 -S /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL3.sam --very-sensitive-local
Calling sqm_counter: Sample DL3, BAM /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL3.bam, Number of reads 42991772
Sorting mapcount table: sort -T /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp -t _ -k 2 -k 3 -n /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/10.DS_Squeezmeta_Results.mapcount > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/mapcount.temp; mv /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/mapcount.temp /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/10.DS_Squeezmeta_Results.mapcount
[1 days, 23 hours, 11 minutes, 15 seconds]: STEP11 -> 11.mcount.pl
Reading contig length from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/01.DS_Squeezmeta_Results.lon
Reading contig taxa from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/09.DS_Squeezmeta_Results.contiglog
Reading contig coverages from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/10.DS_Squeezmeta_Results.contigcov
Writing output to /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/11.DS_Squeezmeta_Results.mcount
[1 days, 23 hours, 11 minutes, 48 seconds]: STEP12 -> 12.funcover.pl
Creating cog coverage output in /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/12.DS_Squeezmeta_Results.cog.funcover
Creating kegg coverage output in /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/12.DS_Squeezmeta_Results.kegg.funcover
Creating cog raw reads output in /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/ext_tables/12.DS_Squeezmeta_Results.cog.stamp
Creating kegg raw reads output in /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/ext_tables/12.DS_Squeezmeta_Results.kegg.stamp
[1 days, 23 hours, 13 minutes, 35 seconds]: STEP13 -> 13.mergeannot2.pl
Creating table in /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/13.DS_Squeezmeta_Results.orftable
Reading GFF in /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/03.DS_Squeezmeta_Results.gff
Reading Diamond hits from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/04.DS_Squeezmeta_Results.nr.diamond
Reading aa sequences from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/03.DS_Squeezmeta_Results.faa
Reading nt sequences
Reading rRNA sequences
Reading tRNA/tmRNA sequences from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/02.DS_Squeezmeta_Results.trnas
Reading ORF information from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/06.DS_Squeezmeta_Results.fun3.tax.wranks
Calculating GC content for genes using /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/03.DS_Squeezmeta_Results.fna
Calculating GC content for RNAs using /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/02.DS_Squeezmeta_Results.rnas
Reading contig information from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/09.DS_Squeezmeta_Results.contiglog
Reading KEGG annotations from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/07.DS_Squeezmeta_Results.fun3.kegg
Reading COGs annotations from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/07.DS_Squeezmeta_Results.fun3.cog
Reading Pfam annotations from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/07.DS_Squeezmeta_Results.fun3.pfam
Reading RPKMs and Coverages from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/10.DS_Squeezmeta_Results.mapcount
GENE TABLE CREATED: /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/13.DS_Squeezmeta_Results.orftable
[1 days, 23 hours, 19 minutes, 10 seconds]: STEP14 -> 14.runbinning.pl
RUNNING concoct
Cutting contigs in pieces!: python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/cut_up_fasta.py /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/01.DS_Squeezmeta_Results.fasta -c 10000 -o 0 --merge_last -b /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.contigs.bed > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.choppedcontigs.fasta
Creating abundance table: PATH=/home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin:$PATH python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/concoct_coverage_table.py /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.contigs.bed /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL2.bam /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL3.bam /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL1.bam > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/coverage_table.tsv
Running concoct: OMP_THREAD_LIMIT=12 python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/bin/concoct --composition_file /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.choppedcontigs.fasta --coverage_file /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/coverage_table.tsv --threads 12 -b /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/concoct_int/ > /dev/null 2>&1
Merging clusters: python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/merge_cutup_clustering.py /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/concoct_int/clustering_gt1000.csv > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/concoct_int/clustering_merged.csv 2> /dev/null
Extracting final bins: python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/extract_fasta_bins.py /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/01.DS_Squeezmeta_Results.fasta /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/concoct_int/clustering_merged.csv --output_path /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct > /dev/null 2>&1
Creating coverage file in /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/metabat2/contigs.depth.txt
jgi_summarize_bam_contig_depths: /lib/x86_64-linux-gnu/libm.so.6: version GLIBC_2.29' not found (required by jgi_summarize_bam_contig_depths) jgi_summarize_bam_contig_depths: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version GLIBCXX_3.4.26' not found (required by jgi_summarize_bam_contig_depths)
[1 days, 23 hours, 31 minutes, 1 seconds]: STEP15 -> 15.dastool.pl
Running DAS Tool for : LD_LIBRARY_PATH=/home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/lib PATH=/home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin:$PATH /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/DAS_Tool/DAS_Tool -i -l -c /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/01.DS_Squeezmeta_Results.fasta --write_bins 1 --score_threshold 0 --search_engine diamond -t 12 -o /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/DAS/DS_Squeezmeta_Results --db_directory /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/database/db
[1 days, 23 hours, 31 minutes, 2 seconds]: STEP19 -> 19.getcontigs.pl
Reading taxa for contigs information from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/09.DS_Squeezmeta_Results.contiglog
Reading GC & length from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/01.DS_Squeezmeta_Results.fasta
Reading number of genes from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/03.DS_Squeezmeta_Results.faa
Reading coverages from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/10.DS_Squeezmeta_Results.contigcov
Reading bins from /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/18.DS_Squeezmeta_Results.contigsinbins
Creating contig table in /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/19.DS_Squeezmeta_Results.contigtable
[1 days, 23 hours, 34 minutes, 29 seconds]: STEP21 -> 21.stats.pl
Deleting temporary files in /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp
[1 days, 23 hours, 35 minutes, 43 seconds]: FINISHED -> Have fun!
[7 seconds]: STEP14 -> 14.runbinning.pl
RUNNING concoct
Cutting contigs in pieces!: python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/cut_up_fasta.py /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/01.DS_Squeezmeta_Results.fasta -c 10000 -o 0 --merge_last -b /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.contigs.bed > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.choppedcontigs.fasta
Creating abundance table: PATH=/home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin:$PATH python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/concoct_coverage_table.py /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.contigs.bed /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL1.bam /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL3.bam /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL2.bam > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/coverage_table.tsv
Running concoct: OMP_THREAD_LIMIT=12 python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/bin/concoct --composition_file /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.choppedcontigs.fasta --coverage_file /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/coverage_table.tsv --threads 12 -b /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/concoct_int/ > /dev/null 2>&1
Merging clusters: python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/merge_cutup_clustering.py /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/concoct_int/clustering_gt1000.csv > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/concoct_int/clustering_merged.csv 2> /dev/null
Extracting final bins: python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/extract_fasta_bins.py /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/01.DS_Squeezmeta_Results.fasta /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/concoct_int/clustering_merged.csv --output_path /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct > /dev/null 2>&1
Creating coverage file in /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/metabat2/contigs.depth.txt
jgi_summarize_bam_contig_depths: /lib/x86_64-linux-gnu/libm.so.6: version GLIBC_2.29' not found (required by jgi_summarize_bam_contig_depths) jgi_summarize_bam_contig_depths: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version GLIBCXX_3.4.26' not found (required by jgi_summarize_bam_contig_depths)
[11 minutes, 57 seconds]: STEP15 -> 15.dastool.pl
Running DAS Tool for : LD_LIBRARY_PATH=/home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/lib PATH=/home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin:$PATH /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/DAS_Tool/DAS_Tool -i -l -c /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/01.DS_Squeezmeta_Results.fasta --write_bins 1 --score_threshold 0 --search_engine diamond -t 12 -o /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/DAS/DS_Squeezmeta_Results --db_directory /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/database/db
Deleting temporary files in /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp
[11 minutes, 57 seconds]: FINISHED -> Have fun!
[3 seconds]: STEP14 -> 14.runbinning.pl
RUNNING concoct
Cutting contigs in pieces!: python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/cut_up_fasta.py /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/01.DS_Squeezmeta_Results.fasta -c 10000 -o 0 --merge_last -b /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.contigs.bed > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.choppedcontigs.fasta
Creating abundance table: PATH=/home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin:$PATH python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/concoct_coverage_table.py /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.contigs.bed /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL2.bam /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL1.bam /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL3.bam > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/coverage_table.tsv
Running concoct: OMP_THREAD_LIMIT=12 python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/bin/concoct --composition_file /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.choppedcontigs.fasta --coverage_file /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/coverage_table.tsv --threads 12 -b /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/concoct_int/ > /dev/null 2>&1
Merging clusters: python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/merge_cutup_clustering.py /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/concoct_int/clustering_gt1000.csv > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/concoct_int/clustering_merged.csv 2> /dev/null
Extracting final bins: python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/extract_fasta_bins.py /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/01.DS_Squeezmeta_Results.fasta /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/concoct_int/clustering_merged.csv --output_path /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct > /dev/null 2>&1
Creating coverage file in /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/metabat2/contigs.depth.txt
jgi_summarize_bam_contig_depths: /lib/x86_64-linux-gnu/libm.so.6: version GLIBC_2.29' not found (required by jgi_summarize_bam_contig_depths) jgi_summarize_bam_contig_depths: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version GLIBCXX_3.4.26' not found (required by jgi_summarize_bam_contig_depths)
[11 minutes, 55 seconds]: STEP15 -> 15.dastool.pl
Running DAS Tool for : LD_LIBRARY_PATH=/home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/lib PATH=/home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin:$PATH /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/DAS_Tool/DAS_Tool -i -l -c /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/01.DS_Squeezmeta_Results.fasta --write_bins 1 --score_threshold 0 --search_engine diamond -t 12 -o /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/DAS/DS_Squeezmeta_Results --db_directory /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/database/db
Deleting temporary files in /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp
[11 minutes, 56 seconds]: FINISHED -> Have fun!
[3 seconds]: STEP14 -> 14.runbinning.pl
RUNNING concoct
Cutting contigs in pieces!: python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/cut_up_fasta.py /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/01.DS_Squeezmeta_Results.fasta -c 10000 -o 0 --merge_last -b /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.contigs.bed > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.choppedcontigs.fasta
Creating abundance table: PATH=/home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin:$PATH python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/concoct_coverage_table.py /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.contigs.bed /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL2.bam /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL1.bam /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/data/bam/DS_Squeezmeta_Results.DL3.bam > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/coverage_table.tsv
Running concoct: OMP_THREAD_LIMIT=12 python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/bin/concoct --composition_file /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp/DS_Squeezmeta_Results.choppedcontigs.fasta --coverage_file /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/coverage_table.tsv --threads 12 -b /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/concoct_int/ > /dev/null 2>&1
Merging clusters: python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/merge_cutup_clustering.py /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/concoct_int/clustering_gt1000.csv > /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/concoct_int/clustering_merged.csv 2> /dev/null
Extracting final bins: python3 /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/extract_fasta_bins.py /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/01.DS_Squeezmeta_Results.fasta /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct/concoct_int/clustering_merged.csv --output_path /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/concoct > /dev/null 2>&1
Creating coverage file in /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/metabat2/contigs.depth.txt
jgi_summarize_bam_contig_depths: /lib/x86_64-linux-gnu/libm.so.6: version GLIBC_2.29' not found (required by jgi_summarize_bam_contig_depths) jgi_summarize_bam_contig_depths: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version GLIBCXX_3.4.26' not found (required by jgi_summarize_bam_contig_depths)
[12 minutes, 8 seconds]: STEP15 -> 15.dastool.pl
Running DAS Tool for : LD_LIBRARY_PATH=/home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/lib PATH=/home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin:$PATH /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/bin/DAS_Tool/DAS_Tool -i -l -c /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/results/01.DS_Squeezmeta_Results.fasta --write_bins 1 --score_threshold 0 --search_engine diamond -t 12 -o /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/intermediate/binners/DAS/DS_Squeezmeta_Results --db_directory /home/ham/Desktop/Metagenome/NGS_Tools/SqueezeMeta/database/db
Deleting temporary files in /media/ham/HAM_lab/Ayush/data/for_squeezemeta/darjeeling/analysis/DS_Squeezmeta_Results/temp
[12 minutes, 9 seconds]: FINISHED -> Have fun!
jgi_summarize_bam_contig_depths: /lib/x86_64-linux-gnu/libm.so.6: version GLIBC_2.29' not found (required by jgi_summarize_bam_contig_depths) jgi_summarize_bam_contig_depths: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version GLIBCXX_3.4.26' not found (required by jgi_summarize_bam_contig_depths)
jgi_summarize_bam_contig_depths: /lib/x86_64-linux-gnu/libm.so.6: version GLIBC_2.29' not found (required by jgi_summarize_bam_contig_depths) jgi_summarize_bam_contig_depths: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version GLIBCXX_3.4.26' not found (required by jgi_summarize_bam_contig_depths)
The problem is here
jgi_summarize_bam_contig_depths: /lib/x86_64-linux-gnu/libm.so.6: version GLIBC_2.29' not found (required by jgi_summarize_bam_contig_depths) jgi_summarize_bam_contig_depths: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version GLIBCXX_3.4.26' not found (required by jgi_summarize_bam_contig_depths)
jgi_summarize_bam_contig_depths (itself part of metabat2) was compiled against a newer version of GLIBC than the one in your system. What linux distribution and version are you using?
An temporary solution would be to avoid metabat2 by adding -binners concoct or -binners concoct,maxbin when calling SqueezeMeta.
A definitive solution would be to compile metabat2 from source in your machine and then instruct SqueezeMeta to use those binaries instead of the ones from conda.
Source code and compilation/testing instructions for metabat2 can be found here https://bitbucket.org/berkeleylab/metabat/src/master/.
Once you have a metabat2 binary that is compatible with your system I can guide you on how to make SqueezeMeta use it.
Currently, I am using glibc_2.29. Thank you for your advice, I will follow your advice and revert back
Update! I have successfully run the pipeline, thank you for your advice.
Glad to hear! What fixed it? Did you compile metabat2 from source?
I ran the metabat2 independently, put the output in the project directory, and restarted the pipeline. It worked fine but again stopped at the checkM step for which some binaries and checkM data were missing again, I did the same thing and put the output file in a proper format in the result directory of the project. It completed all the steps. I am facing some issues with the system itself due to conda environment conflicts for which I guess I have to update the linux.
Yeah I also suspect that some of your system libraries are quite old at this point. Anyways glad you could figure it out. Closing issue