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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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Issue at Diamond FIle splitting and LCA #629

Closed vmevada102 closed 1 year ago

vmevada102 commented 1 year ago

Run started Sat Feb 18 22:02:53 2023 in sequential mode 1 metagenomes found: SRR953529

--- SAMPLE SRR953529 -------- Now creating directories Reading configuration from /home/user/Desktop/squeezemetarun/SRR953529/SqueezeMeta_conf.pl [0 seconds]: STEP1 -> RUNNING ASSEMBLY: 01.run_all_assemblies.pl (megahit) Working for sample SRR953529 Preparing files for pair1: cat /home/user/Desktop/squeezemetarun/raw//SRR953529_1.fastq.gz > /home/user/Desktop/squeezemetarun/SRR953529/data/raw_fastq/par1.fastq.gz Preparing files for pair2: cat /home/user/Desktop/squeezemetarun/raw//SRR953529_2.fastq.gz > /home/user/Desktop/squeezemetarun/SRR953529/data/raw_fastq/par2.fastq.gz Running assembly with megahit: perl /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/lib/SqueezeMeta/assembly_megahit.pl /home/user/Desktop/squeezemetarun/SRR953529 SRR953529 /home/user/Desktop/squeezemetarun/SRR953529/data/raw_fastq/par1.fastq.gz /home/user/Desktop/squeezemetarun/SRR953529/data/raw_fastq/par2.fastq.gz Running prinseq (Schmieder et al 2011, Bioinformatics 27(6):863-4) for selecting contigs longer than 200 Input and filter stats: Input sequences: 1 Input bases: 207 Input mean length: 207.00 Good sequences: 1 (100.00%) Good bases: 207 Good mean length: 207.00 Bad sequences: 0 (0.00%) Sequences filtered by specified parameters: none Renaming contigs Running prinseq for contig statistics: /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/bin/prinseq-lite.pl -fasta /home/user/Desktop/squeezemetarun/SRR953529/results/01.SRR953529.fasta -stats_len -stats_info -stats_assembly > /home/user/Desktop/squeezemetarun/SRR953529/intermediate/01.SRR953529.stats Counting length of contigs Contigs stored in /home/user/Desktop/squeezemetarun/SRR953529/results/01.SRR953529.fasta Number of contigs: 1 [23 seconds]: STEP2 -> RNA PREDICTION: 02.rnas.pl Running barrnap (Seeman 2014, Bioinformatics 30, 2068-9) for predicting RNAs: Bacteria Archaea Eukaryote Mitochondrial Running RDP classifier (Wang et al 2007, Appl Environ Microbiol 73, 5261-7) Running Aragorn (Laslett & Canback 2004, Nucleic Acids Res 31, 11-16) for tRNA/tmRNA prediction [31 seconds]: STEP3 -> ORF PREDICTION: 03.run_prodigal.pl Running prodigal (Hyatt et al 2010, BMC Bioinformatics 11: 119) for predicting ORFs ORFs predicted: 1 [31 seconds]: STEP4 -> HOMOLOGY SEARCHES: 04.rundiamond.pl Setting block size for Diamond AVAILABLE (free) RAM memory: 56.41 Gb We will set Diamond block size to 7.1 (Gb RAM/8, Max 16). You can override this setting using the -b option when starting the project, or changing the $blocksize variable in SqueezeMeta_conf.pl taxa COGS Running Diamond (Buchfink et al 2015, Nat Methods 12, 59-60) for KEGG

[21 minutes, 31 seconds]: STEP5 -> HMMER/PFAM: 05.run_hmmer.pl Running HMMER3 (Eddy 2009, Genome Inform 23, 205-11) for Pfam [22 minutes, 36 seconds]: STEP6 -> TAXONOMIC ASSIGNMENT: 06.lca.pl Splitting Diamond file Starting multithread LCA in 24 threads Thread 2 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.2.m8 Thread 3 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.3.m8 Thread 4 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.4.m8 Thread 5 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.5.m8 Thread 6 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.6.m8 Thread 7 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.7.m8 Thread 8 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.8.m8 Thread 9 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.9.m8 Thread 10 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.10.m8 Thread 11 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.11.m8 Thread 12 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.12.m8 Thread 13 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.13.m8 Thread 14 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.14.m8 Thread 15 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.15.m8 Thread 16 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.16.m8 Thread 17 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.17.m8 Thread 18 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.18.m8 Thread 19 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.19.m8 Thread 20 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.20.m8 Thread 21 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.21.m8 Thread 22 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.22.m8 Thread 23 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.23.m8 Thread 24 terminated abnormally: Cannot open /home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.24.m8 Creating /home/user/Desktop/squeezemetarun/SRR953529/results/06.SRR953529.fun3.tax.wranks file Creating /home/user/Desktop/squeezemetarun/SRR953529/results/06.SRR953529.fun3.tax.noidfilter.wranks file Stopping in STEP6 -> 06.lca.pl. File /home/user/Desktop/squeezemetarun/SRR953529/results/06.SRR953529.fun3.tax.wranks is empty!

If you don't know what went wrong or want further advice, please look for similar issues in https://github.com/jtamames/SqueezeMeta/issues Feel free to open a new issue if you don't find the answer there. Please add a brief description of the problem and upload the /home/user/Desktop/squeezemetarun/SRR953529/syslog file (zip it first) Died at /home/user/miniconda3/envs/squeezemeta/bin/SqueezeMeta.pl line 921.

jtamames commented 1 year ago

Syslog

vmevada102 @.***> escribió:

Run started Sat Feb 18 22:02:53 2023 in sequential mode 1 metagenomes found: SRR953529

--- SAMPLE SRR953529 -------- Now creating directories Reading configuration from
/home/user/Desktop/squeezemetarun/SRR953529/SqueezeMeta_conf.pl [0 seconds]: STEP1 -> RUNNING ASSEMBLY: 01.run_all_assemblies.pl (megahit) Working for sample SRR953529 Preparing files for pair1: cat
/home/user/Desktop/squeezemetarun/raw//SRR953529_1.fastq.gz >
/home/user/Desktop/squeezemetarun/SRR953529/data/raw_fastq/par1.fastq.gz Preparing files for pair2: cat
/home/user/Desktop/squeezemetarun/raw//SRR953529_2.fastq.gz >
/home/user/Desktop/squeezemetarun/SRR953529/data/raw_fastq/par2.fastq.gz Running assembly with megahit: perl
/home/user/miniconda3/envs/squeezemeta/SqueezeMeta/lib/SqueezeMeta/assembly_megahit.pl /home/user/Desktop/squeezemetarun/SRR953529 SRR953529 /home/user/Desktop/squeezemetarun/SRR953529/data/raw_fastq/par1.fastq.gz
/home/user/Desktop/squeezemetarun/SRR953529/data/raw_fastq/par2.fastq.gz Running prinseq (Schmieder et al 2011, Bioinformatics 27(6):863-4)
for selecting contigs longer than 200 Input and filter stats: Input sequences: 1 Input bases: 207 Input mean length: 207.00 Good sequences: 1 (100.00%) Good bases: 207 Good mean length: 207.00 Bad sequences: 0 (0.00%) Sequences filtered by specified parameters: none Renaming contigs Running prinseq for contig statistics:
/home/user/miniconda3/envs/squeezemeta/SqueezeMeta/bin/prinseq-lite.pl
-fasta
/home/user/Desktop/squeezemetarun/SRR953529/results/01.SRR953529.fasta
-stats_len -stats_info -stats_assembly >
/home/user/Desktop/squeezemetarun/SRR953529/intermediate/01.SRR953529.stats Counting length of contigs Contigs stored in
/home/user/Desktop/squeezemetarun/SRR953529/results/01.SRR953529.fasta Number of contigs: 1 [23 seconds]: STEP2 -> RNA PREDICTION: 02.rnas.pl Running barrnap (Seeman 2014, Bioinformatics 30, 2068-9) for
predicting RNAs: Bacteria Archaea Eukaryote Mitochondrial Running RDP classifier (Wang et al 2007, Appl Environ Microbiol 73, 5261-7) Running Aragorn (Laslett & Canback 2004, Nucleic Acids Res 31,
11-16) for tRNA/tmRNA prediction [31 seconds]: STEP3 -> ORF PREDICTION: 03.run_prodigal.pl Running prodigal (Hyatt et al 2010, BMC Bioinformatics 11: 119)
for predicting ORFs ORFs predicted: 1 [31 seconds]: STEP4 -> HOMOLOGY SEARCHES: 04.rundiamond.pl Setting block size for Diamond AVAILABLE (free) RAM memory: 56.41 Gb We will set Diamond block size to 7.1 (Gb RAM/8, Max 16). You can override this setting using the -b option when starting
the project, or changing the $blocksize variable in SqueezeMeta_conf.pl taxa COGS Running Diamond (Buchfink et al 2015, Nat Methods 12,
59-60) for KEGG

[21 minutes, 31 seconds]: STEP5 -> HMMER/PFAM: 05.run_hmmer.pl Running HMMER3 (Eddy 2009, Genome Inform 23, 205-11) for Pfam [22 minutes, 36 seconds]: STEP6 -> TAXONOMIC ASSIGNMENT: 06.lca.pl Splitting Diamond file Starting multithread LCA in 24 threads Thread 2 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.2.m8 Thread 3 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.3.m8 Thread 4 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.4.m8 Thread 5 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.5.m8 Thread 6 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.6.m8 Thread 7 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.7.m8 Thread 8 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.8.m8 Thread 9 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.9.m8 Thread 10 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.10.m8 Thread 11 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.11.m8 Thread 12 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.12.m8 Thread 13 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.13.m8 Thread 14 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.14.m8 Thread 15 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.15.m8 Thread 16 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.16.m8 Thread 17 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.17.m8 Thread 18 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.18.m8 Thread 19 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.19.m8 Thread 20 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.20.m8 Thread 21 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.21.m8 Thread 22 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.22.m8 Thread 23 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.23.m8 Thread 24 terminated abnormally: Cannot open
/home/user/Desktop/squeezemetarun/SRR953529/temp/diamond_lca.24.m8 Creating
/home/user/Desktop/squeezemetarun/SRR953529/results/06.SRR953529.fun3.tax.wranks
file Creating
/home/user/Desktop/squeezemetarun/SRR953529/results/06.SRR953529.fun3.tax.noidfilter.wranks
file Stopping in STEP6 -> 06.lca.pl. File
/home/user/Desktop/squeezemetarun/SRR953529/results/06.SRR953529.fun3.tax.wranks is
empty!

If you don't know what went wrong or want further advice, please
look for similar issues in
https://github.com/jtamames/SqueezeMeta/issues Feel free to open a new issue if you don't find the answer there.
Please add a brief description of the problem and upload the
/home/user/Desktop/squeezemetarun/SRR953529/syslog file (zip it first) Died at /home/user/miniconda3/envs/squeezemeta/bin/SqueezeMeta.pl line 921.

-- Reply to this email directly or view it on GitHub: https://github.com/jtamames/SqueezeMeta/issues/629 You are receiving this because you are subscribed to this thread.

Message ID: @.***>

vmevada102 commented 1 year ago 
Run started Sun Feb 19 10:54:05 2023 in sequential mode

SqueezeMeta v1.6.0, September 2022 - (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 squeezemetarun, Sun Feb 19 10:54:05 2023
Project: SRR953529
Map file: /home/user/Desktop/squeezemetarun/SRR953529.samples
Fastq directory: /home/user/Desktop/squeezemetarun/raw/
Command: /home/user/miniconda3/envs/squeezemeta/bin/SqueezeMeta.pl -m sequential -s /home/user/Desktop/squeezemetarun/SRR953529.samples -f /home/user/Desktop/squeezemetarun/raw/ -t 24
[0 seconds]: STEP0 -> SqueezeMeta.pl
 COGS; KEGG; PFAM;

[0 seconds]: STEP1 -> 01.run_all_assemblies.pl (megahit)
  Preparing files for pair1: cat /home/user/Desktop/squeezemetarun/raw//SRR953529_1.fastq.gz > /home/user/Desktop/squeezemetarun/SRR953529/data/raw_fastq/par1.fastq.gz
  Preparing files for pair2: cat /home/user/Desktop/squeezemetarun/raw//SRR953529_2.fastq.gz > /home/user/Desktop/squeezemetarun/SRR953529/data/raw_fastq/par2.fastq.gz
Running assembly with megahit: perl /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/lib/SqueezeMeta/assembly_megahit.pl /home/user/Desktop/squeezemetarun/SRR953529 SRR953529 /home/user/Desktop/squeezemetarun/SRR953529/data/raw_fastq/par1.fastq.gz /home/user/Desktop/squeezemetarun/SRR953529/data/raw_fastq/par2.fastq.gz
2023-02-19 10:54:06 - MEGAHIT v1.2.9
2023-02-19 10:54:06 - Using megahit_core with POPCNT and BMI2 support
2023-02-19 10:54:06 - Convert reads to binary library
2023-02-19 10:54:08 - b'INFO  sequence/io/sequence_lib.cpp  :   77 - Lib 0 (/home/user/Desktop/squeezemetarun/SRR953529/data/raw_fastq/par1.fastq.gz,/home/user/Desktop/squeezemetarun/SRR953529/data/raw_fastq/par2.fastq.gz): pe, 2244954 reads, 151 max length'
2023-02-19 10:54:08 - b'INFO  utils/utils.h                 :  152 - Real: 2.8839\tuser: 1.9544\tsys: 0.4087\tmaxrss: 161944'
2023-02-19 10:54:08 - k-max reset to: 141 
2023-02-19 10:54:08 - Start assembly. Number of CPU threads 24 
2023-02-19 10:54:08 - k list: 21,29,39,59,79,99,119,141 
2023-02-19 10:54:08 - Memory used: 60514906521
2023-02-19 10:54:08 - Extract solid (k+1)-mers for k = 21 
2023-02-19 10:54:15 - Build graph for k = 21 
2023-02-19 10:54:16 - Assemble contigs from SdBG for k = 21
2023-02-19 10:54:20 - Local assembly for k = 21
2023-02-19 10:54:21 - Extract iterative edges from k = 21 to 29 
2023-02-19 10:54:23 - Build graph for k = 29 
2023-02-19 10:54:24 - Assemble contigs from SdBG for k = 29
2023-02-19 10:54:24 - Local assembly for k = 29
2023-02-19 10:54:25 - Extract iterative edges from k = 29 to 39 
2023-02-19 10:54:26 - Build graph for k = 39 
2023-02-19 10:54:26 - Assemble contigs from SdBG for k = 39
2023-02-19 10:54:26 - Local assembly for k = 39
2023-02-19 10:54:26 - Extract iterative edges from k = 39 to 59 
2023-02-19 10:54:27 - Build graph for k = 59 
2023-02-19 10:54:27 - Assemble contigs from SdBG for k = 59
2023-02-19 10:54:27 - Local assembly for k = 59
2023-02-19 10:54:28 - Extract iterative edges from k = 59 to 79 
2023-02-19 10:54:29 - Merging to output final contigs 
2023-02-19 10:54:29 - 1 contigs, total 207 bp, min 207 bp, max 207 bp, avg 207 bp, N50 207 bp
2023-02-19 10:54:29 - ALL DONE. Time elapsed: 23.106947 seconds 
Running prinseq for selecting contigs longer than 200: /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/bin/prinseq-lite.pl -fasta /home/user/Desktop/squeezemetarun/SRR953529/results/01.SRR953529.fasta -min_len 200 -out_good /home/user/Desktop/squeezemetarun/SRR953529/results/prinseq; mv /home/user/Desktop/squeezemetarun/SRR953529/results/prinseq.fasta /home/user/Desktop/squeezemetarun/SRR953529/results/01.SRR953529.fasta > /dev/null 2>&1
  Running prinseq for contig statistics: /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/bin/prinseq-lite.pl -fasta /home/user/Desktop/squeezemetarun/SRR953529/results/01.SRR953529.fasta -stats_len -stats_info -stats_assembly > /home/user/Desktop/squeezemetarun/SRR953529/intermediate/01.SRR953529.stats
  Running barrnap for Bacteria: /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/bin/barrnap --quiet --threads 24 --kingdom bac --reject 0.1 /home/user/Desktop/squeezemetarun/SRR953529/intermediate/02.SRR953529.maskedrna.fasta --dbdir /home/user/squeezemeta_db/db > /home/user/Desktop/squeezemetarun/SRR953529/temp/bac.gff
Running barrnap for Archaea: /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/bin/barrnap --quiet --threads 24 --kingdom arc --reject 0.1 /home/user/Desktop/squeezemetarun/SRR953529/intermediate/02.SRR953529.maskedrna.fasta --dbdir /home/user/squeezemeta_db/db > /home/user/Desktop/squeezemetarun/SRR953529/temp/arc.gff
Running barrnap for Eukaryote: /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/bin/barrnap --quiet --threads 24 --kingdom euk --reject 0.1 /home/user/Desktop/squeezemetarun/SRR953529/intermediate/02.SRR953529.maskedrna.fasta --dbdir /home/user/squeezemeta_db/db > /home/user/Desktop/squeezemetarun/SRR953529/temp/euk.gff
Running barrnap for Mitochondrial: /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/bin/barrnap --quiet --threads 24 --kingdom mito --reject 0.1 /home/user/Desktop/squeezemetarun/SRR953529/intermediate/02.SRR953529.maskedrna.fasta --dbdir /home/user/squeezemeta_db/db > /home/user/Desktop/squeezemetarun/SRR953529/temp/mito.gff
Running RDP classifier: java -jar /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/lib/classifier/classifier.jar classify /home/user/Desktop/squeezemetarun/SRR953529/temp/16S.fasta -o /home/user/Desktop/squeezemetarun/SRR953529/temp/16S.out -f filterbyconf
Running Aragorn: /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/bin/aragorn -w /home/user/Desktop/squeezemetarun/SRR953529/intermediate/02.SRR953529.maskedrna.fasta -o /home/user/Desktop/squeezemetarun/SRR953529/temp/trnas.aragorn
Creating new gff file: cat /home/user/Desktop/squeezemetarun/SRR953529/temp/*gff.mod > /home/user/Desktop/squeezemetarun/SRR953529/temp/02.SRR953529.rna.gff
Running prodigal for predicting ORFs: /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/bin/prodigal -q -m -p meta -i /home/user/Desktop/squeezemetarun/SRR953529/intermediate/02.SRR953529.maskedrna.fasta -a /home/user/Desktop/squeezemetarun/SRR953529/results/03.SRR953529.faa -d /home/user/Desktop/squeezemetarun/SRR953529/results/03.SRR953529.fna -f gff -o /home/user/Desktop/squeezemetarun/SRR953529/temp/02.SRR953529.cds.gff.temp
Diamond block size set to 7.1 (Free Mem 56.47 Gb)
Running Diamond for taxa: /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/bin/diamond blastp -q /home/user/Desktop/squeezemetarun/SRR953529/results/03.SRR953529.faa -p 24 -d /home/user/squeezemeta_db/db/nr.dmnd -e 0.001 --id 40 -f tab -b 7.1 --quiet -o /home/user/Desktop/squeezemetarun/SRR953529/intermediate/04.SRR953529.nr.diamond
Running Diamond for COGs: /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/bin/diamond blastp -q /home/user/Desktop/squeezemetarun/SRR953529/results/03.SRR953529.faa -p 24 -d /home/user/squeezemeta_db/db/eggnog -e 0.001 --id 30 --quiet -b 7.1 -f 6 qseqid qlen sseqid slen pident length evalue bitscore qstart qend sstart send -o /home/user/Desktop/squeezemetarun/SRR953529/intermediate/04.SRR953529.eggnog.diamond
Running Diamond for KEGG: /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/bin/diamond blastp -q /home/user/Desktop/squeezemetarun/SRR953529/results/03.SRR953529.faa -p 24 -d /home/user/squeezemeta_db/db/keggdb -e 0.001 --id 30 --quiet -b 7.1 -f 6 qseqid qlen sseqid slen pident length evalue bitscore qstart qend sstart send -o /home/user/Desktop/squeezemetarun/SRR953529/intermediate/04.SRR953529.kegg.diamond
Running HMMER3 for Pfam: /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/bin/hmmer/hmmsearch --domtblout /home/user/Desktop/squeezemetarun/SRR953529/intermediate/05.SRR953529.pfam.hmm -E 1e-10 --cpu 24 /home/user/squeezemeta_db/db/Pfam-A.hmm /home/user/Desktop/squeezemetarun/SRR953529/results/03.SRR953529.faa > /dev/null 2>&1
  Splitting Diamond file
  Total lines in Diamond: 25; Allocating 1 in 24 threads
  Opening file 1 in line  (estimated in 1)
  Starting multithread LCA in 24 threads
  Starting thread 1
  Starting thread 2
  Starting thread 3
  Starting thread 4
  Starting thread 5
  Starting thread 6
  Starting thread 7
  Starting thread 8
  Starting thread 9
  Starting thread 10
  Starting thread 11
  Starting thread 12
  Starting thread 13
  Starting thread 14
  Starting thread 15
  Starting thread 16
  Starting thread 17
  Starting thread 18
  Starting thread 19
  Starting thread 20
  Starting thread 21
  Starting thread 22
  Starting thread 23
  Starting thread 24
  Creating /home/user/Desktop/squeezemetarun/SRR953529/results/06.SRR953529.fun3.tax.wranks file: cat /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_1.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_2.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_3.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_4.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_5.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_6.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_7.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_8.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_9.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_10.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_11.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_12.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_13.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_14.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_15.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_16.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_17.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_18.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_19.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_20.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_21.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_22.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_23.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_24.wranks > /home/user/Desktop/squeezemetarun/SRR953529/results/06.SRR953529.fun3.tax.wranks
  Creating /home/user/Desktop/squeezemetarun/SRR953529/results/06.SRR953529.fun3.tax.noidfilter.wranks file: cat /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_1.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_2.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_3.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_4.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_5.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_6.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_7.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_8.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_9.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_10.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_11.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_12.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_13.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_14.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_15.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_16.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_17.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_18.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_19.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_20.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_21.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_22.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_23.noidfilter.wranks /home/user/Desktop/squeezemetarun/SRR953529/temp/fun3tax_24.noidfilter.wranks  > /home/user/Desktop/squeezemetarun/SRR953529/results/06.SRR953529.fun3.tax.noidfilter.wranks
  Removing temporaty diamond files in /home/user/Desktop/squeezemetarun/SRR953529/temp
Linux vnsgu 3.10.0-1160.81.1.el7.x86_64 #1 SMP Fri Dec 16 17:29:43 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
[ 224 Feb 19 10:54]  /home/user/Desktop/squeezemetarun/SRR953529
├── [  82 Feb 19 10:54]  data
│   ├── [  74 Feb 19 10:54]  00.SRR953529.samples
│   ├── [ 124 Feb 19 10:54]  megahit
│   │   ├── [ 150 Feb 19 10:54]  checkpoints.txt
│   │   ├── [   0 Feb 19 10:54]  done
│   │   ├── [4.0K Feb 19 10:54]  intermediate_contigs
│   │   │   ├── [460K Feb 19 10:54]  k21.addi.fa
│   │   │   ├── [  12 Feb 19 10:54]  k21.addi.fa.info
│   │   │   ├── [ 45K Feb 19 10:54]  k21.bubble_seq.fa
│   │   │   ├── [  10 Feb 19 10:54]  k21.bubble_seq.fa.info
│   │   │   ├── [8.0M Feb 19 10:54]  k21.contigs.fa
│   │   │   ├── [  15 Feb 19 10:54]  k21.contigs.fa.info
│   │   │   ├── [   0 Feb 19 10:54]  k21.final.contigs.fa
│   │   │   ├── [   4 Feb 19 10:54]  k21.final.contigs.fa.info
│   │   │   ├── [   0 Feb 19 10:54]  k21.local.fa
│   │   │   ├── [   4 Feb 19 10:54]  k21.local.fa.info
│   │   │   ├── [6.7K Feb 19 10:54]  k29.addi.fa
│   │   │   ├── [   8 Feb 19 10:54]  k29.addi.fa.info
│   │   │   ├── [ 40K Feb 19 10:54]  k29.bubble_seq.fa
│   │   │   ├── [  10 Feb 19 10:54]  k29.bubble_seq.fa.info
│   │   │   ├── [272K Feb 19 10:54]  k29.contigs.fa
│   │   │   ├── [  11 Feb 19 10:54]  k29.contigs.fa.info
│   │   │   ├── [   0 Feb 19 10:54]  k29.final.contigs.fa
│   │   │   ├── [   4 Feb 19 10:54]  k29.final.contigs.fa.info
│   │   │   ├── [ 243 Feb 19 10:54]  k29.local.fa
│   │   │   ├── [   6 Feb 19 10:54]  k29.local.fa.info
│   │   │   ├── [   0 Feb 19 10:54]  k39.addi.fa
│   │   │   ├── [   4 Feb 19 10:54]  k39.addi.fa.info
│   │   │   ├── [1.4K Feb 19 10:54]  k39.bubble_seq.fa
│   │   │   ├── [   7 Feb 19 10:54]  k39.bubble_seq.fa.info
│   │   │   ├── [ 29K Feb 19 10:54]  k39.contigs.fa
│   │   │   ├── [   9 Feb 19 10:54]  k39.contigs.fa.info
│   │   │   ├── [   0 Feb 19 10:54]  k39.final.contigs.fa
│   │   │   ├── [   4 Feb 19 10:54]  k39.final.contigs.fa.info
│   │   │   ├── [   0 Feb 19 10:54]  k39.local.fa
│   │   │   ├── [   4 Feb 19 10:54]  k39.local.fa.info
│   │   │   ├── [   0 Feb 19 10:54]  k59.addi.fa
│   │   │   ├── [   4 Feb 19 10:54]  k59.addi.fa.info
│   │   │   ├── [   0 Feb 19 10:54]  k59.bubble_seq.fa
│   │   │   ├── [   4 Feb 19 10:54]  k59.bubble_seq.fa.info
│   │   │   ├── [ 463 Feb 19 10:54]  k59.contigs.fa
│   │   │   ├── [   5 Feb 19 10:54]  k59.contigs.fa.info
│   │   │   ├── [   0 Feb 19 10:54]  k59.final.contigs.fa
│   │   │   ├── [   4 Feb 19 10:54]  k59.final.contigs.fa.info
│   │   │   ├── [   0 Feb 19 10:54]  k59.local.fa
│   │   │   └── [   4 Feb 19 10:54]  k59.local.fa.info
│   │   ├── [ 76K Feb 19 10:54]  log
│   │   └── [1005 Feb 19 10:54]  options.json
│   └── [  60 Feb 19 10:54]  raw_fastq
│       ├── [ 73M Feb 19 10:54]  par1.fastq.gz
│       └── [ 80M Feb 19 10:54]  par2.fastq.gz
├── [  10 Feb 19 10:54]  ext_tables
├── [ 296 Feb 19 11:14]  intermediate
│   ├── [  14 Feb 19 10:54]  01.SRR953529.lon
│   ├── [ 284 Feb 19 10:54]  01.SRR953529.stats
│   ├── [ 219 Feb 19 10:54]  02.SRR953529.maskedrna.fasta
│   ├── [2.4K Feb 19 11:14]  04.SRR953529.eggnog.diamond
│   ├── [   0 Feb 19 11:14]  04.SRR953529.kegg.diamond
│   ├── [1.7K Feb 19 11:14]  04.SRR953529.nr.diamond
│   ├── [1.2K Feb 19 11:15]  05.SRR953529.pfam.hmm
│   ├── [  10 Feb 19 10:54]  binners
│   └── [  56 Feb 19 10:54]  DB_BUILD_DATE
├── [1.2K Feb 19 11:15]  methods.txt
├── [3.2K Feb 19 10:54]  parameters.pl
├── [ 120 Feb 19 11:15]  progress
├── [4.0K Feb 19 11:17]  results
│   ├── [ 222 Feb 19 10:54]  01.SRR953529.fasta
│   ├── [ 148 Feb 19 10:54]  02.SRR953529.16S.txt
│   ├── [   0 Feb 19 10:54]  02.SRR953529.rnas
│   ├── [   0 Feb 19 10:54]  02.SRR953529.trnas
│   ├── [   0 Feb 19 10:54]  02.SRR953529.trnas.fasta
│   ├── [ 164 Feb 19 10:54]  03.SRR953529.faa
│   ├── [ 268 Feb 19 10:54]  03.SRR953529.fna
│   ├── [ 516 Feb 19 10:54]  03.SRR953529.gff
│   ├── [ 249 Feb 19 11:17]  06.SRR953529.fun3.tax.noidfilter.wranks
│   └── [ 249 Feb 19 11:17]  06.SRR953529.fun3.tax.wranks
├── [8.2K Feb 19 10:54]  SqueezeMeta_conf.pl
├── [ 13K Feb 19 11:17]  syslog
└── [4.0K Feb 19 11:17]  temp
    ├── [ 452 Feb 19 10:54]  02.SRR953529.cds.gff
    ├── [ 440 Feb 19 10:54]  02.SRR953529.cds.gff.temp
    ├── [  64 Feb 19 10:54]  02.SRR953529.rna.gff
    ├── [   0 Feb 19 10:54]  16S.fasta
    ├── [  40 Feb 19 10:54]  16S.out
    ├── [  16 Feb 19 10:54]  arc.gff
    ├── [  16 Feb 19 10:54]  arc.gff.mod
    ├── [  16 Feb 19 10:54]  bac.gff
    ├── [  16 Feb 19 10:54]  bac.gff.mod
    ├── [  16 Feb 19 10:54]  euk.gff
    ├── [  16 Feb 19 10:54]  euk.gff.mod
    ├── [   0 Feb 19 11:16]  fun3tax_10.noidfilter.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_10.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_11.noidfilter.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_11.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_12.noidfilter.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_12.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_13.noidfilter.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_13.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_14.noidfilter.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_14.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_15.noidfilter.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_15.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_16.noidfilter.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_16.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_17.noidfilter.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_17.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_18.noidfilter.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_18.wranks
    ├── [   0 Feb 19 11:17]  fun3tax_19.noidfilter.wranks
    ├── [   0 Feb 19 11:17]  fun3tax_19.wranks
    ├── [ 249 Feb 19 11:16]  fun3tax_1.noidfilter.wranks
    ├── [ 249 Feb 19 11:16]  fun3tax_1.wranks
    ├── [   0 Feb 19 11:17]  fun3tax_20.noidfilter.wranks
    ├── [   0 Feb 19 11:17]  fun3tax_20.wranks
    ├── [   0 Feb 19 11:17]  fun3tax_21.noidfilter.wranks
    ├── [   0 Feb 19 11:17]  fun3tax_21.wranks
    ├── [   0 Feb 19 11:17]  fun3tax_22.noidfilter.wranks
    ├── [   0 Feb 19 11:17]  fun3tax_22.wranks
    ├── [   0 Feb 19 11:17]  fun3tax_23.noidfilter.wranks
    ├── [   0 Feb 19 11:17]  fun3tax_23.wranks
    ├── [   0 Feb 19 11:17]  fun3tax_24.noidfilter.wranks
    ├── [   0 Feb 19 11:17]  fun3tax_24.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_2.noidfilter.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_2.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_3.noidfilter.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_3.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_4.noidfilter.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_4.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_5.noidfilter.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_5.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_6.noidfilter.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_6.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_7.noidfilter.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_7.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_8.noidfilter.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_8.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_9.noidfilter.wranks
    ├── [   0 Feb 19 11:16]  fun3tax_9.wranks
    ├── [  16 Feb 19 10:54]  mito.gff
    ├── [  16 Feb 19 10:54]  mito.gff.mod
    ├── [   0 Feb 19 10:54]  trna.gff.mod
    ├── [  25 Feb 19 10:54]  trnas.aragorn
    └── [  86 Feb 19 11:16]  wc

9 directories, 134 files
vmevada102 commented 1 year ago

I checked the several other samples. Still getting this error

jtamames commented 1 year ago

Sorry for the delay in responding This error is due to the tiny size of the resulting fasta files from the assembly. Your dataset is rather small, then the assembly produce almost nothing, and when LCA tries to split the results in 24 parts for the 24 threads, it fails because there are not enough data. Possible solutions are: 1) Do not assemble (since it is not succeeding) and use sqm_reads or sqm_longrads instead. 2) Specify just 1 thread, using -t 1. I will go for the first option. Best, J

fpusan commented 1 year ago

Closing due to lack of activity, feel free to reopen!