wwood
commented
1 year ago Hi,
Thanks for trying singlem. I think that error is caused by a packaging error in a newly released diamond. Try diamond <2.1 ?
-------------- Ben Woodcroft Group leader, Centre for Microbiome Research, QUT
From: Rainjie-afk @.> Sent: Saturday, February 25, 2023 3:52:26 PM To: wwood/singlem @.> Cc: Subscribed @.***> Subject: [wwood/singlem] Singlem error with (Issue #122)
Hellow wwood, I successfully installed the software Singlem and specified the database path, but when I run it in commond line, it prompts that diamond failed. Is it because my computer doesn't have enough memory to run software B? Or how can I solve this problem?"
This is my error imformation.
(singlem) @.***:/media/hyj/E/singlem-main/bin$ singlem pipe -1 /media/hyj/F/ProjectZLP/2U/ERR1600539_1.fastq.gz -2 /media/hyj/F/ProjectZLP/2U/ERR1600539_2.fastq.gz --otu-table /media/hyj/F/ProjectZLP/2U/1.tsv --threads 8
02/25/2023 03:25:12 AM INFO: SingleM v1.0.0beta5
02/25/2023 03:25:12 AM INFO: Retrieval successful. Location of backpack is: /media/hyj/E/Database/Singlem_DB/S3.1.0.metapackage_20221209.smpkg.zb
02/25/2023 03:25:12 AM INFO: Loaded 59 SingleM packages
02/25/2023 03:25:12 AM INFO: Using as input 1 different pairs of sequence files e.g. /media/hyj/F/ProjectZLP/2U/ERR1600539_1.fastq.gz & /media/hyj/F/ProjectZLP/2U/ERR1600539_2.fastq.gz
02/25/2023 03:25:12 AM INFO: Filtering sequence files through DIAMOND blastx
02/25/2023 03:26:05 AM ERROR: Process (DIAMOND?) failed
Traceback (most recent call last):
File "/media/hyj/E/singlem-main/bin/singlem", line 591, in
singlem.pipe.SearchPipe().run(
File "/media/hyj/E/singlem-main/bin/../singlem/pipe.py", line 63, in run
otu_table_object = self.run_to_otu_table(**kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^File "/media/hyj/E/singlem-main/bin/../singlem/pipe.py", line 334, in run_to_otu_table
raise e
File "/media/hyj/E/singlem-main/bin/../singlem/pipe.py", line 327, in run_to_otu_table
self._num_threads, self._working_directory).run_diamond(
^^^^^^^^^^^^File "/media/hyj/E/singlem-main/bin/../singlem/diamond_spkg_searcher.py", line 34, in run_diamond
fwds = self._prefilter(dmnd, forward_read_files, False, performance_parameters)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^File "/media/hyj/E/singlem-main/bin/../singlem/diamond_spkg_searcher.py", line 94, in _prefilter
qseqid_sseqid = extern.run(cmd)
^^^^^^^^^^^^^^^File "/home/hyj/miniconda3/envs/singlem/lib/python3.11/site-packages/extern/init.py", line 41, in run
raise ExternCalledProcessError(process, command)
extern.ExternCalledProcessError: Command diamond blastx --outfmt 6 qseqid full_qseq sseqid --max-target-seqs 1 --evalue 0.01 --block-size 0.5 --target-indexed -c1 --min-orf 24 --threads 8 --query /media/hyj/F/ProjectZLP/2U/ERR1600539_1.fastq.gz --db /media/hyj/E/Database/Singlem_DB/S3.1.0.metapackage_20221209.smpkg.zb/payload_directory/prefilter.fna.dmnd | tee >(sed 's/^/>/; s/\t/\n/; s/\t.*//' > /tmp/tmp9c2d3ibn/prefilter_forward/ERR1600539_1.fna) | awk '{print $1,$3}' returned non-zero exit status 139.
STDERR was: b"bash\xef\xbc\x9a\xe8\xa1\x8c 1: 37997 \xe6\xae\xb5\xe9\x94\x99\xe8\xaf\xaf \xef\xbc\x88\xe6\xa0\xb8\xe5\xbf\x83\xe5\xb7\xb2\xe8\xbd\xac\xe5\x82\xa8\xef\xbc\x89 diamond blastx --outfmt 6 qseqid full_qseq sseqid --max-target-seqs 1 --evalue 0.01 --block-size 0.5 --target-indexed -c1 --min-orf 24 --threads 8 --query /media/hyj/F/ProjectZLP/2U/ERR1600539_1.fastq.gz --db /media/hyj/E/Database/Singlem_DB/S3.1.0.metapackage_20221209.smpkg.zb/payload_directory/prefilter.fna.dmnd\n 37998 \xe5\xb7\xb2\xe5\xae\x8c\xe6\x88\x90 | tee >(sed 's/^/>/; s/\t/\n/; s/\t.*//' > /tmp/tmp9c2d3ibn/prefilter_forward/ERR1600539_1.fna)\n 37999 \xe5\xb7\xb2\xe5\xae\x8c\xe6\x88\x90 | awk '{print $1,$3}'\n"STDOUT was: b''
When I tested DIAMOND in the singlme environment, the error message was. (singlem) @.***:/media/hyj/E/singlem-main/bin$ diamond blastx --outfmt 6 qseqid full_qseq sseqid --max-target-seqs 1 --evalue 0.01 --block-size 0.5 --target-indexed -c1 --min-orf 24 --threads 7 --query /media/hyj/E/NAFLD_PRJNA373901/data/Metawrap_binning/SRR5275397/metabat2_bins/bin.3.fa --db /media/hyj/E/Database/Singlem_DB/S3.1.0.metapackage_20221209.smpkg.zb/payload_directory/prefilter.fna.dmnd --out /media/hyj/E/NAFLD_PRJNA373901/data/Metawrap_binning/SRR5275397/metabat2_bins/bin.3.fa.otu diamond v2.1.3.157 (C) Max Planck Society for the Advancement of Science Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)
CPU threads: 7
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) Temporary directory: /media/hyj/E/NAFLD_PRJNA373901/data/Metawrap_binning/SRR5275397/metabat2_bins
Target sequences to report alignments for: 1
Opening the database... [0.006s] Database: /media/hyj/E/Database/Singlem_DB/S3.1.0.metapackage_20221209.smpkg.zb/payload_directory/prefilter.fna.dmnd (type: Diamond database, sequences: 65337, letters: 5095531) Block size = 500000000 Algorithm: Double-indexed Loading reference sequences... [0.011s] Masking reference... [0.06s] Initializing temporary storage... [0.005s] Building reference histograms... [0.029s] Allocating buffers... 段错误 (核心已转储)
Many thanks
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Rainjie-afk
Hellow wwood, I successfully installed the software Singlem and specified the database path, but when I run it in command line, it prompts that DIAMOND failed. Is it because my computer doesn't have enough memory to run DIAMOND or how can I solve this problem?"
This is my error information.
(singlem) hyj@hyj:/media/hyj/E/singlem-main/bin$ singlem pipe -1 /media/hyj/F/ProjectZLP/2U/ERR1600539_1.fastq.gz -2 /media/hyj/F/ProjectZLP/2U/ERR1600539_2.fastq.gz --otu-table /media/hyj/F/ProjectZLP/2U/1.tsv --threads 8
02/25/2023 03:25:12 AM INFO: SingleM v1.0.0beta5
02/25/2023 03:25:12 AM INFO: Retrieval successful. Location of backpack is: /media/hyj/E/Database/Singlem_DB/S3.1.0.metapackage_20221209.smpkg.zb
02/25/2023 03:25:12 AM INFO: Loaded 59 SingleM packages
02/25/2023 03:25:12 AM INFO: Using as input 1 different pairs of sequence files e.g. /media/hyj/F/ProjectZLP/2U/ERR1600539_1.fastq.gz & /media/hyj/F/ProjectZLP/2U/ERR1600539_2.fastq.gz
02/25/2023 03:25:12 AM INFO: Filtering sequence files through DIAMOND blastx
02/25/2023 03:26:05 AM ERROR: Process (DIAMOND?) failed
Traceback (most recent call last):
File "/media/hyj/E/singlem-main/bin/singlem", line 591, in
File "/media/hyj/E/singlem-main/bin/../singlem/pipe.py", line 63, in run
File "/media/hyj/E/singlem-main/bin/../singlem/pipe.py", line 334, in run_to_otu_table
File "/media/hyj/E/singlem-main/bin/../singlem/pipe.py", line 327, in run_to_otu_table
File "/media/hyj/E/singlem-main/bin/../singlem/diamond_spkg_searcher.py", line 34, in run_diamond
File "/media/hyj/E/singlem-main/bin/../singlem/diamond_spkg_searcher.py", line 94, in _prefilter
File "/home/hyj/miniconda3/envs/singlem/lib/python3.11/site-packages/extern/init.py", line 41, in run
extern.ExternCalledProcessError: Command diamond blastx --outfmt 6 qseqid full_qseq sseqid --max-target-seqs 1 --evalue 0.01 --block-size 0.5 --target-indexed -c1 --min-orf 24 --threads 8 --query /media/hyj/F/ProjectZLP/2U/ERR1600539_1.fastq.gz --db /media/hyj/E/Database/Singlem_DB/S3.1.0.metapackage_20221209.smpkg.zb/payload_directory/prefilter.fna.dmnd | tee >(sed 's/^/>/; s/\t/\n/; s/\t.*//' > /tmp/tmp9c2d3ibn/prefilter_forward/ERR1600539_1.fna) | awk '{print $1,$3}' returned non-zero exit status 139.
STDERR was: b"bash\xef\xbc\x9a\xe8\xa1\x8c 1: 37997 \xe6\xae\xb5\xe9\x94\x99\xe8\xaf\xaf \xef\xbc\x88\xe6\xa0\xb8\xe5\xbf\x83\xe5\xb7\xb2\xe8\xbd\xac\xe5\x82\xa8\xef\xbc\x89 diamond blastx --outfmt 6 qseqid full_qseq sseqid --max-target-seqs 1 --evalue 0.01 --block-size 0.5 --target-indexed -c1 --min-orf 24 --threads 8 --query /media/hyj/F/ProjectZLP/2U/ERR1600539_1.fastq.gz --db /media/hyj/E/Database/Singlem_DB/S3.1.0.metapackage_20221209.smpkg.zb/payload_directory/prefilter.fna.dmnd\n 37998 \xe5\xb7\xb2\xe5\xae\x8c\xe6\x88\x90 | tee >(sed 's/^/>/; s/\t/\n/; s/\t.*//' > /tmp/tmp9c2d3ibn/prefilter_forward/ERR1600539_1.fna)\n 37999 \xe5\xb7\xb2\xe5\xae\x8c\xe6\x88\x90 | awk '{print $1,$3}'\n"STDOUT was: b''
When I tested DIAMOND in the singlme environment, the error message was. (singlem) hyj@hyj:/media/hyj/E/singlem-main/bin$ diamond blastx --outfmt 6 qseqid full_qseq sseqid --max-target-seqs 1 --evalue 0.01 --block-size 0.5 --target-indexed -c1 --min-orf 24 --threads 7 --query /media/hyj/E/NAFLD_PRJNA373901/data/Metawrap_binning/SRR5275397/metabat2_bins/bin.3.fa --db /media/hyj/E/Database/Singlem_DB/S3.1.0.metapackage_20221209.smpkg.zb/payload_directory/prefilter.fna.dmnd --out /media/hyj/E/NAFLD_PRJNA373901/data/Metawrap_binning/SRR5275397/metabat2_bins/bin.3.fa.otu diamond v2.1.3.157 (C) Max Planck Society for the Advancement of Science Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)
CPU threads: 7
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) Temporary directory: /media/hyj/E/NAFLD_PRJNA373901/data/Metawrap_binning/SRR5275397/metabat2_bins
Target sequences to report alignments for: 1
Opening the database... [0.006s] Database: /media/hyj/E/Database/Singlem_DB/S3.1.0.metapackage_20221209.smpkg.zb/payload_directory/prefilter.fna.dmnd (type: Diamond database, sequences: 65337, letters: 5095531) Block size = 500000000 Algorithm: Double-indexed Loading reference sequences... [0.011s] Masking reference... [0.06s] Initializing temporary storage... [0.005s] Building reference histograms... [0.029s] Allocating buffers... 段错误 (核心已转储)
Many thanks