SQM_LONGREADS.PL died at line 933

[inej90]

Hi,

I have 28 samples of feces and slurry (nanopore sequences) and I am trying to work with SQM using my raw reads (sqm_longreads.pl). The problem bigan with the second sample and it gives me this message:

Running Diamond BlastX (Buchfink et al 2015, Nat Methods 12, 59-60) Error running /pipe/soft/miniconda/miniconda3/envs/SqueezeMeta/SqueezeMeta/bin/diamond blastx -q /base_datos/librerias/librerias_originales/Sistema_pastoreo_SUP/purin_pasto_sup_all/PURIN_pasto_all_sqm_longreads/PP2/P33.27.L4.21.fastq -p 32 -d /pipe/data_base_SQM/db/nr.dmnd -f tab -F 15 --quiet --range-culling -b 5.4 -e 0.001 --id 30 --top 10 -o /base_datos/librerias/librerias_originales/Sistema_pastoreo_SUP/purin_pasto_sup_all/PURIN_pasto_all_sqm_longreads/PP2/P33.27.L4.21.fastq.gz.nr.blastx -f 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen at /pipe/soft/miniconda/miniconda3/envs/SqueezeMeta/bin/sqm_longreads.pl line 933.

You can also find here the syslog generated. syslog.zip

Thank you in advance.

[fpusan]

An error in that step is usually due to a lack of memory. How much available memory do you have?

I would try two things. 1) Run manually the command that failed and record the output, to see if we get a more meaningful error message /pipe/soft/miniconda/miniconda3/envs/SqueezeMeta/SqueezeMeta/bin/diamond blastx -q /base_datos/librerias/librerias_originales/Sistema_pastoreo_SUP/purin_pasto_sup_all/PURIN_pasto_all_sqm_longreads/PP2/P33.27.L4.21.fastq -p 32 -d /pipe/data_base_SQM/db/nr.dmnd -f tab -F 15 --quiet --range-culling -b 5.4 -e 0.001 --id 30 --top 10 -o /base_datos/librerias/librerias_originales/Sistema_pastoreo_SUP/purin_pasto_sup_all/PURIN_pasto_all_sqm_longreads/PP2/P33.27.L4.21.fastq.gz.nr.blastx -f 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen 2) Re-run the command, but changing the value of -b from 5.4 to e.g. 2. This should reduce memory usage. If the command finishes with this new configuration, you can just pass -b 2 to sqm_longreads.pl