Description of the bug
Hi! My nf-mag job is failing at the CAT-pack unbinned contigs stage. Below are some of the error lines from the log.
From what I can tell, CAT-pack won't take multiple .fa file inputs? If I just run the script with one input listed it runs ok. Is there a way around this? alternatively, how important is this step, and can it be skipped?
thank you,
Suzanna
-[nf-core/mag] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_MAG:MAG:CATPACK:CATPACK_UNBINS (barley_01)'
Caused by:
Process NFCORE_MAG:MAG:CATPACK:CATPACK_UNBINS (barley_01) terminated with an error exit status (1)
Command executed:
CAT_pack contigs
--nproc 6
--contigs_fasta FLYE-MetaBAT2-barley_01.unbinned.1.fa FLYE-MetaBAT2-barley_01.unbinned.2.fa
--database_folder db
--taxonomy_folder tax
--out_prefix FLYE-MetaBAT2-barley_01-unbins
\
cat <<-END_VERSIONS > versions.yml
"NFCORE_MAG:MAG:CATPACK:CATPACK_UNBINS":
catpack: $(CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g')
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
error: too many arguments supplied:
FLYE-MetaBAT2-barley_01.unbinned.2.fa
Command used and terminal output
Relevant files
No response
System information
No response
Description of the bug
Hi! My nf-mag job is failing at the CAT-pack unbinned contigs stage. Below are some of the error lines from the log.
From what I can tell, CAT-pack won't take multiple .fa file inputs? If I just run the script with one input listed it runs ok. Is there a way around this? alternatively, how important is this step, and can it be skipped?
thank you,
Suzanna
-[nf-core/mag] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_MAG:MAG:CATPACK:CATPACK_UNBINS (barley_01)'
Caused by:
Process
NFCORE_MAG:MAG:CATPACK:CATPACK_UNBINS (barley_01)terminated with an error exit status (1)Command executed:
CAT_pack contigs
--nproc 6
--contigs_fasta FLYE-MetaBAT2-barley_01.unbinned.1.fa FLYE-MetaBAT2-barley_01.unbinned.2.fa
--database_folder db
--taxonomy_folder tax
--out_prefix FLYE-MetaBAT2-barley_01-unbins
\
cat <<-END_VERSIONS > versions.yml
"NFCORE_MAG:MAG:CATPACK:CATPACK_UNBINS":
catpack: $(CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g')
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
error: too many arguments supplied:
FLYE-MetaBAT2-barley_01.unbinned.2.fa
Command used and terminal output
Relevant files
No response
System information
No response