rnaseq_collapse：Perhaps the program crashes due to excessive thread usage

[bismarck1008]

python3 data/egapx/ui/egapx.py data/input_D_farinae_small.local4.yaml -e docker -w ./temp -o egapx_out

[- ] process > export - [ae/0765b8] NOTE: Process egapx:rnaseq_short_plane:rnaseq_collapse:run_rnaseq_collapse (6) terminated with an error exit status (3) -- Execution is retried (3)
[41/720134] NOTE: Process egapx:rnaseq_short_plane:rnaseq_collapse:run_rnaseq_collapse (5) terminated with an error exit status (3) -- Execution is retried (3) [6d/b77983] NOTE: Process egapx:rnaseq_short_plane:rnaseq_collapse:run_rnaseq_collapse (7) terminated with an error exit status (3) -- Execution is retried (3)
[66/59923f] NOTE: Process egapx:rnaseq_short_plane:rnaseq_collapse:run_rnaseq_collapse (4) terminated with an error exit status (3) -- Execution is retried (2)
[10/c33777] NOTE: Process egapx:rnaseq_short_plane:rnaseq_collapse:run_rnaseq_collapse (1) terminated with an error exit status (3) -- Execution is retried (3)
[54/5d8c25] NOTE: Process egapx:rnaseq_short_plane:rnaseq_collapse:run_rnaseq_collapse (9) terminated with an error exit status (3) -- Execution is retried (3)
ERROR ~ Error executing process > 'egapx:rnaseq_short_plane:rnaseq_collapse:run_rnaseq_collapse (10)'

Caused by:
Process egapx:rnaseq_short_plane:rnaseq_collapse:run_rnaseq_collapse (10) terminated with an error exit status (3)

Command executed:

njobs=wc -l <job.009
if [ $njobs -lt 16 ]; then
threads=$njobs
else
threads=16
fi

[boukn]

its a lot of threads but it that shouldnt crash anything by itself... Can you provide the contents of the ./temp/41/720134 workdir?

[bismarck1008]

its a lot of threads but it that shouldnt crash anything by itself... Can you provide the contents of the ./temp/41/720134 workdir?

The file has been deleted. After reducing the input file to a pair of sequences, I still encountered similar errors.
[- ] process > export
[03/b488e2] NOTE: Process egapx:rnaseq_short_plane:rnaseq_collapse:run_rnaseq_collapse (9) terminated with an error exit status (3) -- Execution is retried (3)
[ee/72b6e2] NOTE: Process egapx:rnaseq_short_plane:rnaseq_collapse:run_rnaseq_collapse (3) terminated with an error exit status (3) -- Execution is retried (2)
[f5/917462] NOTE: Process egapx:rnaseq_short_plane:rnaseq_collapse:run_rnaseq_collapse (1) terminated with an error exit status (3) -- Execution is retried (3)
[a0/c9f280] NOTE: Process egapx:rnaseq_short_plane:rnaseq_collapse:run_rnaseq_collapse (7) terminated with an error exit status (3) -- Execution is retried (3)
ERROR ~ Error executing process > 'egapx:rnaseq_short_plane:rnaseq_collapse:run_rnaseq_collapse (10)'

Caused by:
Process egapx:rnaseq_short_plane:rnaseq_collapse:run_rnaseq_collapse (10) terminated with an error exit status (3)

Command executed:

njobs=wc -l <job.009
if [ $njobs -lt 16 ]; then
threads=$njobs
else
threads=16
fi

ll 03/b488e2
GCA_040085125.1_ASM4008512v1_genomic-bin1.align.asnb.gz -> /data/dell/CNI.2024.10.5/anotation/temp/c1/b07c7e05b63c1bb7014234c2d71813/GCA_040085125.1_ASM4008512v1_genomic-bin1.align.asnb.gz
130 10:22 GCA_040085125.1_ASM4008512v1_genomic-bin17.align.asnb.gz -> /data/dell/CNI.2024.10.5/anotation/temp/53/cfb8104531b57a2768b405aa103d19/GCA_040085125.1_ASM4008512v1_genomic-bin17.align.asnb.gz
4096 10:22 genome/
81 10:22 job.008 -> /data/dell/CNI.2024.10.5/anotation/temp/af/7d3e2c5828ef6dd2d549b59abc9be1/job.008
0 10:22 .command.out
0 10:22 .command.trace
1071 10:22 scaffold_list.mft
34 10:22 metadata.mft
1017 10:22 align.mft
884736 10:22 genome_lds
4096 10:22 interim/
140778 10:23 .command.log
140778 10:23 .command.err
1 10:23 .exitcode
4096 10:23 ./

ll ee/72b6e2

1017  10:21 align.mft
 0   10:21 .command.begin

149960 10:23 .command.err
149960 10:23 .command.log
0 10:21 .command.out
19973 10:21 .command.run
3475 10:21 .command.sh
0 10:21 .command.trace
92 10:21 egapx_reads_metadata_ns63yaxv.tsv -> /data/dell/CNI.2024.10.5/anotation/egapx_GCA_040085125_out/egapx_reads_metadata_ns63yaxv.tsv
1 10月 8 10:23 .exitcode
GCA_040085125.1_ASM4008512v1_genomic-bin10.align.asnb.gz -> /data/dell/CNI.2024.10.5/anotation/temp/c2/df2abb714d4f40524588daa8d2efdf/GCA_040085125.1_ASM4008512v1_genomic-bin10.align.asnb.gz
4096 10:21 genome/
884736 10:22 genome_lds
4096 10:22 interim/
81 10:21 job.002 -> /data/dell/CNI.2024.10.5/anotation/temp/af/7d3e2c5828ef6dd2d549b59abc9be1/job.002
34 10:21 metadata.mft
1071 10:21 scaffold_list.mft