(base) dhwani@dhwani:/DATA1/RNASeq/Aeron$ snakemake --cores=10 all
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 10
Rules claiming more threads will be scaled down.
Job counts:
count jobs
2 align
1 all
1 assign_reads_to_transcripts
1 generateCountMatrix
1 output_assignment_statistics
2 postprocess
8
/usr/bin/bash: tmp/aligner_stdout.txt: No such file or directory
[Thu Jul 13 18:15:26 2023]
Error in rule align:
jobid: 1
output: output/aln_324848_hg38_all.gam
shell:
/usr/bin/time -v /DATA1/RNASeq/Aeron/Binaries/GraphAligner -g input/hg38.gfa -f input/324848.fastq --try-all-seeds --seeds-mxm-length 17 --seeds-mem-count 15 --seeds-mxm-cache-prefix tmp/seedcache -a output/aln_324848_hg38_all.gam -t 10 -b 35 --greedy-length 1> tmp/aligner_stdout.txt 2> tmp/aligner_stderr.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /DATA1/RNASeq/Aeron/.snakemake/log/2023-07-13T181526.504064.snakemake.log
[Thu Jul 13 18:15:26 2023] rule align: input: input/hg38.gfa, input/324848.fastq output: output/aln_324848_hg38_all.gam jobid: 1 benchmark: benchmark/aln_324848_hg38_all.txt wildcards: reads=324848, graph=hg38 threads: 10
/usr/bin/bash: tmp/aligner_stdout.txt: No such file or directory [Thu Jul 13 18:15:26 2023] Error in rule align: jobid: 1 output: output/aln_324848_hg38_all.gam shell: /usr/bin/time -v /DATA1/RNASeq/Aeron/Binaries/GraphAligner -g input/hg38.gfa -f input/324848.fastq --try-all-seeds --seeds-mxm-length 17 --seeds-mem-count 15 --seeds-mxm-cache-prefix tmp/seedcache -a output/aln_324848_hg38_all.gam -t 10 -b 35 --greedy-length 1> tmp/aligner_stdout.txt 2> tmp/aligner_stderr.txt (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /DATA1/RNASeq/Aeron/.snakemake/log/2023-07-13T181526.504064.snakemake.log