quantification issue (Error in rule allig JobID 7)

[karlowatz]

Hey

I am having a problem similar to Bodoko except when running the quantification step.

/Aeron$ snakemake --cores=all Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 24 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

[Fri Apr 16 15:43:57 2021] rule align: input: input/hg19.gfa, input/hg19.fa output: output/aln_hg19_hg19_all.gam jobid: 7 benchmark: benchmark/aln_hg19_hg19_all.txt wildcards: reads=hg19, graph=hg19 threads: 15

/usr/bin/bash: tmp/aligner_stdout.txt: No such file or directory [Fri Apr 16 15:43:57 2021] Error in rule align: jobid: 7 output: output/aln_hg19_hg19_all.gam shell: /usr/bin/time -v Binaries/GraphAligner -g input/hg19.gfa -f input/hg19.fa --try-all-seeds --seeds-mxm-length 17 --seeds-mem-count 15 --seeds-mxm-cache-prefix tmp/seedcache -a output/aln_hg19_hg19_all.gam -t 15 -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: /home/nickk/Aeron/.snakemake/log/2021-04-16T154357.466981.snakemake.log

Could someone help me with this issue? I also dont see the log files (.snakemake) in my Aeron folder.

My Config file is as follow

graph: hg19.gfa transcripts: hg19.fa

seedsize: 17 maxseeds: 15 fusion_max_error_rate: 0.2 fusion_min_score_difference: 200 alignment_selection: --greedy-length alignment_E_cutoff: 1

bandwidth for the aligner. Higher means more accurate but slower alignment.

aligner_bandwidth: 35 gtffile: home/nickk/Aeron/ensembl75.gtf

https://bitbucket.org/dilipdurai/aeron/

scripts: AeronScripts

https://github.com/maickrau/GraphAligner

binaries: Binaries

needed to convert mummer seeds to .gam seeds

vgpath: home/nickk/vg

[RDorney]

I also have run into an identical problem. Is there a solution???

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

[Fri Feb 10 16:40:54 2023] rule align: input: input/hg38.gfa, input/gencode.v42.transcripts.fa output: output/aln_gencode_hg38_all.gam jobid: 7 benchmark: benchmark/aln_gencode_hg38_all.txt wildcards: reads=gencode, graph=hg38 threads: 10

/usr/bin/bash: tmp/aligner_stdout.txt: No such file or directory [Fri Feb 10 16:40:54 2023] Error in rule align: jobid: 7 output: output/aln_gencode_hg38_all.gam shell: /usr/bin/time -v /MMCI/MS/LongRNA/work/mikko/AERON_runs/run_20200515_threeprime/Aeron/Binaries/GraphAligner -g input/hg38.gfa -f input/gencode.v42.transcripts.fa --try-all-seeds --seeds-mxm-length 17 --seeds-mem-count 20 --seeds-mxm-cache-prefix tmp/seedcache -a output/aln_gencode_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: /opt/Aeron/.snakemake/log/2023-02-10T164054.584629.snakemake.log