Hi everyone, I’m trying to run LoFreq to call variants on sorted BAM, with default settings.
I’ve used it for long time and it’s always worked fine
Since a couple days it keeps crashing with this error message:
“cat: can’t open ‘/jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallel*/*.log’: No such file or directory”
any clue? what’s wrong?
thx
Luca
Hi @LUCA_MOLOGNI
maybe submit error report: click at any output of failed job, click at error icon, the one looking like ladybird bug, in the middle window provide any info relevant to the failed job (optional but helpful to support people) and hit Report.
Kind regards,
Igor
Dear Igor,
thank you for your reply.
Here is the error report from Galaxy
Dataset | 94921136 (bbd44e69cb8906b55884c1d3dfb7be88) |
- | - |
History | 3916736 (932e860747bb9352) |
Failed Job | 973: Call variants on data 947 (f9cad7b01a47213560aa91eeda719002) |
Job ID | 51231981 (bbd44e69cb8906b573341c47583a8294) |
- | - |
Tool ID | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2 |
Tool Version | 2.1.5+galaxy2 |
Job PID or DRM id | 51231981 |
Job Tool Version | 2.1.5 |
ln -s '/jetstream2/scratch/main/jobs/51231981/inputs/dataset_1fd63bdb-91c2-4d7c-b0b2-9bf1c5e03474.dat' reads.bam && ln -s -f '/jetstream2/scratch/main/jobs/51231981/inputs/metadata_metadata_254480b5-65fa-4c3f-8c89-652a6bea7a13.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref '/cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa)' --out variants.vcf --sig 0.01 --bonf dynamic reads.bam 2>&1 || (tool_exit_code=$? && cat "$TMPDIR/lofreq2_call_parallel*/*.log" 1>&2 && exit $tool_exit_code) && echo set_lofreq_standard
cat: can't open '/jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallel*/*.log': No such file or directory
INFO [2023-06-27 17:09:41,198]: Using 8 threads with following basic args: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam
INFO [2023-06-27 17:09:41,222]: Adding 27 commands to mp-pool
CRITICAL [2023-06-27 17:09:41,287]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr8:1-145138636" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/10.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/10.log 2>&1
CRITICAL [2023-06-27 17:09:41,288]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr6:1-170805979" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/8.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/8.log 2>&1
CRITICAL [2023-06-27 17:09:41,289]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chrX:1-156040895" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/25.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/25.log 2>&1
CRITICAL [2023-06-27 17:09:41,289]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr4:1-190214555" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/6.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/6.log 2>&1
CRITICAL [2023-06-27 17:09:41,289]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr7:1-159345973" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/9.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/9.log 2>&1
CRITICAL [2023-06-27 17:09:41,289]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr11:1-135086622" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/13.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/13.log 2>&1
CRITICAL [2023-06-27 17:09:41,290]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr5:1-181538259" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/7.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/7.log 2>&1
CRITICAL [2023-06-27 17:09:41,292]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr9:1-138394717" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/11.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/11.log 2>&1
CRITICAL [2023-06-27 17:09:41,302]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr10:1-133797422" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/12.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/12.log 2>&1
CRITICAL [2023-06-27 17:09:41,303]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr2:1-121096764" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/2.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/2.log 2>&1
CRITICAL [2023-06-27 17:09:41,303]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr12:1-133275309" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/14.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/14.log 2>&1
CRITICAL [2023-06-27 17:09:41,304]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr2:121096765-242193529" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/3.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/3.log 2>&1
CRITICAL [2023-06-27 17:09:41,304]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr1:124478212-248956422" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/1.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/1.log 2>&1
CRITICAL [2023-06-27 17:09:41,306]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr13:1-114364328" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/15.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/15.log 2>&1
CRITICAL [2023-06-27 17:09:41,307]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr14:1-107043718" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/16.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/16.log 2>&1
CRITICAL [2023-06-27 17:09:41,314]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr15:1-101991189" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/17.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/17.log 2>&1
CRITICAL [2023-06-27 17:09:41,314]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr1:1-124478211" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/0.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/0.log 2>&1
CRITICAL [2023-06-27 17:09:41,315]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr3:99147780-198295559" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/5.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/5.log 2>&1
CRITICAL [2023-06-27 17:09:41,318]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr3:1-99147779" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/4.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/4.log 2>&1
CRITICAL [2023-06-27 17:09:41,319]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr16:1-90338345" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/18.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/18.log 2>&1
CRITICAL [2023-06-27 17:09:41,322]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr20:1-64444167" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/22.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/22.log 2>&1
CRITICAL [2023-06-27 17:09:41,322]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr18:1-80373285" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/20.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/20.log 2>&1
CRITICAL [2023-06-27 17:09:41,324]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr17:1-83257441" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/19.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/19.log 2>&1
CRITICAL [2023-06-27 17:09:41,328]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr19:1-58617616" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/21.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/21.log 2>&1
CRITICAL [2023-06-27 17:09:41,329]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chrY:1-57227415" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/26.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/26.log 2>&1
CRITICAL [2023-06-27 17:09:41,329]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr22:1-50818468" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/24.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/24.log 2>&1
CRITICAL [2023-06-27 17:09:41,332]: Following command failed with status 1: lofreq call --verbose --ref /cvmfs/[data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa](http://data.galaxyproject.org/byhand/hg38/sam_index/hg38.fa) --sig 0.01 --bonf dynamic reads.bam --no-default-filter -r "chr21:1-46709983" -o /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/23.vcf.gz > /jetstream2/scratch/main/jobs/51231981/_job_tmp/lofreq2_call_parallelgo23nzea/23.log 2>&1
CRITICAL [2023-06-27 17:09:41,336]: Some commands in pool failed. Can't continue
None
None
There seems to be a server side problem at UseGalaxy.org.
We’ll get back to you here once we know more, but maybe also try a rerun since we are still exploring the scope?
We’ve had a misconfiguration of the temporary directories for containerized jobs on usegalaxy.org. It should be resolved now, please try running again. Sorry for the inconvenience and thanks for using Galaxy.
Thank you Marius,
it works now!