Configuration issue snippy 4.6.0+galaxy0 && 4.5.0

[jennaj]

toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.5.0

Notice that the string is using the default -m 0M (which is probably 1 M?) for the samtools sort step.

[02:17:39] Running: bwa mem -Y -M -R '@rg\tID:a_1_fastq_gz\tSM:a_1_fastq_gz' -t 1 reference/ref.fa /corral4/main/objects/0/4/7/dataset_0473a2ba-93ec-4439-bb44-9bac95e09e92.dat /corral4/main/objects/a/b/b/dataset_abb12b58-6772-4a58-bad2-bbd9b3ca7d42.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/075/403/75403025/tmp --threads 1 -m 0M | samtools fixmate -m - - | samtools sort -l 0 -T /corral4/main/jobs/075/403/75403025/tmp --threads 1 -m 0M | samtools markdup -T /corral4/main/jobs/075/403/75403025/tmp -r -s - - > snps.bam 2>> snps.log
[bam_sort] -m setting (0 bytes) is less than the minimum required (1M).

Is this passing through to the tool?
https://github.com/galaxyproject/tpv-shared-database/blob/9ae4db0fadf902dafc18872a4388a414e7e7904e/tools.yml#L583-L585

Testing histories
https://usegalaxy.org/u/jen-galaxyproject/h/test-snippy
Eu pending (can't test rn!)

Container issue?

Workaround for end-users
Toggle to use version Snippy 4.4.5+galaxy2 or earlier
https://galaxyproject.github.io/training-material/faqs/galaxy/tools_change_version.html

Reported at https://help.galaxyproject.org/t/need-help-running-snippy-for-bacterial-genome/17572/2 and via bug reports

[jennaj]

Hi @natefoo -- seems like this needs one more change at jetstream2:

jetstream2

ln -sf '/jetstream2/scratch/main/jobs/sanitized/inputs/dataset_sanitized.dat' 'ref.fna' && snippy --outdir 'genome.fasta' --cpus ${GALAXY_SLOTS:-1} --ram $((${GALAXY_MEMORY_MB:-4096}/1024)) --ref 'ref.fna' --mapqual 60 --mincov 10 --minfrac 0.9 --minqual 100.0 --ctgs '/jetstream2/scratch/main/jobs/sanitized/inputs/dataset_sanitized.dat' && cp -r 'sanitized' out && tar -czf out.tgz 'sanitized'

[23:26:48] Running: bwa mem -Y -M -R '@rg\tID:sanitized\tsanitized' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/077/535/sanitized/tmp --threads 0 -m 0M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/077/535/sanitized/tmp --threads 0 -m 0M | samtools markdup -T /corral4/main/jobs/077/535/sanitized/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[bam_sort] -m setting (0 bytes) is less than the minimum required (1M).

slurm/local

ln -sf '/corral4/main/objects/f/b/e/dataset_sanitized.dat' 'ref.fna' && snippy --outdir 'sanitized' --cpus ${GALAXY_SLOTS:-1} --ram $((${GALAXY_MEMORY_MB:-4096}/1024)) --ref 'ref.fna' --mapqual 60 --mincov 10 --minfrac 0.9 --minqual 100.0 --ctgs '/corral4/main/objects/9/7/d/dataset_sanitized.dat' && cp -r 'sanitized' out && tar -czf out.tgz 'sanitized'

[23:26:52] Running: bwa mem -Y -M -R '@rg\tID:sanitized\tSM:sanitized' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/sanitized/tmp --threads 0 -m 14000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/sanitized/tmp --threads 0 -m 14000M | samtools markdup -T /jetstream2/scratch/main/jobs/sanitized/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log

[natefoo]

You mentioned on Slack checking on EU, did it work there?