only histo file outputs from smoove call

[Ana1335]

Hello developers, I have started running smoove This is my running command:

smoove call --outdir ${OUT_DIR} --exclude ${BED} --name ${SAMPLE_ID} --fasta ${FASTA} -p 1 --genotype ${INPUT_DIR}/${SAMPLE_ID}.rmdup1.bam

However the only output I get is just ${sample}.histo files as outputs. I think I am running the right command but I do not get any vcf files. Am I doing something wrong?

Thanks

[brentp]

hi, can you show the stderr and stdout from the command?

[Ana1335]

Hi, thanks for your reply. When I run the command above I only get the following outputs: (for now I am running only on three cell lines)

GCT-rmdup1.histo RD-rmdup1.histo SW982-rmdup1.histo

head GCT-rmdup1.histo
0   0.005097314201
1   0.006356269899
2   0.006353033509
3   0.006309342244
4   0.006260796395
5   0.006285069319

and the log file I get

Current working directory: /oak/stanford/groups/analysis/shaghayegh/scripts/SR-scripts
Starting run at: Mon Dec  4 22:03:41 PST 2023

Job Array ID / Job ID: 37319724 / 37319725
This is job 1 out of 3 jobs.

[smoove] 2023/12/04 22:03:43 starting with version 0.2.8
[smoove] 2023/12/04 22:03:43 calculating bam stats for 1 bams
[smoove]: ([E]lumpy-filter) 2023/12/04 22:03:43 /bin/bash: lumpy_filter: command not found
[smoove]:2023/12/04 22:03:43 finished process: lumpy-filter (set -eu; lumpy_filter -f /oak/stanford/groups/emoding/sequencing/pipeline/indices/hg19.fa /oak/stanf) in user-time:1.787ms system-time:815µs
[smoove]:2023/12/04 22:03:43 error running command: set -eu; lumpy_filter -f /oak/stanford/groups/sequencing/pipeline/indices/hg19.fa /oak/stanford/groups/emoding/analysis/shaghayegh/shortreads-SV/alignment-BWA/dedupped_BAMs_picard/GCT.rmdup1.bam /oak/stanford/groups/emoding/analysis/shaghayegh/shortreads-SV/results-smoove/GCT-rmdup1.split.bam.tmp.bam /oak/stanford/groups/emoding/analysis/shaghayegh/shortreads-SV/results-smoove/GCT-rmdup1.disc.bam.tmp.bam 2 && mv /oak/stanford/groups/emoding/analysis/shaghayegh/shortreads-SV/results-smoove/GCT-rmdup1.split.bam.tmp.bam /oak/stanford/groups/emoding/analysis/shaghayegh/shortreads-SV/results-smoove/GCT-rmdup1.split.bam && mv /oak/stanford/groups/emoding/analysis/shaghayegh/shortreads-SV/results-smoove/GCT-rmdup1.disc.bam.tmp.bam /oak/stanford/groups/emoding/analysis/shaghayegh/shortreads-SV/results-smoove/GCT-rmdup1.disc.bam && cp /oak/stanford/groups/emoding/analysis/shaghayegh/shortreads-SV/results-smoove/GCT-rmdup1.split.bam /oak/stanford/groups/emoding/analysis/shaghayegh/shortreads-SV/results-smoove/GCT-rmdup1.split.bam.orig.bam && cp /oak/stanford/groups/emoding/analysis/shaghayegh/shortreads-SV/results-smoove/GCT-rmdup1.disc.bam /oak/stanford/groups/emoding/analysis/shaghayegh/shortreads-SV/results-smoove/GCT-rmdup1.disc.bam.orig.bam -> exit status 127
[smoove] 2023/12/04 22:03:52 done calculating bam stats
panic: exit status 127

goroutine 1 [running]:
github.com/brentp/smoove/lumpy.Lumpy(0x7ffc8f2b4ea0, 0x3, 0x7ffc8f2b4eac, 0x40, 0x7ffc8f2b4dd8, 0x4d, 0xc0002307e0, 0x1, 0x1, 0xc000117900, ...)
    /home/brentp/src/smoove/lumpy/lumpy.go:141 +0x587
github.com/brentp/smoove/lumpy.Main()
    /home/brentp/src/smoove/lumpy/lumpy.go:351 +0x29b
main.main()
    /home/brentp/src/smoove/cmd/smoove/smoove.go:121 +0x1c4
Job finished with exit code 2 at: Mon Dec  4 22:03:52 PST 2023

These are the only files I get so far by running the command above

[brentp]

Hi, you need to set up so that lumpy_filter is on your $PATH. Note this in the output:

 lumpy_filter: command not found

and the non-zero exit code. Once you have lumpy_filter and the other required programs it should get further.

[Ana1335]

Great, thanks

[Ana1335]

Hey @brentp . I am still dealing with smoke running and no lumpy_filter error. I installed smoove via conda and the version I have installed is 0.2.8 (https://anaconda.org/bioconda/smoove). when I run smoove with no arguments, see a list of tools but it seems there is no lumpy_filter.

smoove version: 0.2.8

smoove calls several programs. Those with 'Y' are found on your $PATH. Only those with '*' are required.

 *[Y] bgzip [ sort   -> (compress) ->   index ]
 *[Y] gsort [(sort)  ->  compress   ->  index ]
 *[Y] tabix [ sort   ->  compress   -> (index)]
 *[Y] lumpy
 *[ ] lumpy_filter
 *[Y] samtools
 *[Y] svtyper
 *[Y] mosdepth [extra filtering of split and discordant files for better scaling]

  [Y] duphold [(optional) annotate calls with depth changes]
  [Y] svtools [only needed for large cohorts].

Available sub-commands are below. Each can be run with -h for additional help.

call        : call lumpy (and optionally svtyper)
merge       : merge and sort (using svtools) calls from multiple samples
genotype    : parallelize svtyper on an input VCF
paste       : square final calls from multiple samples (each with same number of variants)
plot-counts : plot counts of split, discordant reads before, after smoove filtering
annotate    : annotate a VCF with gene and quality of SV call
hipstr      : run hipSTR in parallel
duphold     : run duphold in parallel (this can be done by adding a flag to call or genotype)

is it just an old version of conda for smoove? why lumpy_filter is not installed? Thanks a lot in advance for your help.