mv: cannot stat './/20201012.split.bam.tmp.bam': No such file or directory

[lindenb]

Hi @brentp , I'm trying to run smoove with singularity and the image from "docker://brentp/smoove". A set of two CRAMs on GRCh38 . I tested various combinations of parameters (set workdir/home, etc...) but it always raises the same kind of error:

cd /sandbox/shares/u1087/lindenb/work/NEXTFLOW/20201019.SND.GRCh38 && singularity exec\
        --workdir /sandbox/shares/u1087/lindenb/work/NEXTFLOW/20201019.SND.GRCh38 \
        --home /sandbox/shares/u1087/lindenb/work/NEXTFLOW/20201019.SND.GRCh38 \
        --bind  /sandbox/shares/u1087/lindenb/work/20201014.testmap/samples/B00I4CH/mapping/:/data1 \
        --bind  /sandbox/shares/u1087/lindenb/work/20201014.testmap/samples/B00I4CI/mapping/:/data2 \
        --bind /sandbox/resources/species/human/broadinstitute.org/bundle/hg38/v0/:/ref \
        --bind /sandbox/shares/u1087/lindenb/work/NEXTFLOW/20201019.SND.GRCh38/:/outdir \
        /sandbox/shares/u1087/lindenb/work/NEXTFLOW/20201019.SND.GRCh38/smoove.simg \
        smoove call -x --name 20201019.SND.GRCh38 \  
        --fasta /ref/Homo_sapiens_assembly38.fasta \ 
        --duphold \
        -p 16 --genotype /data1/20201012.testmap.B00I4CH.cram /data2/20201012.testmap.B00I4CI.cram
[smoove] 2020/10/19 16:43:44 starting with version 0.2.5
[smoove] 2020/10/19 16:43:44 calculating bam stats for 2 bams
[smoove] 2020/10/19 16:43:49 done calculating bam stats
[smoove]: ([E]lumpy-filter) 2020/10/19 16:57:15 Failed to populate reference for id 166
[smoove]:([E]lumpy-filter) 2020/10/19 16:57:31 Failed to populate reference for id 552
[smoove]:([E]lumpy-filter) 2020/10/19 16:57:31 Failed to populate reference for id 576
[smoove]:([E]lumpy-filter) 2020/10/19 16:57:31 Failed to populate reference for id 602
[smoove]:([E]lumpy-filter) 2020/10/19 16:57:39 Failed to populate reference for id 804
[smoove]:([E]lumpy-filter) 2020/10/19 16:57:39 Failed to populate reference for id 850
[smoove]:([E]lumpy-filter) 2020/10/19 16:57:40 Failed to populate reference for id 871
[smoove]:([E]lumpy-filter) 2020/10/19 16:57:40 Failed to populate reference for id 890
[smoove]:([E]lumpy-filter) 2020/10/19 16:57:40 Failed to populate reference for id 919
[smoove]:([E]lumpy-filter) 2020/10/19 16:57:40 Failed to populate reference for id 940
[smoove]:([E]lumpy-filter) 2020/10/19 16:57:40 Failed to populate reference for id 954
[smoove]:([E]lumpy-filter) 2020/10/19 16:57:40 Failed to populate reference for id 968
[smoove]:([E]lumpy-filter) 2020/10/19 16:57:40 Failed to populate reference for id 978
[smoove]:([E]lumpy-filter) 2020/10/19 16:57:40 Failed to populate reference for id 995
[smoove]:([E]lumpy-filter) 2020/10/19 16:57:40 Failed to populate reference for id 1010
(....)
[smoove]:([E]lumpy-filter) 2020/10/19 17:08:30 Failed to populate reference for id 2700
[smoove]:([E]lumpy-filter) 2020/10/19 17:08:31 Failed to populate reference for id 2770
[smoove]:([E]lumpy-filter) 2020/10/19 17:08:41 [lumpy_filter] extracted splits and discordants from 746074924 total aligned reads
[smoove]:([E]lumpy-filter) 2020/10/19 17:08:41 mv: cannot stat './/20201012.split.bam.tmp.bam': No such file or directory
[smoove]:2020/10/19 17:08:41 finished process: lumpy-filter (set -eu; lumpy_filter -f /ref/Homo_sapiens_assembly38.fasta /data1/20201012.testmap.B00I4CH.cram .//) in user-time:49m44.575705s system-time:1m5.422232s
[smoove]:2020/10/19 17:08:41 error running command: set -eu; lumpy_filter -f /ref/Homo_sapiens_assembly38.fasta /data1/20201012.testmap.B00I4CH.cram .//20201012.split.bam.tmp.bam .//20201012.disc.bam.tmp.bam 2 && mv .//20201012.split.bam.tmp.bam .//20201012.split.bam && mv .//20201012.disc.bam.tmp.bam .//20201012.disc.bam && cp .//20201012.split.bam .//20201012.split.bam.orig.bam && cp .//20201012.disc.bam .//20201012.disc.bam.orig.bam -> exit status 1
panic: exit status 1

can you help me please ?

[brentp]

Hi Pierre,

1. are you sure you're using the correct reference? I guess it could mean that there are no reads for those chromosomes?
2. are you sure this isn't running concurrently somewhere else? for example, maybe another process moved the file?
3. can you try exporting TMPDIR
4. did you bind your pwd?

[lindenb]

I wonder if there is a race condition between those two filenames ?

 /data1/20201012.testmap.B00I4CH.cram
/data2/20201012.testmap.B00I4CI.cram

are you using the path to the first dot as a temporary name ?

[brentp]

oh. yes. that's it.

[lindenb]

ok thanks ! do you think a symbolic link will work ?

[brentp]

you can soft-link to a different name to by-pass. i'll try to get in a fix for this.

[brentp]

yes. soft-link should work

[lindenb]

thanks you !

[brentp]

hi Pierre, I pushed v0.2.6 and updated docker images with a fix for this. Thanks for reporting and let me know if you have any problems.

[lindenb]

@brentp thank you !