samtools and docker
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3.4 years ago
genya35 ▴ 40

Hello,

I've pull and image secessfully and now trying to run samtools sort, however, docker is not finding the bam file. Any suggestions?

Here is the code:

docker run -v /home/yey/mdl3/results:/data --rm biocontainers/samtools sort \
-T /tmp/HD753_IonXpress_007.sorted  \
-o /home/yey/mdl3/results/HD753_IonXpress_007.sorted.bam /home/yley/mdl3/results/HD753_IonXpress_007.bam

I get an error message "sort: cannot read: /home/yey/mdl3/results/HD753_IonXpress_007.bam: No such file or directory"

Thanks

software docker • 1.9k views
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1
Entering edit mode
3.4 years ago
Eric Lim ★ 1.7k

Your volume is mounted to /data, so you'd need to change your command line to reflect that.

docker run -v /home/yey/mdl3/results:/data --rm biocontainers/samtools sort \
-T /tmp/HD753_IonXpress_007.sorted  \
-o /data/HD753_IonXpress_007.sorted.bam /data/HD753_IonXpress_007.bam
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0
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sort command seems to be working but not index command. I get the following error. docker: Error response from daemon: OCI runtime create failed: container_linux.go:348: starting container process caused "exec: \"index\": executable file not found in $PATH": unknown. Is this a known issue?

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0
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Instead of using ... biocontainers/samtools index ..., try ... biocontainers/samtools samtools index ... and it should work.

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0
Entering edit mode

Thanks, sort and index seem to work, however, can't get view command to work. Does not produce any error messages but doesn't make a smaller bam based on the position provided. I've tested this code and file on a different machine where samtools was intalled and it worked.

Here is the code:

my $bam_file_sorted = "/data/HD753_IonXpress_007.sorted.bam"; 
my $bam_folder_dir = "/home/yey/mdl3/results/SN2-280-OFA_TL127067_051418_AAB";

my $chr = 7;
my $new_start_position = 55242330;
my $new_end_position = 55242615;

my $position_string = "chr".$chr.":".$new_start_position."-".$new_end_position;
my $smaller_bam_name = "/data/HD753_IonXpress_007_region_EGFR_e20.bam";

my $cmd3 = `docker run -v $bam_folder_dir:/data --rm biocontainers/samtools samtools view -hb $bam_file_sorted $position_string > $smaller_bam_name`;
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