Speedseq is runnning infinitely

[vivekruhela]

Hello,

I am trying to get somatic mutations from speedseq somatic but it has been more than 24 hours but it is still running and no output is generated. Here is the command I am using:

time /home/akansha/speedseq/bin/speedseq somatic -v -t 20 -o /home/akansha/vivekruhela/ega_data_1901/speedseq_analysis/CR-MGUS-10_10/test.vcf /home/akansha/vivekruhela/refs/human_g1k_v37/human_g1k_v37.fasta /home/akansha/vivekruhela/ega_data_1901/bam_files/CR-MGUS-10_10/CR-MGUS-10_10-PB_dedup.realigned.bam /home/akansha/vivekruhela/ega_data_1901/bam_files/CR-MGUS-10_10/CR-MGUS-10_10-BM_dedup.realigned.bam

Here is the response generated from above command:

Sourcing executables from /home/akansha/speedseq/bin/speedseq.config ...
Calling somatic variants...

    create temporary directory

    /home/akansha/speedseq//bin/sambamba view -H /home/akansha/vivekruhela/ega_data_1901/bam_files/CR-MGUS-10_10/CR-MGUS-10_10-PB_dedup.realigned.bam | grep "^@SQ" | cut -f 2- | awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' > test.vcf.QZXqY0BQByf5/windows.bed

    /home/akansha/speedseq//bin/freebayes -f /home/akansha/vivekruhela/refs/human_g1k_v37/human_g1k_v37.fasta \
        --pooled-discrete \
        --min-repeat-entropy 1 \
        --genotype-qualities \
        --min-alternate-fraction 0.05 \
        --min-alternate-count 2 \
        --region $chrom:$start..$end \
        /home/akansha/vivekruhela/ega_data_1901/bam_files/CR-MGUS-10_10/CR-MGUS-10_10-PB_dedup.realigned.bam /home/akansha/vivekruhela/ega_data_1901/bam_files/CR-MGUS-10_10/CR-MGUS-10_10-BM_dedup.realigned.bam \
        | somatic_filter 1e-5 18 0 \
        > test.vcf.QZXqY0BQByf5/test.vcf.$chrom:$start..$end.vcf

    cat test.vcf.QZXqY0BQByf5/var_command.txt | /home/akansha/speedseq//bin/parallel -j 20

Neither there is any errror message or any progress I have observed from yesterday. Please suggest if I have missed anything. Thanks.

[vivekruhela]

Please respond.

@ahwagner @cc2qe @s-boardman