No output in nextsv2

[Fu-Yilei]

When I was using nextsv2, the program found the input fastq file, while it seems that the program cannot output anything. The ngmlr is not running. The program output is pasted below.

`[01/21/2019 14:43:37] program started
[01/21/2019 14:43:37] reading config file
[01/21/2019 14:43:37] creating output directories
[01/21/2019 14:43:37] output directory is: /home/fuyilei96/10Xresult_7/10X
[01/21/2019 14:43:37] listing input files
[01/21/2019 14:43:37] 1 fastq files were found in the input folder: /data/tjiang/rCANID/sim_reads/10X
[01/21/2019 14:43:37] checking samtools version
[01/21/2019 14:43:37] checking input files
[01/21/2019 14:43:37] generating tasks for Minimap2
[01/21/2019 14:43:37] generating tasks for Minimap2-Sniffles
[01/21/2019 14:43:37] bam to cram for Minimap2 bam
[01/21/2019 14:43:37] generating tasks for NGMLR
[01/21/2019 14:43:37] generating tasks for NGMLR-Sniffles
[01/21/2019 14:43:37] bam to cram for NGMLR bam`

[fangli80]

Please go to the output directory: /home/fuyilei96/10Xresult_7/10X

There should be a work.sh in the directory. You need to run work.sh locally or submit it to the cluster.

Thank you for using NextSV. I will add this in the Readme.

[fangli80]

Currently it only generates two vcf files. I will soon add some features to generate consensus calls from the two vcf files.

[Fu-Yilei]

Thanks and running work.sh works for me.