Tips

• cwltool may occupy all the system disk by tmp directory. If you suspect the situation, check /tmp or avoid by cwltool's option. The example is below. You can also delete the dir by --rm-tmpdir.

cwltool --tmp-outdir-prefix=/home/yyasumizu/tmp_cwl/ \
--tmpdir-prefix=/home/yyasumizu/tmp_cwl/ \
~/yyoshiaki-git/VIRTUS/workflow/VIRTUS.PE.cwl \
--fastq1 /home/yyasumizu/NGS_public/PRJEB31829_Blimph_EB/donor1_day0_1.fastq.gz \
--fastq2 /home/yyasumizu/NGS_public/PRJEB31829_Blimph_EB/donor1_day0_2.fastq.gz \
--genomeDir_human /home/yyasumizu/yyoshiaki-git/VIRTUS/test/STAR_index_human \
--genomeDir_virus /home/yyasumizu/yyoshiaki-git/VIRTUS/test/STAR_index_virus \
--salmon_index_human /home/yyasumizu/yyoshiaki-git/VIRTUS/test/salmon_index_human \
--salmon_quantdir_human donor1_day0/salmon_human \
--outFileNamePrefix_human /home/yyasumizu/EB_VIRTUS/donor1_day0/human --nthreads 20

• when you specify .cwl files in the absolute path, error may occur. use the relative path.
• note that you cannnot use \in --outFileNamePrefix_*
• STAR will require memory at least 30GB. Check your resources.
• Some options instead of docker are available. Specify cwltool option --user-space-docker-cmd=udocker, --singularity.
• You can specify another host's reference URL such as the mouse in createindex steps, but note that virus references are designed for human viruses. We don't guarantee the result when you changed the reference species.
• When you feel the sequence depth may be insufficient, see virusAligned.filtered.sortedByCoord.out.bam which conteins mapped reads assigned to viruses. Users can adjust the cutoff by --hit_cutoff. For screening viruses, we recommend users set the cutoff to a low number such as 50.