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holab-hku / Vulture

AWS Batch based scalable microbial reads calling pipeline
MIT License
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Error running scvh_filter_matrix.r #2

Closed malonzm1 closed 1 year ago

malonzm1 commented 1 year ago

Hi,

When running scvh_filter_matrix.r I get the following error:

Sig FALSE TRUE FALSE 1915 0 TRUE 42 5850 Analyze bam in /scratch/cs/pan-autoimmune/data/vulture/scRNAseq/GSE215237/SRR21863020 Getting the barcodes of the non-host genes that have potential interaction with host [Mon Sep 18 13:18:12 EEST 2023] gene: gene-PestiV1gp1 bcs: CTGGTCTAGAAGGCCT

/scratch/cs/pan-autoimmune/data/vulture/scRNAseq/GSE215237/SRR21863020/alignment_outs/Aligned.sortedByCoord.out.bam is not present or is empty Looping over STARsolo BAM file to store host read IDS and output non-host BAM [Mon Sep 18 13:18:14 EEST 2023]

Please advise.

Thanks and good day.

hiyin commented 1 year ago

@juychen

juychen commented 1 year ago

Hi,

When running scvh_filter_matrix.r I get the following error:

Sig FALSE TRUE FALSE 1915 0 TRUE 42 5850 Analyze bam in /scratch/cs/pan-autoimmune/data/vulture/scRNAseq/GSE215237/SRR21863020 Getting the barcodes of the non-host genes that have potential interaction with host [Mon Sep 18 13:18:12 EEST 2023] gene: gene-PestiV1gp1 bcs: CTGGTCTAGAAGGCCT

/scratch/cs/pan-autoimmune/data/vulture/scRNAseq/GSE215237/SRR21863020/alignment_outs/Aligned.sortedByCoord.out.bam is not present or is empty Looping over STARsolo BAM file to store host read IDS and output non-host BAM [Mon Sep 18 13:18:14 EEST 2023]

Please advise.

Thanks and good day.

Sorry for my late reply, what files are in your alignment_outs folder?

malonzm1 commented 1 year ago

Thanks.

        4096 9/18/23 12:47 _STARgenome 11600494733 9/18/23 12:58 Aligned.out.bam         4096 9/18/23 12:58 Solo.out     9254511 9/18/23 12:58 SJ.out.tab         1308 9/18/23 12:59 Log.progress.out       52278 9/18/23 12:59 Log.out         2037 9/18/23 12:59 Log.final.out

juychen commented 1 year ago

Thanks.

        4096 9/18/23 12:47 _STARgenome 11600494733 9/18/23 12:58 Aligned.out.bam         4096 9/18/23 12:58 Solo.out     9254511 9/18/23 12:58 SJ.out.tab         1308 9/18/23 12:59 Log.progress.out       52278 9/18/23 12:59 Log.out         2037 9/18/23 12:59 Log.final.out

Seems that you did not get the sorted bam file.

did you set --outSAMtype "BAM SortedByCoordinate" when runing alignment using scvh_map_reads.pl?

malonzm1 commented 1 year ago

Thanks!