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Hoohm / dropSeqPipe

A SingleCell RNASeq pre-processing snakemake workflow
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Hi, i have a question about using dropSeqPipe #9

Closed kkjjhhk closed 6 years ago

kkjjhhk commented 6 years ago

Hi,

I'm doing follow the wiki and,

have a problem in generate-meta step.

here is error massages :

[Mon Oct 30 19:16:47 2017] IndexError in line 5 of /usr/lib/python3.6/site-packages/dropSeqPipe/Snakefiles/generate_meta.snake: [Mon Oct 30 19:16:47 2017] list index out of range [Mon Oct 30 19:16:47 2017] File "/usr/lib/python3.6/site-packages/dropSeqPipe/Snakefiles/generate_meta.snake", line 5, in Traceback (most recent call last): File "/usr/bin/dropSeqPipe", line 11, in load_entry_point('dropSeqPipe==0.23a0', 'console_scripts', 'dropSeqPipe')() File "/usr/lib/python3.6/site-packages/dropSeqPipe/main.py", line 81, in main complementory_args)) File "/usr/lib/python3.6/site-packages/snakemake/shell.py", line 100, in new raise sp.CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command ' set -euo pipefail; snakemake -s /usr/lib/python3.6/site-packages/dropSeqPipe/Snakefiles/generate_meta.snake --cores 5 -pT -d ../../hg19_dropseqpipe --configfile ./config.yaml ' returned non-zero exit status 1.

and this is my config.yaml:

config.yaml

Samples: SRR5250848: fraction: 0.001 expected_cells: 100 GENOMEREF: /storage/hd2/jina/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa REFFLAT: /storage/hd2/jina/Homo_sapiens/UCSC/hg19/Annotation/Genes/refFlat.txt METAREF: /storage/hd2/jina/hg19_STAR/ RRNAINTERVALS: /storage/hd2/jina/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.rRNA.interval_list GTF: /storage/hd2/jina/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf SPECIES:

can you tell me about which commend is wrong?

thanks,

Hoohm commented 6 years ago

Hello,

this is probably linked to a wrong genome file extension. In the folder containing the genome and the annotation you should have exactly two files: One file is the genome and has to end in .fa The second is the annotation file and has to end with .gtf

That should fix it.

Hoohm commented 6 years ago

@kkjjhhk Could you fix it? Can I close the issue?

kkjjhhk commented 6 years ago

Yes, I fixed it.

Thanks and have a nice day!

From: Patrick Roelli [mailto:notifications@github.com] Sent: Monday, January 01, 2018 7:47 PM To: Hoohm/dropSeqPipe Cc: kkjjhhk; Mention Subject: Re: [Hoohm/dropSeqPipe] Hi, i have a question about using dropSeqPipe (#9)

@kkjjhhk https://github.com/kkjjhhk Could you fix it? Can I close the issue?

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