Unable to run ChIP-seq pipeline

[Liene....@mdc-berlin.de]

Dear PiGx team,

I am having issues with running the chipseq pipeline. 

I have been trying figure out what is actually causing the error, but with no success. Any help would be appreciated. I assume I have specified something in one of the files wrong...

The sample sheet:

SampleName, Read, Read2

FLAG_ChIP_rep1, FLAG-dmCTCF_rep1_ChIP-seq_i13_R1.fastq.gz, FLAG-dmCTCF_rep1_ChIP-seq_i13_R2.fastq.gz

FLAG_ChIP_rep2, FLAG-dmCTCF_rep2_ChIP-seq_i14_R1.fastq.gz, FLAG-dmCTCF_rep2_ChIP-seq_i14_R2.fastq.gz

input_rep1, FLAG-dmCTCF_input1_i15_R1.fastq.gz, FLAG-dmCTCF_input1_i15_R2.fastq.gz

input_rep2, FLAG-dmCTCF_input1_i16_R1.fastq.gz, FLAG-dmCTCF_input1_i16_R2.fastq.gz

I have also attached the settings file.

The error I get is: 

SyntaxError:

Input and output files have to be specified as strings or lists of strings.

  File "/gnu/store/1d1y4d7j8p4cnad7q9mswhbvs18falp6-pigx-chipseq-0.0.52/libexec/pigx_chipseq/Snake_ChIPseq.py", line 364, in <module>

  File "/gnu/store/1d1y4d7j8p4cnad7q9mswhbvs18falp6-pigx-chipseq-0.0.52/libexec/pigx_chipseq/Rules/Prepare_Annotation.py", line 11, in <module>

Thank you in advance!

Best,
Liene.

-------------------------------------------------------------------------
Liene Astica

PhD Student
AG Zinzen & AG Lupíáñez
Berlin Institute for Medical Systems Biology (BIMSB)
at the Max Delbrueck Center (MDC)
Hannoversche Str. 28
Rm. 1.60
10115 Berlin, Germany
-------------------------------------------------------------------------

[Alexander Blume]

Hi Liene,

Thanks for giving the chipseq pipeline a try :) 

Sorry, the error that you got is not very informative, but I checked the corresponding location in the code and figured it has something to do with the gtf file (gene annotation), which we are expecting, but unfortunately not properly validating.

To fix this error you should provide a gtf annotation to the ‘gff-file’ argument of the locations section. Please make sure that it matches your genome assembly, i.e uses the same chromosome naming scheme.

 

Unfortunately (again), you will also have to remove all header lines in the gtf file, meaning all lines starting with ‘#’. You can use the following command to achieve this, which will delete lines starting with ‘#’ and writes the output to a new file: 

'cat test.gtf | sed '/^#/d' > test_noHeader.gtf’  .

 

I hope this solves your problem, but please ask again if there are more errors popping up.

Best,

Alex

Alexander Blume

PhD Student

Berlin Institute for 

Medical Systems Biology (BIMSB)

at Max Delbrueck Center (MDC)

Hannoversche Str. 28

10115 Berlin, Germany

Phone: +49 30 9406 1422

Email: alexand...@mdc-berlin.de

Web: https://www.mdc-berlin.de/bioinformatics

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<settings.yaml>