Done with the quality check. Facing the following issues.!!

[ritikgarg1234]

Issue.txt

[tadKeys]

Hi,

seems like Bismark is failing. Can you please provide me the output of

head /home/gm-database/Desktop/tabsat-master/tabsat_test_output_tmap/PGM_316D_IonXpress_028_1_NONDIR_tmap/PGM_316D_IonXpress_028_1_trimmed.fastq

and

ls -la /home/gm-database/Desktop/tabsat-master/tabsat_test_output_tmap/PGM_316D_IonXpress_028_1_NONDIR_tmap/

Thanks

[ritikgarg1234]

output_issue.txt

This is the output I'm getting.

[tadKeys]

Thanks.

1. Did you run "tabsat/reference/prepareReference.sh" before starting tabsat?

2. Could you please send me the output of
   /home/gm-database/Desktop/tabsat-master/tabsat_test_output_tmap/PGM_316D_IonXpress_028_1_NONDIR_tmap/bismark.log

Thanks

[ritikgarg1234]

Hello,
Thank you for your prompt reply.

1. I did run "tabsat/reference/prepareReference.sh" before starting tabsat.
2. Afterwhich, I tried executing /home/gm-database/Desktop/tabsat-master/tabsat_test_output_tmap/PGM_316D_IonXpress_028_1_NONDIR_tmap/bismark.log and attached herewith (issue3) is the permission error that I get.
   Also, find the bismark log file that was generated in the output folder, while using tabsat.

bismark.log

issue3.txt

[tadKeys]

Hi,

it seems like that the reference genome was not prepared correctly. Could you please make an ls -lR in the reference directory and send me the output.

Also you could try afterwards to remove the Bisulfite_Genome folder and rerun the prepare reference script.

Thanks

[ritikgarg1234]

Hello,

Please find attached, the output for the above mentioned command (ls -lR).
issue3 output.txt

As per your suggestion, I removed the Bisulfite_Genome folder and tried running the prepare reference script, again. But I think the mm10.fasta file is either missing or corrupted.

Here, is the output for (ls -lR) command after re running the prepare reference script.
issue3output2.txt

[tadKeys]

Hi,

as far as I can see, the reason for the errors are the *.2bit files. These files need to be extracted before they can be used.

Please see
http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/
and
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

Also the references need to be name *.fasta - not *.fa, please rename if this is the case (mv hg19.fa hg19.fasta)

Thanks

[ritikgarg1234]

Hi,
Done with the extraction and preparation of reference genome. Please see the run and let me know if it is alright (reference file prepared.txt).
reference file prepared.txt
After this I tried executing ./test_tabsat_tmap.sh command and attached here is the output I am getting.
tabsat output.txt
I think some files are still missing.
Please help!!

Thanks.

[tadKeys]

Hi,

I think bismark is still failing - could you please send me again the content of:

/home/gm-database/Desktop/tabsat-master/tabsat_test_output_tmap/PGM_316D_IonXpress_028_1_NONDIR_tmap/bismark.log

and ls -lR in the reference directory?

Thanks

[ritikgarg1234]

Hello,

Please find attached, the content of bismark.log file and the output of ls -lR.

Awaiting your response.

Thanks.

output_bismark_log.txt
output_ls-lR.txt

[tadKeys]

Hi,

seems like the bowtie2 index was not built sucessfully. Could you please remove the folders bismark_bowtie2 and bismark_tmap in the human directory and rerun the prepareReference script?

Also the bismark_log file was not present as your output showed.

Best wishes