#70 hg19 DB not recognised in the assembly stage

[Jose]

Hello MOCAT team,

First of all, thanks for puting together this amazing pipeline.

I've tried the runMOCAT script but it has crashed while trying to perform the assembly, with this last message:

Tue Aug 8 23:38:51 2017: PERFORMING ASSEMBLY... Tue Aug 8 23:38:51 2017: Checking files... ERROR & EXIT: Missing pair and/or single reads files for Suelo -r|reads 'hg19' is not any of the following: a) 'reads.processed' (and the reads have been trimmed and filtered) b) 'DATABASE NAME' (and the reads have been screened using this database) c) 'FASTA FILE' (and the reads have been screened using a fasta file). Perhaps you meant either of these for the -r option: - reads.processed

If I try the direct MOCAT.pl command for assembly with different sample files (in my project root or inside the logs/processing/ tree) I get the same result, so it seems it is not a problem of the sample or config files, since previous step recognized the hg19.

I've attached the logs.

Thank you very much in advance!
Jose

[jxcui]

hey, I met the same problem as yours. have you solved it?

[MOCAT]

You have to specify -r hg19 or -r reads.processed

On Wed, Dec 13, 2017 at 04:29 jxcui cjx13@users.sf.net wrote:

hey, I met the same problem as yours. have you solved it?

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** [tickets:#70] hg19 DB not recognised in the assembly stage**

Status: New
Labels: assembly runMOCAT
Created: Tue Aug 08, 2017 09:49 PM UTC by Jose
Last Updated: Tue Aug 08, 2017 09:49 PM UTC
Owner: MOCAT
Attachments:

• logs.tar.gz (11.1
  kB; application/x-gzip)

Hello MOCAT team,

First of all, thanks for puting together this amazing pipeline.

I've tried the runMOCAT script but it has crashed while trying to perform
the assembly, with this last message:

Tue Aug 8 23:38:51 2017: PERFORMING ASSEMBLY... Tue Aug 8 23:38:51 2017: Checking files... ERROR & EXIT: Missing pair and/or single reads files for Suelo -r|reads 'hg19' is not any of the following: a) 'reads.processed' (and the reads have been trimmed and filtered) b) 'DATABASE NAME' (and the reads have been screened using this database) c) 'FASTA FILE' (and the reads have been screened using a fasta file). Perhaps you meant either of these for the -r option: - reads.processed

If I try the direct MOCAT.pl command for assembly with different sample
files (in my project root or inside the logs/processing/ tree) I get the
same result, so it seems it is not a problem of the sample or config files,
since previous step recognized the hg19.

I've attached the logs.

Thank you very much in advance!
Jose

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[Jose]

As you can clearly see in the logs that I uploaded, -r hg19 was specified, but MOCAT crashed miserabily:
EXECUTE COMMAND : -sf /scratch/MOCAT/MOCAT.samples -cfg /scratch/MOCAT/logs/tmp//user.MOCAT.samples.20170808_224339.assemble_revise_predict_genes_with_hg19_screen/MOCAT.cfg -a -r hg19

[jxcui]

As Jose said, we used the wrapper script runMOCAT.sh with the parameter "4：assemble_revise_predict_genes_with_hg19_screen" , and in the log file, -r hg19 was specified.

[Jose]

No, I didn't solve it, sorry!

[jxcui]

hi Jose, I found the problem. The parameter "-screened_files" for screen was missing in the file "MOCAT/scripts/assemble_revise_predict_genes_with_hg19_screen". You shoud add "-screened_files" to the line "[command] -s hg19 -identity 90".
Hope this helps. Though there are still other problems in subsequent steps that I can't solve.

[Jose]

Hi Jxcui! Thank you very much for the feedback! Yes... it seems not a very tested pipeline anyway...