A quick question on SAMMate with reference genome and bam files

[sunghee OH]

Hi,

I just ran SAMMate with neurospora_crassa_7_transcripts.gtf and bam files for RNA-seq samples. 

But, the process is cancelled in the beginning of running with this log file :

<Console>  12:55:53  <INFO>  The estimated time to process the data is more than 8 hour(s).

12:55:53  <INFO>  1.0 % is done...

<Console>  12:55:53  <INFO>  Start parsing annotation file in GTF format...

<Console>  12:55:54  <INFO>  Parsing annotation file is complete.

<Console>  12:55:54  <INFO>  Start parsing alignment results in BAM format...

12:55:54  <WARN>  Chromosome Supercontig_1 is not in the annotation file.

12:56:8  <WARN>  Chromosome Supercontig_2 is not in the annotation file.

12:56:16  <WARN>  Chromosome Supercontig_3 is not in the annotation file.

12:56:23  <WARN>  Chromosome Supercontig_4 is not in the annotation file.

12:56:31  <WARN>  Chromosome Supercontig_5 is not in the annotation file.

12:56:42  <WARN>  Chromosome Supercontig_6 is not in the annotation file.

12:56:47  <WARN>  Chromosome Supercontig_7 is not in the annotation file.

12:56:53  <WARN>  Chromosome Supercontig_8 is not in the annotation file.

12:56:55  <WARN>  Chromosome Supercontig_9 is not in the annotation file.

12:56:55  <WARN>  Chromosome Supercontig_12 is not in the annotation file.

12:56:55  <WARN>  Chromosome Supercontig_18 is not in the annotation file.

<Console>  12:56:55  <WARN>  The process is cancelled.

 

Could you please let me know what the problems are now and how i can address this to run SAMMate? 

Thanks Sunghee

[Nan Deng]

I think the chromosome name in your annotation file and in BAM file are not consistent. If your can not change the names, you can make a file for matching these names. You can find how to make it in the guide line documentation.

Best,

Nan

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