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Question: Error with featureCounts
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gravatar for syrttgump
3.8 years ago by
syrttgump20
United States
syrttgump20 wrote:

Hi,

I am using featureCounts to count reads for every gene from refSeq annotation file. But it went to error:

featureCounts -a ../refGeneReviewed.gtf -t exon -g gene_id -p -Q 10 -o ../../result/fc_accepted_hits.txt accepted_hits.bam

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
      v1.4.6

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           P accepted_hits.bam                              ||
||                                                                            ||
||             Output file : ../../result/fc_accepted_hits.txt                ||
||             Annotations : ../refGeneReviewed.gtf (GTF)                     ||
||                                                                            ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||              Paired-end : yes                                              ||
||         Strand specific : no                                               ||
||      Multimapping reads : not counted                                      ||
|| Multi-overlapping reads : not counted                                      ||
||                                                                            ||
||          Chimeric reads : counted                                          ||
||        Both ends mapped : not required                                     ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file ../refGeneReviewed.gtf ...                            ||
||    Features : 304046                                                       ||
||    Meta-features : 24154                                                   ||
||    Chromosomes : 35                                                        ||
||                                                                            ||
|| Process BAM file accepted_hits.bam...                                      ||
||    Paired-end reads are included.                                          ||
||    Assign fragments (read pairs) to features...                            ||
||    Found reads that are not properly paired.                               ||
||    (missing mate or the mate is not the next read)                         ||
Cannot load read part from the tmp file!
featureCounts: input-files.c:2216: sort_SAM_finalise: Assertion `0' failed.
Aborted

 

This bam and gtf file should be right, because I have used them to run HTSeq-count

ADD COMMENTlink modified 3.8 years ago by Yang Liao70 • written 3.8 years ago by syrttgump20

Hi,

I found similar error:

featureCounts: input-files.c:4675: SAM_pairer_run: Assertion `0 == corrected_run' failed.

And tried the -p and -P option, but still run into this error. Can you suggestion why and what could be the solution?

ADD REPLYlink written 2.5 years ago by hn.biotech0

Also having the same problem, and not able to fix it with -p -P ...

ADD REPLYlink written 23 months ago by Darya Vanichkina100
3
gravatar for Yang Liao
3.8 years ago by
Yang Liao70
Australia
Yang Liao70 wrote:

It looks that the current directory has no enough space, or some reads in the SAM file are extremely long (e.g., longer than 1200 bps). 

ADD COMMENTlink written 3.8 years ago by Yang Liao70

That is the problem, I used the parameter -p -P, and it works now. Thanks.

ADD REPLYlink written 3.8 years ago by syrttgump20

I can confirm that changing the tmpDir option to featureCounts to a drive where I have storage solved the issue for me, no longer terminating the with the error:

 

||    Assign reads to features...                                             ||
ERROR: cannot write into the temporary file. Please check the empty space in the output directory.
||                                                                            ||

 

 

ADD REPLYlink modified 7 months ago • written 7 months ago by Malcolm Cook1.5k
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