FelixKrueger
commented
3 years ago Hi Debora,
This is somewhat odd. This die statement should come directly after the sequences were C>T transformed, and closing the filehandles is required to ensure that the transcribed files are not truncated.
A couple of things I have noticed:
- is there a chance that you don't have enough disk space? Maybe you can lose the
--temp_dirso that the temp files are (temporarily) written to the output file (where tehy will be removed by the end of the run)? - aligning to the human genome in non-directional mode probably takes ~5 cores, and 20GB of RAM for a single thread, so
--parallel 4will take at least 20 cores and >80GB of RAM. Is there chance that the job scheduler is unhappy about that and kills it? - the file names do not look like they have beend trimmed. it is almost never a good idea to align reads without and trimming, I can only recommend you your Trim Galore for this purpose. Also, if the data is non-directional there is a good chance the data will need additional trimming on the 5' ends (e.g. ~10-20bp for the Zymo Pico-Methyl kit... see here for recommendations: https://github.com/FelixKrueger/Bismark/tree/master/Docs#ix-notes-about-different-library-types-and-commercial-kits)
DLGisch
Hello, I have this error with --parallel and without too.
Reading in the sequence files /N/slate/dg/ILMN_678/S15_R1_001.fastq.gz.temp.1 and /N/slate/dg/ILMN_678/S15_R2_001.fastq.gz.temp.1
Created C -> T as well as G -> A converted versions of the FastQ file S15_R2_001.fastq.gz.temp.3 (83911887 sequences in total)
Failed to close filehandle Input/output error
Created C -> T as well as G -> A converted versions of the FastQ file S15_R2_001.fastq.gz.temp.4 (83911887 sequences in total)
Failed to close filehandle Input/output error
Command without --parallel 4
Bismark-0.23.1/bismark --genome genomes_homo_sapiens_GRCh38 -q --non_directional -o ILMN_678 --temp_dir ILMN_678 --nucleotide_coverage \ -1 /N/project/hongao_transfer/ILMN_678/S15_R1_001.fastq.gz -2 /N/project/hongao_transfer/ILMN_678/S15_R2_001.fastq.gz
When I receive this error WITHOUT --parallel 4 command I just resubmitted the then the program run, but very slow run 60h and Processed 190000000 sequence pairs so far.
When I received this error WITH --parallel 4 I try to run again, but received the same error again.
Can you help me understand this error?
Thank you, Debora