Comments (5)
rotifergirl
commented on August 16, 2024
I am having a similar problem, but earlier in the process, here is the contents of the log file
*** This is BWISE - High order De Bruijn graph assembler ***
Binaries are in: /users/jblommaert/BWISE/bin
The command line was: /users/jblommaert/BWISE/Bwise.py -x OHJ82_allclean.fa -S 10 -t 40 -o OHJ82_BWISE_S10.1
Results will be stored in: /automounts/workspace/workspace/markwelchlab/HIMBplic/OHJ82/OHJ82_V3/OHJ82_BWISE_S10.1
[09:24:44 04/12/2017] --> Starting Read Correction with Bloocoo...
Correction step 1
/users/jblommaert/BWISE/bin/Bloocoo32 -file /automounts/workspace/workspace/markwelchlab/HIMBplic/OHJ82/OHJ82_V3/OHJ82_allclean.fa -slow -kmer-size 31 -nbits-bloom 24 -abundance-min 10 -out reads_corrected1.fa -nb-cores 40
ln -fs /automounts/workspace/workspace/markwelchlab/HIMBplic/OHJ82/OHJ82_V3/OHJ82_BWISE_S10.1/reads_corrected1.fa /automounts/workspace/workspace/markwelchlab/HIMBplic/OHJ82/OHJ82_V3/OHJ82_BWISE_S10.1/reads_corrected.fa
[09:40:08 04/12/2017] --> Correction Done
Correction took: 0:15:23
[09:40:08 04/12/2017] --> Starting Graph construction and Super Reads generation...
#Graph 1: Construction...
/users/jblommaert/BWISE/bin/bcalm -max-memory 10000 -in /automounts/workspace/workspace/markwelchlab/HIMBplic/OHJ82/OHJ82_V3/OHJ82_BWISE_S10.1/bankBcalm.txt -kmer-size 63 -abundance-min 2 -out /automounts/workspace/workspace/markwelchlab/HIMBplic/OHJ82/OHJ82_V3/OHJ82_BWISE_S10.1/out -nb-cores 40
#Graph cleaning...
/users/jblommaert/BWISE/bin/btrim -u out.unitigs.fa -k 63 -t 124 -T 3 -o dbg63.fa -c 40 -h 8 -f 10
[ERROR] There was a problem writing "/automounts/workspace/workspace/markwelchlab/HIMBplic/OHJ82/OHJ82_V3/OHJ82_BWISE_S10.1/dbg63.fa".
[FATAL ERROR] One or more files could not be written.
Try `Bwise --help` for more information
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jnarayan81
commented on August 16, 2024
Can you double check your input file, it should be interleaved PE " Fasta" file.
I got this error because I used fastq sequence :( ...
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rotifergirl
commented on August 16, 2024
Maybe the problem is that I don't have interleaved PEs in my fasta file, I concatenated them based on the help:
-x PAIRED_READFILES input fasta or (compressed .gz if -c option is != 0) paired-end read files. Several read files must be concatenated
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jflot
commented on August 16, 2024
The sentence "Several read files must be concatenated." is quite ambiguous I realize: what we meant here is that if you have for instance two paired-end librairies (e.g. libA and libB), you have four read files (libA_1.fq, libA_2.fq, libB_1.fq, and libA_2.fq) among which you should first interleave the forward and reverse reads for each library (fq2fa --merge libA_1.fq libA_2.fq interleavedlibA.fa; fq2fa --merge libB_1.f libB_2.fq interleavedlibB.fa using for instance the tool fq2fa of the IDBA package), then concatenate the two resulting files (cat interleavedlibA.fa interleavedlibB.fa > interleavedlibsA+B.fa) in order to generate the PAIRED_READFILES input fasta.
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rotifergirl
commented on August 16, 2024
Thanks, that seems to have fixed my problem!
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Related Issues (18)
- Parameter for multi libraries HOT 1
- ZeroDivisionError: division by zero HOT 8
- Running time HOT 2
- What is the final file ? HOT 1
- BWISE stops working properly when k=220
- replace "integral information" by something like "fully uses paired-end information"
- Default output directory should be "." but is ".." instead, leading to a crash HOT 1
- add information about the output in the README
- Checking dependencies?
- Unexpected error during graph construction: <class 'FileNotFoundError'> HOT 1
- Create a "dev" branch separate from the "stable" branch
- Add option to crush isolated bubbles HOT 2
- Haplo contigs not generated
- Test fails at Graph3: Construction
- Please add a copy of the AGPL to the source code
- One or several files could not be generated
- Problem with binary compilation of BWISE. HOT 4
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