malfoy / bcool Goto Github PK

Could you add a check in BCool.py to check that the required executables are installed and runnable before failing later?

Maybe as a -c or --check option too?

This will avoid:
/bin/sh: /home/tseemann/tmp/BCOOL-untagged-5f0c9c78ec34735ca8e2/bin/ntcard: No such file or directory

wen -> went

Hi,

I installed BCOOL as suggested, and got the following messages:
./install.sh -t 8
use 8 threads
I put binaries in /fs/scratch/PHS0338/appz/BCOOL/bin
PHASE ONE, kmer spectrum estimator ntcard
PHASE THREE, READ MAPPING ON THE DBG: BGREAT
PHASE FOUR GRAPH CLEANING: BTRIM
The end !
[jpac1984@p0076 BCOOL]$

But, then I tried the test, and it failed:
./test.sh

*** This is Bcool - de Bruin graph based corrector ***
Binaries are in: /fs/scratch/PHS0338/appz/BCOOL/bin
The command line was: ../Bcool -u lambda_virus.200bp.50x.1percentError.fa.gz -k 61 -o testFixedK -t 4
Results will be stored in: /fs/scratch/PHS0338/appz/BCOOL/test/testFixedK
Kmer selected : k=61 Spectrum analysis duration 0:00:00
[21:18:55 18/02/2021] --> Building the graph...
#Graph dbg61.fa: Construction...
Unexpected error during graph construction: <class 'FileNotFoundError'>
[FATAL ERROR]
Try BCOOL --help for more information
FAIL the install went wrong
*** This is Bcool - de Bruin graph based corrector ***
Binaries are in: /fs/scratch/PHS0338/appz/BCOOL/bin
The command line was: ../Bcool -u lambda_virus.200bp.50x.1percentError.fa.gz -o testNtcard -t 4
Results will be stored in: /fs/scratch/PHS0338/appz/BCOOL/test/testNtcard
No kmer size selected, launching kmer spctrum analysis with Ntcard
Kmer selected : k=61 Spectrum analysis duration 0:00:17
[21:19:13 18/02/2021] --> Building the graph...
#Graph dbg61.fa: Construction...
Unexpected error during graph construction: <class 'FileNotFoundError'>
[FATAL ERROR]
Try BCOOL --help for more information
FAIL ntcard install went wrong

What did I do wrong?
Is there any particular way how should I have ran test.sh?

Hi I ran the below, which resulted in outputs for all of the intermediate files except the reads_corrected.fa file
Bcool.py -u cat_unmap.fq -t 15 -o Bcool
Any suggestions to why the final file is empty?

I've also attached my log files
logBgreat.txt
logTips.txt
logBcalm.txt

`Bcool.py --version

*** This is Bcool - de Bruin graph based corrector ***

Binaries are in: /space/home/rosales/local/bin/BCOOL/bin
Bcool.py 0.0.1`