tsolver.py can't find partitioned read files

[webbchen]

Dear Ka-Kit Lam

I've tried to run tsolver.py after running your main finishing tool and it seems to struggle to find the raw reads files:
(...)
ERROR: The following critical files could not be used
/main/projects/anne_webb/fungi/Septoria/smartdenovo_assembly/Pilon/Zt_02_pilon/Zt_02_smis/raw_reads.part-20.fasta
Check your paths and file permissions and try again
ERROR: Could not parse delta file, /main/projects/anne_webb/fungi/Septoria/smartdenovo_assembly/Pilon/Zt_02_pilon/Zt_02_smis/seedReads20.delta
error no: 400
20
len(dataList) 0
I think it tries to look for the partitioned raw read files 1-20 in my case, which are named as follows, e.g for the 20th: tmp_rawreads.part-20.fasta

I renamed them to raw_reads.part-<0to20>.fasta and for the time being, it seems to work.

Kind regards,

A. Webb

[kakitone]

Tsolver only works under fairly restricted setting. It is an experimental module. While you are encouraged to try it, I recommend the output from the main FinisherSC more.

[jnarayan81]

It would be great to know how to fix this problem. I would be more than happy to test and report you the result on our genome assembly.

python2 ~/tools/finishingTool/experimental/tSolver.py /mnt/sdc1/Jit/genomes_polished/3C_genome/B_polishing/ /home/lege/.conda/envs/align-env/bin/

It return an error

ERROR: The following critical files could not be used
/mnt/sdc1/Jit/genomes_polished/3C_genome/B_polishing/raw_reads.part-01.fasta
Check your paths and file permissions and try again
ERROR: Could not parse delta file, /mnt/sdc1/Jit/genomes_polished/3C_genome/B_polishing/seedReads01.delta
error no: 400

Is that critical ?
Note: I am using the old out folder location of finisherSC !