Thanks a lot for HAPHPIPE, I've used it successfully and pretty easily for HRSV and HIV assembly, it did great!
Now we want to get to the next level with HIV haplotype reconstruction, but I am facing issues with predict_haplo. First I only used it with corrected fastq reads and final assembly from a denovo assembly, as exemplified in your tutorial; it looks like bwa-mem did ok but then i get:
Reconstruction region PH01: RBF254|RBF254|RBF254:1-9024
[--- predict_haplo:PH01_RBF254 command 1 ---]
cd \
/tmp/tmpHP_predict_haplonazqau_x
I wonder if this is related to the lack of an interval_txt option, but:
there's no example file to helps build one
when I try to use the option with an empty file (--interval_txt interval.txt), I get:
haphpipe: error: unrecognized arguments: --interval_txt interval.txt
Please can you help me out of this? I attach a log file for the run with no --interval_txt option:
slurm-48131535.out.txt
Hi guys,
Thanks a lot for HAPHPIPE, I've used it successfully and pretty easily for HRSV and HIV assembly, it did great!
Now we want to get to the next level with HIV haplotype reconstruction, but I am facing issues with predict_haplo. First I only used it with corrected fastq reads and final assembly from a denovo assembly, as exemplified in your tutorial; it looks like bwa-mem did ok but then i get:
Reconstruction region PH01: RBF254|RBF254|RBF254:1-9024
[--- predict_haplo:PH01_RBF254 command 1 ---] cd \ /tmp/tmpHP_predict_haplonazqau_x
[--- predict_haplo:PH01_RBF254 command 2 ---] PredictHaplo-Paired \ PH01_RBF254.config \ &> PH01_RBF254.config.log /bin/sh : ligne 1 : 3424 Erreur de segmentation PredictHaplo-Paired PH01_RBF254.config &>PH01_RBF254.config.log
[--- FAILED: predict_haplo:PH01_RBF254 ---] Command: cd /tmp/tmpHP_predict_haplonazqau_x && PredictHaplo-Paired PH01_RBF254.config &> PH01_RBF254.config.log returncode: 139 PredictHaplo segfaulted
I wonder if this is related to the lack of an interval_txt option, but:
Please can you help me out of this? I attach a log file for the run with no --interval_txt option: slurm-48131535.out.txt
as well as the ref fasta file: RBF254_denovo_consensus.fas.txt
Please let me know if you need more to figure this out. Cheers, Marie