Falcon Unzip crashed at 0-phasing (blasr ?)

[agroppi]

I'm using the last version of falcon-unzip after an assembly with the lastest version of falcon. I have blasr 5.3 python 2.7.12 The first step 3-unzip/reads ended but at the 0-phasing step Directories are created (here is an exemple : 0-phasing/000011F) But after that the pipeline stops Here is my cfg file :

[General]
job_type = local

[Unzip]
# list of fasta files
input_fofn = /mnt/cbib/sWAGMAN/Marouch/Falcon_0.5_Marouch/input_Marouch_falcon_0.5.fofn
# input_bam_fofn= input_bams.fofn

# path to bin directory containing samtools, blasr, and various GenomicConsensus utilities
smrt_bin=/module/apps/samtools/1.4/bin/ /module/apps/blasr/5.3/blasr/blasr /module/apps/python/2.7.12/bin/ /home/ag/GenomicConsensus/bin/

sge_phasing= --nodes 1 --ntasks-per-node 6
sge_quiver= --nodes 1 --ntasks-per-node 10
sge_track_reads= --nodes 1 --ntasks-per-node 6
sge_blasr_aln= --nodes 1 --ntasks-per-node 10
sge_hasm= --nodes 1 --ntasks-per-node 20
unzip_concurrent_jobs = 20
quiver_concurrent_jobs = 20

and here attached the all.log : all.log.txt

[nottwy]

Can you check if there is a file called '000191F_reads.fa' under the directory 3-unzip/reads/ ?

[agroppi]

Hi YES there is a file called 000191F_reads.fa under the directory 3-unzip/reads/

[nottwy]

You can attach your file '3-unzip/0-phasing/000191F/blasr/pwatcher/stderr' here.

[agroppi]

I don't have 3-unzip/0-phasing/000191F/blasr/pwatcher/stderr In the directory 3-unzip there is only the directory reads

But in the directory readsI have a symbolic link to mypwatcher/jobs/P4e06e95c523470/stderr

Here is this file : stderr.zip

[nottwy]

You have to change the name of your fofn file into input.fofn. Unzip only supports this name so fat. It didn't parse the name in your unzip.cfg.

[agroppi]

Thanks for your quick answer. I've changed the names of my config and fofn files I've just relaunched Falcon Unzip I'll keep you informed