Open shannonekj opened 4 years ago
Hi, I get exactly the same error with exactly the same files in the tmp (with file size 0 for both try.out and align2.dat). Was there a solution?
Best and thanks
Many thanks for all your bug reporting efforts. I spent some time on this and sorry to say I haven't found the bug or the problem. VGP used a lot on scaff10x and it seems that they didn't have this issue and also I never had this problem. If any of the users had this problem and also put the data (reads and assembly) in a location for download, I would be really grateful! My problem is that I need to repeat this issue and then fix the bug. For the time being, please use scaffolding_reads to decode the barcodes and then use the paired reads for scaffolding.
Best regards,
Zemin
Hi all,
Apologies for not posting when I got things up and running. I believe I "solved" this (or at least I no longer run into the) problem by supplying the input 10X fastq's through -data input.dat
(see format below) and sym-linking the reference genome to be in the working directory .
input.dat file format:
q1=/group/millermrgrp2/shannon/projects/assembly_genome_Hypomesus-transpacificus/00-raw_data/data-10X_M/Male2_S63_L004_R1_001.fastq.gz
q2=/group/millermrgrp2/shannon/projects/assembly_genome_Hypomesus-transpacificus/00-raw_data/data-10X_M/Male2_S63_L004_R2_001.fastq.gz
Run command:
scaff10x -nodes $((SLURM_CPUS_PER_TASK-2)) -longread 1 -gap 100 -matrix 2000 -reads 10 -link 8 -score 20 -edge 50000 -block 50000 -data input.dat sym-linked.reference.fasta output.scaff10x.fasta
which was run in the following working directory : /group/millermrgrp2/shannon/projects/assembly_genome_Hypomesus-transpacificus/03-assemblies/sandbox_hicanu/
As a note I installed scaff10x with conda.
@zning-sanger I'd be happy to upload the original files I used to a server if you'd like/it would be useful. I haven't tried to recreate the error since it was happening but maybe knowing how I fixed it helps??
Hi there,
I am encountering a segmentation fault when running Scaff10X.
Here is the stderr file associated with the error: test_assembly.j23957420.run_scaff10x.hi.err.txt
Here is the stdout file associated with the job: test_assembly.j23957420.run_scaff10x.hi.out.txt
I have the following lines in the
tmp_rununik_10443
and my
align.dat
file looks like this:I ran Scaff10X with the following parameters:
and used the following command to run scaff10x:
I didn't think this step much memory and indeed it fails at the same place if I use a partition with less memory (62000M/node).
Please advise! Thank you for your time :)