These are chat archives for dereneaton/ipyrad

7th
Mar 2018
Glib Mazepa
@mazepago_twitter
Mar 07 2018 14:39
@isaacovercast and @eaton-lab another short question: I have completed steps 12, and created new params files by branching: for each such a branch that differ in clustering threshold i was firstly changing this value in the maternal params_file and then executing the branching 'ipyrad -p maternal_params_file_changed_for_branch_n -b branch_n'. But if i ran two the branches of s3 simultaneously, it seems like they both writing to the _edits folder, which is a product of step 2... so we cannot run branches s3 simultaneously, can we?
Isaac Overcast
@isaacovercast
Mar 07 2018 15:59
@gissella_pineda_twitter Can you email me the ipyrad_log.txt file? I'll pm you my address
@mazepago_twitter That command looks okay and there's no error message so it's hard to say. If you copy/paste and run this whole command it might give you more info:
/home/gmazepa/miniconda2/lib/python2.7/site-packages/bin/vsearch-linux-x86_64 --fastq_mergepairs /scratch/beegfs/monthly/gmazepa/ipyrad_02_March/pairddrad_02_March_edits/tmpQplW8IR1.fastq --reverse /scratch/beegfs/monthly/gmazepa/ipyrad_02_March/pairddrad_02_March_edits/tmpr_rm3VR2.fastq --fastqout /scratch/beegfs/monthly/gmazepa/ipyrad_02_March/pairddrad_02_March_edits/tmpTWGl_8_merged.fastq --fastqout_notmerged_fwd /scratch/beegfs/monthly/gmazepa/ipyrad_02_March/pairddrad_02_March_edits/tmpmX5CKl_nonmergedR1.fastq --fastqout_notmerged_rev /scratch/beegfs/monthly/gmazepa/ipyrad_02_March/pairddrad_02_March_edits/tmpcv1Vzm_nonmergedR2.fastq --fasta_width 0 --fastq_minmergelen 35 --fastq_maxns 5 --fastq_minovlen 20 --fastq_maxdiffs 4 --label_suffix _m1 --fastq_qmax 1000 --threads 2 --fastq_allowmergestagger
@mazepago_twitter Yes, correct, in general you should not run the same step on branched assemblies simultaneously because it'll overwrite itself. This is just a limitation of the implementation.