Segmentation fault in process_radtags

[florawf]

Hi,

I am attempting to run process_radtags, and keep running into a segmentation fault.

I have tried this with two different versions of stacks - both downloaded via conda and a direct download from stacks. 

I have also tried this zipped and unzipped files, and with one node and multiple nodes.

I have also checked that there aren't any blank lines in the fastq files, using:

zless filename.fastq.gz | grep -v "."

This fails pretty quickly after I set it up.

The commands I use are as follows (for the zipped version, using the conda version):

process_radtags -p ${reads} -i gzfastq -b ${barcodes} -o ${outdir} -c -q -r --index_index --renz_1 pstI --renz_2 mspI 

The error given is this:

Processing single-end data.

Using Phred+33 encoding for quality scores.

Found 2 input file(s).

Searching for single and paired-end, indexed barcodes.

Loaded 2 barcodes (8bp / 8bp).

Will attempt to recover barcodes with at most 1 / 1 mismatches.

Processing file 1 of 2

  Processing RAD-Tags.../tmp/slurmd/job1235086/slurm_script: line 22: 353223 Segmentation fault      (core dumped) ./process_radtags -p ${reads} -i gzfastq -b ${barcodes} -o ${outdir} -c -q -r --index_index --renz_1 pstI --renz_2 mspI --threads ${cpus}

I've been attempting to run this on two of my files to test this out.

The barcode file looks like this:

GTGTGAGC GCTTCGTG 28648_001

TGAGTGCC GCTTCGTG 29593_026

And a small section of the fastq looks like this, which is the first row:

@AV241004:Aviti2_Run_045_08_26_24:2344617575:1:10102:0376:0049 1:N:0:GTGTGAGC+GCTTCGTG

TCACGCTCATGCAGTGCCCGCCCCGTCCCCAGCTCCCAACGAGGAGACAGCTATCCTCCAGCGCCTTAATCCGAGGGCCCCCCCAGTGTTCGATCCCGCTGTCTCTTATACACATCTCCGAGCCCACGAGACGTGTCAGCATCTCGTATG

+

GLLLLLLLNNNNNE=>I;F5LENL>2&NN4N>NLFMILLKMNM1NMHNMDNBFNNL'LL@5=NKM/FMMI.NAIE1MDI8MLAN$LNN08L@MCKJL8IFM?40C'LM6ML;BI64J?L)MLLL@JLJK8IJ$8JE%G6KC9>?IG6F;*

@AV241004:Aviti2_Run_045_08_26_24:2344617575:1:10102:0114:0053 1:N:0:GTGTGAGC+GCTTCGTG

TGCAGGGGAGGATGGGGATGAGCGGGTCTGGATGTAGGATGTGGAGCCCAGGCAGAGCAGAGGCTCCGCTGTCTCTTATACACATCTCCGAGCCCACGAGACGTGTGAGCATCTCGTATGCCGTCTTCTGCTTGATACGGCGACCACCGA

+

As far as I'm aware, my data is single-end data, with two indexed barcodes.

I would be very grateful for any help you could give me!

Many thanks,

Flora

[Catchen, Julian]

Hi, what version of Stacks/process_radtags are you running? -julian

[florawf]

The conda version I used is 1.44, the self-installed version is 2.68 - I get the same error with both.

Many thanks,

Flora

[Catchen, Julian]

If you can send me a few thousand lines of your raw input file, along with your barcodes file, say via Dropbox, I can try to debug it. -julian

 

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Stacks website: http://catchenlab.life.illinois.edu/stacks/
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[florawf]

Hi Julian,

I have worked out my problem was a basic misunderstanding - my data was already demultiplexed, it then ran fine without the barcodes file or index_index argument.

Thanks for your help and quick replies!

Many thanks,

Flora