Parallel_Draft stop abruptly

[Ninh Vu]

I tried your latest AftrRAD_Parallel_Draft.pl script on a relatively small dataset (55 individuals, fastq -uncompressed ~ 52 GB). The species of interest has a relatively small genome size ~1.9 GB, and the restriction enzyme used was SbfI-HF.

I tried running the pipeline on a small truncated fastq file (~6 GB) and it seems to work.

Am I setting very stringent parameters causing this failure? Is "minDepth" of 5 too low? Be that as it may, the terminal read out for complete fastq file: 

genetics@genetics:~/software/AftrRADv4.1$ perl AftrRAD_Parallel_Draft.pl maxProcesses-20 re-TGCAGG minQual-20 minDepth-5 minIden-0.9 numIndels-3 P2-TTCCGATC minParalog-5 Phred-33 dplexedData-0 stringLength-15 MaxH-0.9

Arguments entered are...

Help 0

Phred 33

numIndels 3

P2 TTCCGATC

BarcodePath Barcodes/

minDepth 5

minQual 20

stringLength 15

MaxH 0.9

DataPath Data/

minParalog 5

re TGCAGG

minIden 0.9

maxProcesses 20

dplexedData 0

Running AftrRAD...

Recognized 1 data files.

File names are...

 fish.txt 

The barcodes you entered for data file 0.0 (file fish.txt) are...

 AAACGG ACTCTT ATTCCG CGAGGC GAAATG GGACTT TAAGCT TCTTCT AACGTT ACTGGC CAAAAA CGCAGA GAACCA GGCAAG TAATTC TGAACC AACTGA AGCCAT CAATCG CGCGTG GACGAC GGGCGC TACACA TGACAA AAGACG AGCGCA CACCTC CGGTCC GACTCT GGGGCG TACGGG TGCCCG AAGCTA AGGGTC CAGGCA CGTCTA GAGAGA GGTACA TAGTAT TGCTTA AATATC AGGTGT CATACT CGTGAT GATCGT GGTTTG TATCAC TGGGGA AATGAG AGTAGG CCATTT CTACAG GCAGAT GTAAGT TCAAAG TTATGA ACAAGA AGTTAA CCCGGT CTCGCC GCATGG 

The names you entered for data file 0.0 (file fish.txt) are...

 F1 F2 F3 F4 F5 F6 F7 F8 F9 F10 F11 F12 F13 F14 F15 F16 F17 F18 F19 F20 F21 F22 F23 F24 F25 M1 M2 M3 M4 M5 M6 M7 M8 M9 M10 M11 M12 M13 M14 M15 M16 M17 M18 M19 M20 M21 M22 M23 M24 M25 F26 F27 F28 F29 F30 F31 M26 M27 M28 M29 M30 

Demultiplexing samples for data file fish.txt.

Identifying unique sequences for each individual.

mv: cannot stat ‘TempFiles/SubTemp_0/UniqueWith*’: No such file or directory

Identifying all unique sequences within the dataset.

sort: write failed: /tmp/sortLYubhn: No space left on device

Creating file to test mean read counts.

No such file or directory at AftrRAD_Parallel_Draft.pl line 2458.

efgl@efgl:~/software/AftrRADv4.1$ 

[Ninh Vu]

I forgot to include a log report. See attachment

[Mike Sovic]

Hi Ninh,

Is it possible you don't have enough free disk space for the run?  See my posts under the topic "Perl errors in AftrRAD.pl" on April 9 and 10 regarding disk space.  The line "sort: write failed: /tmp/sortLYubhn: No space left on device" is what's leading me in this direction at the moment.  Check this out and if this doesn't seem to be the problem we'll go from there.

                           Mike