Nonpareil exiting after "Evaluating consistency"

[sterrettJD]

Hi Nonpareil team,

Thanks for the cool tool! I've been trying to use it on my data, but it seems like the program is exiting at the "evaluating consistency" step. It is outputting the .npl, .npo, .npa, and .npc files, but it doesn't seem to be running to completion. Do you have any ideas why this might be happening?

Does resource utilization increase during this step? I am running it on a cluster with max memory 30 GB, using 16 threads and in kmer mode.

Here is the command I used to run it: nonpareil -s ${outpath}/temp_unzipped_input.fq -T kmer -f fastq -b ${outpath} -t 16

Here is the full output:

Nonpareil v3.401 [ 0.0] reading hiv.t32.concat.n40/DM065/temp_unzipped_input.fq [ 0.0] Picking 10000 random sequences [ 0.0] Started counting [ 37.3] Read file with 97916184 sequences [ 37.3] Average read length is 136.097897bp [ 37.3] Sub-sampling library [ 37.3] Sampling at 0.000000% [ 37.3] Sampling at 0.000002% [ 37.3] Sampling at 0.000003% [ 37.3] Sampling at 0.000004% [ 37.3] Sampling at 0.000005% [ 37.3] Sampling at 0.000007% [ 37.3] Sampling at 0.000011% [ 37.3] Sampling at 0.000015% [ 37.3] Sampling at 0.000022% [ 37.3] Sampling at 0.000031% [ 37.3] Sampling at 0.000045% [ 37.3] Sampling at 0.000064% [ 37.3] Sampling at 0.000091% [ 37.3] Sampling at 0.000130% [ 37.4] Sampling at 0.000186% [ 37.4] Sampling at 0.000265% [ 37.4] Sampling at 0.000379% [ 37.4] Sampling at 0.000541% [ 37.4] Sampling at 0.000773% [ 37.4] Sampling at 0.001104% [ 37.4] Sampling at 0.001578% [ 37.4] Sampling at 0.002254% [ 37.4] Sampling at 0.003220% [ 37.4] Sampling at 0.004600% [ 37.4] Sampling at 0.006571% [ 37.4] Sampling at 0.009387% [ 37.4] Sampling at 0.013411% [ 37.4] Sampling at 0.019158% [ 37.4] Sampling at 0.027369% [ 37.4] Sampling at 0.039098% [ 37.4] Sampling at 0.055855% [ 37.4] Sampling at 0.079792% [ 37.4] Sampling at 0.113989% [ 37.4] Sampling at 0.162841% [ 37.4] Sampling at 0.232631% [ 37.4] Sampling at 0.332329% [ 37.4] Sampling at 0.474756% [ 37.5] Sampling at 0.678223% [ 37.5] Sampling at 0.968890% [ 37.5] Sampling at 1.384129% [ 37.5] Sampling at 1.977327% [ 37.5] Sampling at 2.824752% [ 37.5] Sampling at 4.035361% [ 37.5] Sampling at 5.764801% [ 37.5] Sampling at 8.235430% [ 37.5] Sampling at 11.764900% [ 37.5] Sampling at 16.807000% [ 37.5] Sampling at 24.010000% [ 37.5] Sampling at 34.300000% [ 37.5] Sampling at 49.000000% [ 37.6] Sampling at 70.000000% [ 37.6] Sampling at 100.000000% [ 37.6] Evaluating consistency