+ minimap2 -ax map-ont ../../data/Pmulti/Pmulti_dabA_CDS.fa ../../data/Pmulti/pmulti-sup_nanoFilt.fastq.gz -o pmulti-ont.minimap.dabA.sam -t 24
[M::mm_idx_gen::0.002*1.00] collected minimizers
[M::mm_idx_gen::0.003*1.00] sorted minimizers
[M::main::0.003*1.00] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.003*1.00] mid_occ = 10
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.003*0.89] distinct minimizers: 271 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.125; total length: 1389
[M::worker_pipeline::17.195*0.99] mapped 232832 sequences
[M::worker_pipeline::32.595*1.00] mapped 245404 sequences
[M::worker_pipeline::47.635*1.00] mapped 264201 sequences
[M::worker_pipeline::62.142*1.00] mapped 253223 sequences
[M::worker_pipeline::76.987*1.00] mapped 196325 sequences
[M::worker_pipeline::91.737*1.00] mapped 190050 sequences
[M::worker_pipeline::106.176*1.00] mapped 189717 sequences
[M::worker_pipeline::120.874*1.00] mapped 191178 sequences
[M::worker_pipeline::135.401*1.00] mapped 191192 sequences
[M::worker_pipeline::150.027*1.00] mapped 192280 sequences
[M::worker_pipeline::164.560*1.00] mapped 194335 sequences
[M::worker_pipeline::179.272*1.00] mapped 195356 sequences
[M::worker_pipeline::193.842*1.00] mapped 197421 sequences
[M::worker_pipeline::208.382*1.00] mapped 198952 sequences
[M::worker_pipeline::223.056*1.00] mapped 200602 sequences
[M::worker_pipeline::237.621*1.00] mapped 197209 sequences
[M::worker_pipeline::252.226*1.00] mapped 203164 sequences
[M::worker_pipeline::267.019*1.00] mapped 211253 sequences
[M::worker_pipeline::281.612*1.00] mapped 223551 sequences
[M::worker_pipeline::296.465*1.00] mapped 232924 sequences
[M::worker_pipeline::311.180*1.00] mapped 245526 sequences
[M::worker_pipeline::325.954*1.00] mapped 263691 sequences
[M::worker_pipeline::340.772*1.00] mapped 253229 sequences
[M::worker_pipeline::355.384*1.00] mapped 196319 sequences
[M::worker_pipeline::369.977*1.00] mapped 190018 sequences
[M::worker_pipeline::384.520*1.00] mapped 190028 sequences
[M::worker_pipeline::398.991*1.00] mapped 190835 sequences
[M::worker_pipeline::413.673*1.00] mapped 191190 sequences
[M::worker_pipeline::428.002*1.00] mapped 192385 sequences
[M::worker_pipeline::442.756*1.00] mapped 194291 sequences
[M::worker_pipeline::457.288*1.00] mapped 195346 sequences
[M::worker_pipeline::471.763*1.00] mapped 197464 sequences
[M::worker_pipeline::486.353*1.00] mapped 198917 sequences
[M::worker_pipeline::500.842*1.00] mapped 200682 sequences
[M::worker_pipeline::515.513*1.00] mapped 197075 sequences
[M::worker_pipeline::530.126*1.00] mapped 203261 sequences
[M::worker_pipeline::544.827*1.00] mapped 211367 sequences
[M::worker_pipeline::557.647*1.00] mapped 220043 sequences
[M::main] Version: 2.29-r1283
[M::main] CMD: minimap2 -ax map-ont -o pmulti-ont.minimap.dabA.sam -t 24 ../../data/Pmulti/Pmulti_dabA_CDS.fa ../../data/Pmulti/pmulti-sup_nanoFilt.fastq.gz
[M::main] Real time: 557.648 sec; CPU: 555.263 sec; Peak RSS: 2.118 GB
+ minimap2 -ax map-ont ../../data/Pmulti/Pmulti_dabA_CDS.fa ../../data/Pmulti/Pmultiseries_S471_L004_R1_001.fastq.gz -o pmulti-R1.minimap.dabA.sam -t 24
[M::mm_idx_gen::0.005*0.41] collected minimizers
[M::mm_idx_gen::0.006*0.54] sorted minimizers
[M::main::0.006*0.54] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.006*0.54] mid_occ = 10
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.006*0.55] distinct minimizers: 271 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.125; total length: 1389
[M::worker_pipeline::16.309*0.99] mapped 3320529 sequences
[M::worker_pipeline::30.303*0.99] mapped 3320588 sequences
[M::worker_pipeline::43.698*0.99] mapped 3320585 sequences
[M::worker_pipeline::57.226*0.99] mapped 3320623 sequences
[M::worker_pipeline::70.508*0.99] mapped 3320538 sequences
[M::worker_pipeline::83.838*1.00] mapped 3320549 sequences
[M::worker_pipeline::97.270*1.00] mapped 3320561 sequences
[M::worker_pipeline::110.481*1.00] mapped 3320609 sequences
[M::worker_pipeline::123.727*1.00] mapped 3320540 sequences
[M::worker_pipeline::137.003*1.00] mapped 3320511 sequences
[M::worker_pipeline::150.209*1.00] mapped 3320576 sequences
[M::worker_pipeline::163.561*1.00] mapped 3320606 sequences
[M::worker_pipeline::176.935*1.00] mapped 3320577 sequences
[M::worker_pipeline::190.234*1.00] mapped 3320509 sequences
[M::worker_pipeline::203.602*1.00] mapped 3320538 sequences
[M::worker_pipeline::216.804*1.00] mapped 3320598 sequences
[M::worker_pipeline::229.897*1.00] mapped 3320604 sequences
[M::worker_pipeline::243.245*1.00] mapped 3320575 sequences
[M::worker_pipeline::256.494*1.00] mapped 3320604 sequences
[M::worker_pipeline::269.803*1.00] mapped 3320626 sequences
[M::worker_pipeline::283.042*1.00] mapped 3320630 sequences
[M::worker_pipeline::296.330*1.00] mapped 3320589 sequences
[M::worker_pipeline::309.517*1.00] mapped 3320585 sequences
[M::worker_pipeline::322.821*1.00] mapped 3320610 sequences
[M::worker_pipeline::336.228*1.00] mapped 3320624 sequences
[M::worker_pipeline::349.395*1.00] mapped 3320624 sequences
[M::worker_pipeline::362.638*1.00] mapped 3320539 sequences
[M::worker_pipeline::376.093*1.00] mapped 3320543 sequences
[M::worker_pipeline::389.084*1.00] mapped 3320604 sequences
[M::worker_pipeline::402.462*1.00] mapped 3320610 sequences
[M::worker_pipeline::415.692*1.00] mapped 3320511 sequences
[M::worker_pipeline::429.074*1.00] mapped 3320537 sequences
[M::worker_pipeline::442.476*1.00] mapped 3320584 sequences
[M::worker_pipeline::455.689*1.00] mapped 3320597 sequences
[M::worker_pipeline::469.024*1.00] mapped 3320512 sequences
[M::worker_pipeline::482.300*1.00] mapped 3320538 sequences
[M::worker_pipeline::495.511*1.00] mapped 3320563 sequences
[M::worker_pipeline::508.801*1.00] mapped 3320571 sequences
[M::worker_pipeline::522.180*1.00] mapped 3320532 sequences
[M::worker_pipeline::535.557*1.00] mapped 3320520 sequences
[M::worker_pipeline::548.787*1.00] mapped 3320591 sequences
[M::worker_pipeline::562.042*1.00] mapped 3320575 sequences
[M::worker_pipeline::575.316*1.00] mapped 3320557 sequences
[M::worker_pipeline::588.450*1.00] mapped 3320592 sequences
[M::worker_pipeline::601.830*1.00] mapped 3320620 sequences
[M::worker_pipeline::615.009*1.00] mapped 3320640 sequences
[M::worker_pipeline::628.233*1.00] mapped 3320621 sequences
[M::worker_pipeline::641.546*1.00] mapped 3320595 sequences
[M::worker_pipeline::654.822*1.00] mapped 3320620 sequences
[M::worker_pipeline::667.932*1.00] mapped 3320630 sequences
[M::worker_pipeline::681.149*1.00] mapped 3320636 sequences
[M::worker_pipeline::685.721*1.00] mapped 1610829 sequences
[M::main] Version: 2.29-r1283
[M::main] CMD: minimap2 -ax map-ont -o pmulti-R1.minimap.dabA.sam -t 24 ../../data/Pmulti/Pmulti_dabA_CDS.fa ../../data/Pmulti/Pmultiseries_S471_L004_R1_001.fastq.gz
[M::main] Real time: 685.722 sec; CPU: 682.686 sec; Peak RSS: 2.831 GB
+ minimap2 -ax map-ont ../../data/Pmulti/Pmulti_dabA_CDS.fa ../../data/Pmulti/Pmultiseries_S471_L004_R2_001.fastq.gz -o pmulti-R2.minimap.dabA.sam -t 24
[M::mm_idx_gen::0.001*1.22] collected minimizers
[M::mm_idx_gen::0.003*1.12] sorted minimizers
[M::main::0.003*1.12] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.003*1.12] mid_occ = 10
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.003*1.12] distinct minimizers: 271 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.125; total length: 1389
[M::worker_pipeline::16.278*0.99] mapped 3320328 sequences
[M::worker_pipeline::30.552*0.99] mapped 3320408 sequences
[M::worker_pipeline::44.007*1.00] mapped 3320424 sequences
[M::worker_pipeline::57.631*1.00] mapped 3320437 sequences
[M::worker_pipeline::71.161*1.00] mapped 3320315 sequences
[M::worker_pipeline::84.502*1.00] mapped 3320398 sequences
[M::worker_pipeline::98.158*1.00] mapped 3320432 sequences
[M::worker_pipeline::111.645*1.00] mapped 3320428 sequences
[M::worker_pipeline::125.030*1.00] mapped 3320352 sequences
[M::worker_pipeline::138.653*1.00] mapped 3320330 sequences
[M::worker_pipeline::152.046*1.00] mapped 3320414 sequences
[M::worker_pipeline::165.390*1.00] mapped 3320419 sequences
[M::worker_pipeline::179.015*1.00] mapped 3320385 sequences
[M::worker_pipeline::192.516*1.00] mapped 3320313 sequences
[M::worker_pipeline::205.843*1.00] mapped 3320412 sequences
[M::worker_pipeline::219.240*1.00] mapped 3320414 sequences
[M::worker_pipeline::232.584*1.00] mapped 3320457 sequences
[M::worker_pipeline::246.225*1.00] mapped 3320388 sequences
[M::worker_pipeline::259.289*1.00] mapped 3320466 sequences
[M::worker_pipeline::272.909*1.00] mapped 3320475 sequences
[M::worker_pipeline::286.329*1.00] mapped 3320474 sequences
[M::worker_pipeline::299.679*1.00] mapped 3320438 sequences
[M::worker_pipeline::313.243*1.00] mapped 3320381 sequences
[M::worker_pipeline::326.495*1.00] mapped 3320436 sequences
[M::worker_pipeline::339.784*1.00] mapped 3320488 sequences
[M::worker_pipeline::353.293*1.00] mapped 3320455 sequences
[M::worker_pipeline::366.786*1.00] mapped 3320336 sequences
[M::worker_pipeline::380.488*1.00] mapped 3320387 sequences
[M::worker_pipeline::393.671*1.00] mapped 3320442 sequences
[M::worker_pipeline::407.013*1.00] mapped 3320435 sequences
[M::worker_pipeline::420.501*1.00] mapped 3320326 sequences
[M::worker_pipeline::433.840*1.00] mapped 3320367 sequences
[M::worker_pipeline::447.107*1.00] mapped 3320403 sequences
[M::worker_pipeline::460.645*1.00] mapped 3320439 sequences
[M::worker_pipeline::474.302*1.00] mapped 3320333 sequences
[M::worker_pipeline::487.675*1.00] mapped 3320334 sequences
[M::worker_pipeline::500.975*1.00] mapped 3320415 sequences
[M::worker_pipeline::514.393*1.00] mapped 3320420 sequences
[M::worker_pipeline::527.726*1.00] mapped 3320337 sequences
[M::worker_pipeline::541.220*1.00] mapped 3320376 sequences
[M::worker_pipeline::554.756*1.00] mapped 3320434 sequences
[M::worker_pipeline::568.409*1.00] mapped 3320462 sequences
[M::worker_pipeline::581.712*1.00] mapped 3320410 sequences
[M::worker_pipeline::595.141*1.00] mapped 3320435 sequences
[M::worker_pipeline::608.635*1.00] mapped 3320472 sequences
[M::worker_pipeline::621.985*1.00] mapped 3320467 sequences
[M::worker_pipeline::635.579*1.00] mapped 3320479 sequences
[M::worker_pipeline::648.930*1.00] mapped 3320426 sequences
[M::worker_pipeline::662.303*1.00] mapped 3320473 sequences
[M::worker_pipeline::675.839*1.00] mapped 3320489 sequences
[M::worker_pipeline::689.316*1.00] mapped 3320482 sequences
[M::worker_pipeline::693.970*1.00] mapped 1619329 sequences
[M::main] Version: 2.29-r1283
[M::main] CMD: minimap2 -ax map-ont -o pmulti-R2.minimap.dabA.sam -t 24 ../../data/Pmulti/Pmulti_dabA_CDS.fa ../../data/Pmulti/Pmultiseries_S471_L004_R2_001.fastq.gz
[M::main] Real time: 693.981 sec; CPU: 690.728 sec; Peak RSS: 2.852 GB
+ samtools view -F 4 pmulti-ont.minimap.dabA.sam
/var/spool/slurmd/job25633971/slurm_script: line 48: samtools: command not found