c2997108/centos6:2-bwa-0.7.17-r1198-dirty centos:centos6 quay.io/biocontainers/samtools:1.9--h91753b0_3
using docker
++ docker pull quay.io/biocontainers/samtools:1.9--h91753b0_3
1.9--h91753b0_3: Pulling from biocontainers/samtools
a3ed95caeb02: Already exists
77c6c00e8b61: Already exists
3aaade50789a: Already exists
00cf8b9f3d2a: Already exists
7ff999a2256f: Already exists
d2ba336f2e44: Already exists
dfda3e01f2b6: Already exists
a3ed95caeb02: Already exists
10c3bb32200b: Already exists
6c71d22e98f8: Pulling fs layer
6c71d22e98f8: Verifying Checksum
6c71d22e98f8: Download complete
6c71d22e98f8: Pull complete
Digest: sha256:3613d6560fda1bb60322d7f3eb1e3992477b4a4712a5e5e6060a3b1c56b316b2
Status: Downloaded newer image for quay.io/biocontainers/samtools:1.9--h91753b0_3
++ set +ex
+ set -o pipefail
+ ref=input_1/ecoli.pilon.ERR348742.fasta
+ r1=input_2/DRR015801_1.fastq.gz
+ r2=input_3/DRR015801_2.fastq.gz
+ '[' '!' -e input_1/ecoli.pilon.ERR348742.fasta.bwt ']'
+ docker run -v /data/user2/work/86:/data/user2/work/86 -w /data/user2/work/86 -u root -i --rm c2997108/centos6:2-bwa-0.7.17-r1198-dirty bwa index input_1/ecoli.pilon.ERR348742.fasta
[bwa_index] Pack FASTA... 0.05 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 2.74 seconds elapse.
[bwa_index] Update BWT... 0.03 sec
[bwa_index] Pack forward-only FASTA... 0.03 sec
[bwa_index] Construct SA from BWT and Occ... 0.74 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: bwa index input_1/ecoli.pilon.ERR348742.fasta
[main] Real time: 4.256 sec; CPU: 3.643 sec
+ docker run -v /data/user2/work/86:/data/user2/work/86 -w /data/user2/work/86 -u root -i --rm quay.io/biocontainers/samtools:1.9--h91753b0_3 samtools faidx input_1/ecoli.pilon.ERR348742.fasta
++ basename input_2/DRR015801_1.fastq.gz
+ outname=DRR015801_1.fastq.gz
+ docker run -v /data/user2/work/86:/data/user2/work/86 -w /data/user2/work/86 -u root -i --rm c2997108/centos6:2-bwa-0.7.17-r1198-dirty bwa mem -t 8 -M -R '@RG\tID:DRR015801_1.fastq.gz\tSM:DRR015801_1.fastq.gz\tPL:Illumina\tLB:DRR015801_1.fastq.gz' input_1/ecoli.pilon.ERR348742.fasta input_2/DRR015801_1.fastq.gz input_3/DRR015801_2.fastq.gz
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 800000 sequences (80000000 bp)...
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (565, 173317, 19, 572)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (163, 336, 735)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1879)
[M::mem_pestat] mean and std.dev: (455.06, 411.58)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2451)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (197, 269, 368)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 710)
[M::mem_pestat] mean and std.dev: (287.72, 129.05)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 881)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (95, 190, 1170)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3320)
[M::mem_pestat] mean and std.dev: (337.88, 421.12)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 4395)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (168, 350, 750)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1914)
[M::mem_pestat] mean and std.dev: (438.96, 384.56)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2496)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 800000 reads in 73.663 CPU sec, 9.405 real sec
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (575, 173261, 27, 594)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (169, 322, 696)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1750)
[M::mem_pestat] mean and std.dev: (415.21, 355.32)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2277)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (196, 267, 367)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 709)
[M::mem_pestat] mean and std.dev: (286.56, 129.43)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 880)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (157, 252, 1549)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4333)
[M::mem_pestat] mean and std.dev: (671.08, 978.70)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 5725)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (198, 408, 780)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1944)
[M::mem_pestat] mean and std.dev: (491.63, 415.26)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2526)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 800000 reads in 73.691 CPU sec, 8.998 real sec
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (570, 172017, 17, 562)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (164, 333, 735)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1877)
[M::mem_pestat] mean and std.dev: (443.37, 397.44)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2448)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (194, 265, 363)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 701)
[M::mem_pestat] mean and std.dev: (283.58, 127.74)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 870)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (64, 350, 3554)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10534)
[M::mem_pestat] mean and std.dev: (1682.82, 2327.64)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 14024)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (179, 385, 835)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2147)
[M::mem_pestat] mean and std.dev: (526.20, 483.75)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2803)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 800000 reads in 75.622 CPU sec, 9.219 real sec
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (552, 172475, 26, 566)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (156, 327, 693)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1767)
[M::mem_pestat] mean and std.dev: (425.65, 383.52)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2304)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (192, 261, 358)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 690)
[M::mem_pestat] mean and std.dev: (279.65, 125.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 856)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (143, 281, 1312)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3650)
[M::mem_pestat] mean and std.dev: (438.67, 603.36)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 4819)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (180, 342, 732)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1836)
[M::mem_pestat] mean and std.dev: (451.93, 394.04)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2388)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 800000 reads in 70.463 CPU sec, 8.648 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (573, 172210, 16, 548)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (187, 372, 744)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1858)
[M::mem_pestat] mean and std.dev: (467.10, 390.05)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2415)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (194, 266, 364)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 704)
[M::mem_pestat] mean and std.dev: (284.34, 128.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 874)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (83, 220, 1948)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5678)
[M::mem_pestat] mean and std.dev: (772.20, 1215.93)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 7543)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (184, 375, 772)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1948)
[M::mem_pestat] mean and std.dev: (467.66, 401.46)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2536)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_process_seqs] Processed 800000 reads in 67.981 CPU sec, 8.178 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (603, 173551, 28, 559)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (195, 389, 824)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2082)
[M::mem_pestat] mean and std.dev: (505.41, 440.40)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2711)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (196, 268, 369)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 715)
[M::mem_pestat] mean and std.dev: (287.78, 130.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 888)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (87, 141, 335)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 831)
[M::mem_pestat] mean and std.dev: (165.50, 149.44)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1079)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (182, 368, 770)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1946)
[M::mem_pestat] mean and std.dev: (467.90, 406.59)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2534)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_process_seqs] Processed 800000 reads in 66.069 CPU sec, 8.005 real sec
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (576, 172367, 20, 579)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (179, 375, 807)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2063)
[M::mem_pestat] mean and std.dev: (497.49, 467.42)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2691)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (194, 265, 365)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 707)
[M::mem_pestat] mean and std.dev: (284.53, 128.99)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 878)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (65, 171, 1644)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4802)
[M::mem_pestat] mean and std.dev: (948.10, 1373.37)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 6442)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (174, 362, 754)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1914)
[M::mem_pestat] mean and std.dev: (451.52, 391.67)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2494)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 800000 reads in 68.869 CPU sec, 8.419 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (547, 173051, 16, 527)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (170, 343, 742)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1886)
[M::mem_pestat] mean and std.dev: (450.70, 397.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2458)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (193, 263, 360)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 694)
[M::mem_pestat] mean and std.dev: (281.45, 126.55)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 861)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (89, 167, 1086)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3080)
[M::mem_pestat] mean and std.dev: (355.64, 638.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 4077)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (186, 387, 767)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1929)
[M::mem_pestat] mean and std.dev: (479.04, 409.94)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2510)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_process_seqs] Processed 800000 reads in 70.417 CPU sec, 8.515 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (573, 171834, 27, 535)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (189, 347, 739)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1839)
[M::mem_pestat] mean and std.dev: (457.49, 397.36)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2389)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (194, 264, 362)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 698)
[M::mem_pestat] mean and std.dev: (283.16, 127.33)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 866)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (79, 166, 1082)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3088)
[M::mem_pestat] mean and std.dev: (384.17, 573.25)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 4091)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (175, 368, 798)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2044)
[M::mem_pestat] mean and std.dev: (483.04, 427.25)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2667)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 800000 reads in 58.562 CPU sec, 7.081 real sec
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (520, 172600, 23, 525)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (182, 385, 722)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1802)
[M::mem_pestat] mean and std.dev: (467.39, 389.87)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2342)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (194, 265, 364)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 704)
[M::mem_pestat] mean and std.dev: (284.50, 128.27)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 874)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (49, 126, 1724)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5074)
[M::mem_pestat] mean and std.dev: (891.13, 1349.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 6749)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (181, 386, 732)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1834)
[M::mem_pestat] mean and std.dev: (462.82, 395.65)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2385)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_process_seqs] Processed 800000 reads in 66.571 CPU sec, 8.010 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (570, 172372, 23, 534)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (165, 357, 766)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1968)
[M::mem_pestat] mean and std.dev: (433.43, 381.66)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2569)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (192, 263, 359)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 693)
[M::mem_pestat] mean and std.dev: (280.82, 126.28)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 860)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (94, 219, 266)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 610)
[M::mem_pestat] mean and std.dev: (154.95, 86.62)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 782)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (177, 372, 769)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1953)
[M::mem_pestat] mean and std.dev: (469.40, 412.38)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2545)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_process_seqs] Processed 800000 reads in 65.045 CPU sec, 7.893 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (530, 172208, 22, 489)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (162, 341, 744)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1908)
[M::mem_pestat] mean and std.dev: (447.62, 396.67)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2490)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (189, 259, 355)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 687)
[M::mem_pestat] mean and std.dev: (277.11, 125.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 853)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (141, 411, 1612)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4554)
[M::mem_pestat] mean and std.dev: (1008.45, 1251.77)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 6025)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (165, 355, 724)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1842)
[M::mem_pestat] mean and std.dev: (441.39, 395.34)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2401)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_process_seqs] Processed 800000 reads in 64.850 CPU sec, 7.846 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (560, 172492, 33, 543)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (178, 396, 812)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2080)
[M::mem_pestat] mean and std.dev: (514.08, 479.28)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2714)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (194, 265, 363)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 701)
[M::mem_pestat] mean and std.dev: (283.28, 127.69)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 870)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (133, 238, 952)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2590)
[M::mem_pestat] mean and std.dev: (395.00, 522.61)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 3409)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (194, 386, 768)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1916)
[M::mem_pestat] mean and std.dev: (459.04, 382.14)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2490)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_process_seqs] Processed 800000 reads in 61.493 CPU sec, 7.390 real sec
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (580, 172500, 29, 573)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (185, 381, 825)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2105)
[M::mem_pestat] mean and std.dev: (508.07, 442.10)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2745)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (197, 270, 372)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 722)
[M::mem_pestat] mean and std.dev: (289.93, 131.60)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 897)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (89, 214, 1654)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4784)
[M::mem_pestat] mean and std.dev: (978.52, 1301.02)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 6349)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (198, 388, 828)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2088)
[M::mem_pestat] mean and std.dev: (499.85, 425.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2718)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 800000 reads in 68.403 CPU sec, 8.400 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (554, 171876, 22, 569)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (183, 356, 726)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1812)
[M::mem_pestat] mean and std.dev: (456.77, 382.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2355)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (194, 266, 367)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 713)
[M::mem_pestat] mean and std.dev: (285.97, 130.04)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 886)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (155, 1102, 2058)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5864)
[M::mem_pestat] mean and std.dev: (1187.41, 1279.63)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 7767)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (175, 366, 803)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2059)
[M::mem_pestat] mean and std.dev: (496.21, 442.96)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2687)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_process_seqs] Processed 800000 reads in 65.975 CPU sec, 7.915 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (534, 171800, 20, 563)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (170, 347, 752)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1916)
[M::mem_pestat] mean and std.dev: (439.78, 373.41)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2498)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (193, 264, 362)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 700)
[M::mem_pestat] mean and std.dev: (282.70, 127.75)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 869)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (117, 186, 868)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2370)
[M::mem_pestat] mean and std.dev: (249.88, 286.76)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 3121)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (166, 346, 721)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1831)
[M::mem_pestat] mean and std.dev: (450.75, 404.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2386)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_process_seqs] Processed 800000 reads in 62.645 CPU sec, 7.621 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (564, 171823, 25, 554)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (172, 363, 809)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2083)
[M::mem_pestat] mean and std.dev: (499.42, 449.28)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2720)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (192, 263, 361)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 699)
[M::mem_pestat] mean and std.dev: (281.60, 127.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 868)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (67, 195, 1056)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3034)
[M::mem_pestat] mean and std.dev: (388.39, 467.49)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 4023)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (184, 372, 803)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2041)
[M::mem_pestat] mean and std.dev: (508.80, 459.49)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2660)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_process_seqs] Processed 800000 reads in 64.922 CPU sec, 7.824 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (632, 172148, 21, 612)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (174, 363, 809)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2079)
[M::mem_pestat] mean and std.dev: (492.48, 457.84)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2714)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (197, 270, 371)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 719)
[M::mem_pestat] mean and std.dev: (289.85, 131.45)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 893)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (59, 136, 3291)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9755)
[M::mem_pestat] mean and std.dev: (1224.10, 2199.60)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 12987)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (186, 365, 799)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2025)
[M::mem_pestat] mean and std.dev: (482.40, 425.54)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2638)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_process_seqs] Processed 800000 reads in 65.979 CPU sec, 8.104 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (563, 171132, 21, 524)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (183, 382, 762)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1920)
[M::mem_pestat] mean and std.dev: (481.26, 417.95)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2499)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (194, 266, 365)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 707)
[M::mem_pestat] mean and std.dev: (284.78, 129.07)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 878)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (54, 190, 433)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1191)
[M::mem_pestat] mean and std.dev: (194.83, 169.93)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1570)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (184, 388, 754)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1894)
[M::mem_pestat] mean and std.dev: (473.01, 415.76)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2464)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_process_seqs] Processed 800000 reads in 65.182 CPU sec, 7.871 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (556, 171588, 16, 521)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (169, 321, 717)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1813)
[M::mem_pestat] mean and std.dev: (422.78, 361.70)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2361)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (192, 263, 362)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 702)
[M::mem_pestat] mean and std.dev: (282.27, 127.96)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 872)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (143, 350, 2651)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7667)
[M::mem_pestat] mean and std.dev: (1376.33, 2022.47)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 10175)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (182, 344, 657)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1607)
[M::mem_pestat] mean and std.dev: (410.54, 331.36)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2082)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_process_seqs] Processed 800000 reads in 63.177 CPU sec, 7.640 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (601, 171487, 19, 556)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (182, 363, 707)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1757)
[M::mem_pestat] mean and std.dev: (434.50, 363.80)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2282)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (193, 264, 361)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 697)
[M::mem_pestat] mean and std.dev: (281.74, 126.88)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 865)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (157, 347, 3580)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10426)
[M::mem_pestat] mean and std.dev: (1632.05, 2190.14)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 13849)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (166, 362, 717)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1819)
[M::mem_pestat] mean and std.dev: (457.28, 411.32)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2370)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_process_seqs] Processed 800000 reads in 64.604 CPU sec, 7.819 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (605, 172869, 20, 569)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (182, 344, 719)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1793)
[M::mem_pestat] mean and std.dev: (440.18, 366.75)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2330)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (196, 268, 367)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 709)
[M::mem_pestat] mean and std.dev: (286.72, 129.20)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 880)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (88, 266, 1703)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4933)
[M::mem_pestat] mean and std.dev: (711.53, 1076.98)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 6548)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (192, 407, 880)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2256)
[M::mem_pestat] mean and std.dev: (549.56, 508.32)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2944)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_process_seqs] Processed 800000 reads in 64.962 CPU sec, 7.856 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (541, 172539, 18, 596)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (172, 367, 787)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2017)
[M::mem_pestat] mean and std.dev: (480.88, 431.49)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2632)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (193, 263, 361)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 697)
[M::mem_pestat] mean and std.dev: (282.22, 127.46)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 865)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (109, 148, 1219)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3439)
[M::mem_pestat] mean and std.dev: (488.35, 746.39)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 4549)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (176, 356, 753)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1907)
[M::mem_pestat] mean and std.dev: (441.39, 384.10)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2484)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::process] read 800000 sequences (80000000 bp)...
[M::mem_process_seqs] Processed 800000 reads in 67.044 CPU sec, 8.094 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (507, 171408, 30, 546)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (172, 347, 748)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1900)
[M::mem_pestat] mean and std.dev: (438.96, 385.41)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2476)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (191, 261, 357)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 689)
[M::mem_pestat] mean and std.dev: (279.12, 125.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 855)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (62, 135, 521)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1439)
[M::mem_pestat] mean and std.dev: (204.73, 231.40)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1898)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (171, 347, 685)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1713)
[M::mem_pestat] mean and std.dev: (432.64, 363.12)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2227)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::process] read 647074 sequences (64707400 bp)...
[M::mem_process_seqs] Processed 800000 reads in 64.837 CPU sec, 7.884 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (408, 138113, 19, 434)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (169, 330, 790)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2032)
[M::mem_pestat] mean and std.dev: (475.69, 438.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2653)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (189, 259, 353)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 681)
[M::mem_pestat] mean and std.dev: (276.10, 123.47)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 845)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (32, 149, 399)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1133)
[M::mem_pestat] mean and std.dev: (236.22, 282.44)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1500)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (179, 352, 806)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2060)
[M::mem_pestat] mean and std.dev: (462.58, 433.10)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2687)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 647074 reads in 54.480 CPU sec, 6.794 real sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: bwa mem -t 8 -M -R @RG\tID:DRR015801_1.fastq.gz\tSM:DRR015801_1.fastq.gz\tPL:Illumina\tLB:DRR015801_1.fastq.gz input_1/ecoli.pilon.ERR348742.fasta input_2/DRR015801_1.fastq.gz input_3/DRR015801_2.fastq.gz
[main] Real time: 209.559 sec; CPU: 1659.648 sec
+ cat DRR015801_1.fastq.gz.sam
+ grep -v '^@'
+ docker run -v /data/user2/work/86:/data/user2/work/86 -w /data/user2/work/86 -u root -i --rm c2997108/centos6:2-bwa-0.7.17-r1198-dirty awk '-F\t' '{a=$6; gsub(/[0-9]+[^0-9M]/,"",a); split(a,arr,"M"); map=0; for(i in arr){map+=arr[i]}; b=$6; gsub(/[^0-9]/,",",b); split(b,arr,","); total=0; for(i in arr){total+=arr[i]}; for(i=12;i<=NF;i++){if($i~"^MD:Z:"){c=$i; gsub(/^MD:Z:/,"",c); gsub(/[0-9]/,"",c); if((map-length(c))/total>=0.8){print map"\t"$0}}}}'
+ docker run -v /data/user2/work/86:/data/user2/work/86 -w /data/user2/work/86 -u root -i --rm c2997108/centos6:2-bwa-0.7.17-r1198-dirty awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME==ARGV[2]{a[$4]+=$1} END{for(i in a){print i"\t"a[i]/len[i]"\t"a[i]"\t"len[i]}}' input_1/ecoli.pilon.ERR348742.fasta.fai DRR015801_1.fastq.gz.sam2
+ echo 'library(Cairo); a=read.table("DRR015801_1.fastq.gz.sam2.cov",sep="\t",row.names=1); CairoPNG(file="DRR015801_1.fastq.gz.sam2.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()'
+ docker run -v /data/user2/work/86:/data/user2/work/86 -w /data/user2/work/86 -u root -i --rm c2997108/centos6:2-bwa-0.7.17-r1198-dirty R --vanilla

R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Cairo); a=read.table("DRR015801_1.fastq.gz.sam2.cov",sep="\t",row.names=1); CairoPNG(file="DRR015801_1.fastq.gz.sam2.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()
null device 
          1 
> 
+ cat DRR015801_1.fastq.gz.sam
+ docker run -v /data/user2/work/86:/data/user2/work/86 -w /data/user2/work/86 -u root -i --rm quay.io/biocontainers/samtools:1.9--h91753b0_3 samtools view -Sb -@ 8 -
+ docker run -v /data/user2/work/86:/data/user2/work/86 -w /data/user2/work/86 -u root -i --rm quay.io/biocontainers/samtools:1.9--h91753b0_3 samtools sort -T DRR015801_1.fastq.gz -@ 8 -o DRR015801_1.fastq.gz.bam
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
+ docker run -v /data/user2/work/86:/data/user2/work/86 -w /data/user2/work/86 -u root -i --rm quay.io/biocontainers/samtools:1.9--h91753b0_3 samtools view -SH DRR015801_1.fastq.gz.sam
+ docker run -v /data/user2/work/86:/data/user2/work/86 -w /data/user2/work/86 -u root -i --rm quay.io/biocontainers/samtools:1.9--h91753b0_3 samtools view -Sb -@ 8 -
+ docker run -v /data/user2/work/86:/data/user2/work/86 -w /data/user2/work/86 -u root -i --rm quay.io/biocontainers/samtools:1.9--h91753b0_3 samtools sort -T DRR015801_1.fastq.gz.clean -@ 8 -o DRR015801_1.fastq.gz.clean.bam
+ cut -f 2- DRR015801_1.fastq.gz.sam2
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
+ rm -f DRR015801_1.fastq.gz.sam DRR015801_1.fastq.gz.sam2
+ docker run -v /data/user2/work/86:/data/user2/work/86 -w /data/user2/work/86 -u root -i --rm quay.io/biocontainers/samtools:1.9--h91753b0_3 samtools index DRR015801_1.fastq.gz.bam
+ docker run -v /data/user2/work/86:/data/user2/work/86 -w /data/user2/work/86 -u root -i --rm quay.io/biocontainers/samtools:1.9--h91753b0_3 samtools index DRR015801_1.fastq.gz.clean.bam
+ post_processing
+ '[' 1 = 1 ']'
+ '[' 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' = 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' ']'
+ docker run -v /data/user2/work/86:/data/user2/work/86 -w /data/user2/work/86 -u root -i --rm centos:centos6 chmod -R a=rXw .
+ echo 0
+ exit