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Failed to HRA000524 dataset (https://ngdc.cncb.ac.cn/gsa-human/browse/HRA000524) #28

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JianGuoZhou3 opened this issue Mar 21, 2022 · 7 comments
Open

Failed to HRA000524 dataset (https://ngdc.cncb.ac.cn/gsa-human/browse/HRA000524) #28

JianGuoZhou3 opened this issue Mar 21, 2022 · 7 comments

Comments

@JianGuoZhou3
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@chiangtw Failed to HRA000524 dataset (https://ngdc.cncb.ac.cn/gsa-human/browse/HRA000524)
I'm not sure this error belongs to bulk RNAseq or this NCLsan?

[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1459500 sequences (200000044 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 48831, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (5, 250)
[M::mem_pestat] mean and std.dev: (129.20, 36.71)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 299)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1459500 reads in 1016.941 CPU sec, 56.230 real sec
[M::process] read 1459110 sequences (200000243 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49116, 7, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (5, 250)
[M::mem_pestat] mean and std.dev: (129.23, 36.75)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 299)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1459110 reads in 992.290 CPU sec, 52.926 real sec
[M::process] read 1459194 sequences (200000262 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49321, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (104, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (8, 248)
[M::mem_pestat] mean and std.dev: (129.25, 36.32)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 296)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1459194 reads in 968.674 CPU sec, 50.918 real sec
[M::process] read 1459290 sequences (200000047 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 48946, 3, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (5, 250)
[M::mem_pestat] mean and std.dev: (129.41, 36.93)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 299)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1459290 reads in 1006.104 CPU sec, 53.871 real sec
[M::process] read 1458558 sequences (200000037 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49319, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (5, 250)
[M::mem_pestat] mean and std.dev: (129.54, 36.73)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 299)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458558 reads in 980.635 CPU sec, 51.559 real sec
[M::process] read 1458978 sequences (200000190 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49488, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (5, 250)
[M::mem_pestat] mean and std.dev: (129.40, 36.85)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 299)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458978 reads in 1027.241 CPU sec, 55.992 real sec
[M::process] read 1459092 sequences (200000115 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49601, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (5, 250)
[M::mem_pestat] mean and std.dev: (129.39, 36.63)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 299)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1459092 reads in 926.529 CPU sec, 47.778 real sec
[M::process] read 1458614 sequences (200000272 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49148, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (5, 250)
[M::mem_pestat] mean and std.dev: (129.19, 36.43)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 299)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458614 reads in 915.569 CPU sec, 47.252 real sec
[M::process] read 1458626 sequences (200000165 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49108, 2, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (104, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (8, 248)
[M::mem_pestat] mean and std.dev: (129.27, 36.38)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 296)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458626 reads in 920.436 CPU sec, 48.297 real sec
[M::process] read 1458596 sequences (200000103 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 48968, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (104, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (8, 248)
[M::mem_pestat] mean and std.dev: (129.27, 36.24)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 296)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458596 reads in 915.353 CPU sec, 47.793 real sec
[M::process] read 1458894 sequences (200000202 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49077, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 153)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (3, 253)
[M::mem_pestat] mean and std.dev: (129.79, 37.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 303)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458894 reads in 890.525 CPU sec, 46.475 real sec
[M::process] read 1458130 sequences (200000111 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49474, 3, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (104, 125, 153)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (6, 251)
[M::mem_pestat] mean and std.dev: (129.68, 36.81)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 300)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458130 reads in 927.785 CPU sec, 49.609 real sec
[M::process] read 1457986 sequences (200000155 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 48962, 3, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (104, 125, 153)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (6, 251)
[M::mem_pestat] mean and std.dev: (129.82, 36.73)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 300)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1457986 reads in 940.115 CPU sec, 47.941 real sec
[M::process] read 1458122 sequences (200000167 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49188, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (5, 250)
[M::mem_pestat] mean and std.dev: (129.47, 36.57)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 299)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458122 reads in 901.964 CPU sec, 46.761 real sec
[M::process] read 1458412 sequences (200000049 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49015, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 153)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (3, 253)
[M::mem_pestat] mean and std.dev: (129.61, 36.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 303)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458412 reads in 927.537 CPU sec, 49.110 real sec
[M::process] read 1459228 sequences (200000175 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 48765, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (5, 250)
[M::mem_pestat] mean and std.dev: (129.33, 36.55)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 299)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1459228 reads in 977.491 CPU sec, 51.023 real sec
[M::process] read 1458902 sequences (200000145 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49399, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (5, 250)
[M::mem_pestat] mean and std.dev: (129.03, 36.52)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 299)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458902 reads in 928.514 CPU sec, 49.106 real sec
[M::process] read 1458100 sequences (200000293 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49260, 1, 1)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (104, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (8, 248)
[M::mem_pestat] mean and std.dev: (129.48, 36.45)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 296)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458100 reads in 979.312 CPU sec, 51.421 real sec
[M::process] read 1458556 sequences (200000084 bp)...
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 48654, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 153)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (3, 253)
[M::mem_pestat] mean and std.dev: (129.79, 37.33)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 303)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458556 reads in 988.138 CPU sec, 54.278 real sec
[M::process] read 1458812 sequences (200000236 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 48691, 2, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (5, 250)
[M::mem_pestat] mean and std.dev: (129.21, 36.41)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 299)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458812 reads in 976.227 CPU sec, 53.732 real sec
[M::process] read 1457400 sequences (200000178 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 48924, 3, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (104, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (8, 248)
[M::mem_pestat] mean and std.dev: (129.34, 36.63)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 296)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1457400 reads in 964.268 CPU sec, 54.671 real sec
[M::process] read 1458444 sequences (200000207 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 48659, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (104, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (8, 248)
[M::mem_pestat] mean and std.dev: (129.32, 36.41)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 296)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458444 reads in 937.059 CPU sec, 48.506 real sec
[M::process] read 1457486 sequences (200000275 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 48623, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (104, 126, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (8, 248)
[M::mem_pestat] mean and std.dev: (129.55, 36.39)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 296)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1457486 reads in 916.761 CPU sec, 47.589 real sec
[M::process] read 1457914 sequences (200000105 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 48403, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (104, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (8, 248)
[M::mem_pestat] mean and std.dev: (129.46, 36.30)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 296)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1457914 reads in 963.780 CPU sec, 51.202 real sec
[M::process] read 1458806 sequences (200000048 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49613, 3, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 153)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (3, 253)
[M::mem_pestat] mean and std.dev: (129.73, 36.97)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 303)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458806 reads in 909.499 CPU sec, 47.299 real sec
[M::process] read 1458322 sequences (200000066 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49072, 1, 1)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (5, 250)
[M::mem_pestat] mean and std.dev: (129.50, 36.87)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 299)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458322 reads in 941.458 CPU sec, 49.166 real sec
[M::process] read 1458718 sequences (200000132 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 48867, 2, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 151)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (7, 247)
[M::mem_pestat] mean and std.dev: (128.95, 36.19)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 295)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458718 reads in 939.347 CPU sec, 48.485 real sec
[M::process] read 1458066 sequences (200000205 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 48982, 2, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 153)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (3, 253)
[M::mem_pestat] mean and std.dev: (129.93, 37.11)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 303)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458066 reads in 906.176 CPU sec, 51.577 real sec
[M::process] read 1019634 sequences (139758293 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 34344, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 151)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (7, 247)
[M::mem_pestat] mean and std.dev: (129.20, 36.33)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 295)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1019634 reads in 634.245 CPU sec, 33.307 real sec
[main] Version: 0.7.17-r1188
[main] CMD: /home/zhou/miniconda2/envs/kn/bin/bwa mem -t 20 /home/zhou/t12b/reference/hg38_ek12/AllRef.fa /home/zhou/t12a/HRA000524/raw/HRR179719_f1.fastq.gz /home/zhou/t12a/HRA000524/raw/HRR179719_r2.fastq.gz
[main] Real time: 10099.346 sec; CPU: 27381.559 sec
[M::process] read 1459500 sequences (200000044 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 48831, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (5, 250)
[M::mem_pestat] mean and std.dev: (129.20, 36.71)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 299)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1459500 reads in 1033.685 CPU sec, 56.620 real sec
[M::process] read 1459110 sequences (200000243 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49116, 7, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (5, 250)
[M::mem_pestat] mean and std.dev: (129.23, 36.75)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 299)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1459110 reads in 986.020 CPU sec, 50.488 real sec
[M::process] read 1459194 sequences (200000262 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49321, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (104, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (8, 248)
[M::mem_pestat] mean and std.dev: (129.25, 36.32)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 296)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1459194 reads in 1003.990 CPU sec, 57.107 real sec
[M::process] read 1459290 sequences (200000047 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 48946, 3, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (5, 250)
[M::mem_pestat] mean and std.dev: (129.41, 36.93)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 299)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1459290 reads in 1112.787 CPU sec, 72.229 real sec
[M::process] read 1458558 sequences (200000037 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49319, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (5, 250)
[M::mem_pestat] mean and std.dev: (129.54, 36.73)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 299)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458558 reads in 895.650 CPU sec, 55.889 real sec
[M::process] read 1458978 sequences (200000190 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49488, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (5, 250)
[M::mem_pestat] mean and std.dev: (129.40, 36.85)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 299)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1458978 reads in 971.154 CPU sec, 67.426 real sec
[M::process] read 1459092 sequences (200000115 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 49601, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (103, 125, 152)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (5, 250)
[M::mem_pestat] mean and std.dev: (129.39, 36.63)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 299)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1459092 reads in 905.292 CPU sec, 46.837 real sec
# novoalign (AVX2) (V3.09.00 - Build Jun 12 2018 @ 08:54:15) - A short read aligner with qualities.
# (C) 2008-2016 Novocraft Technologies Sdn Bhd.
# License file: /home/zhou/miniconda2/envs/kn/bin/novoalign.lic
# Licensed to Jian-Guo Zhou MD
#  novoalign -r A 1 -n 30 -d /home/zhou/t12b/reference/hg38_ek12/AllRef.ndx -f /home/zhou/t12a/HRA000524/NCLscan/HRR179719.output/raw.main.bwa.unmapped_1.fastq /home/zhou/t12a/HRA000524/NCLscan/HRR179719.output/raw.main.bwa.unmapped_2.fastq -o SAM

Read 60669 genes, 228048 transcripts and 1378888 exons from the gtf file.
# novoindex (3.9) - Universal k-mer index constructor.
# (C) 2008 - 2011 NovoCraft Technologies Sdn Bhd
# novoindex /home/zhou/t12a/HRA000524/NCLscan/HRR179719.output/raw.JS.ndx /home/zhou/t12a/HRA000524/NCLscan/HRR179719.output/raw.JS.fa 
# Building with 9-mer and step of 1 bp.
# novoindex construction dT = 0.0s
# Index memory size   0.001Gbyte.
# Done.
# Creating 95 indexing threads.
# novoalign (AVX2) (V3.09.00 - Build Jun 12 2018 @ 08:54:15) - A short read aligner with qualities.
# (C) 2008-2016 Novocraft Technologies Sdn Bhd.
# License file: /home/zhou/miniconda2/envs/kn/bin/novoalign.lic
# Licensed to Jian-Guo Zhou MD
#  novoalign -r A 1 -g 99 -x 99 -d /home/zhou/t12a/HRA000524/NCLscan/HRR179719.output/raw.JS.ndx -f /home/zhou/t12a/HRA000524/NCLscan/HRR179719.output/raw.main.unmapped_1.fastq -o SAM
# Starting at Mon Mar 21 02:49:41 2022
# Interpreting input files as Sanger FASTQ.
# Index Build Version: 3.9
#   Hash length:    9
#     Step size:    1
#     Read Sequences:   115527
#   Unique Alignment:        0 ( 0.0%)
#       Multi Mapped:        1 ( 0.0%)
#   No Mapping Found:   115526 (100.0%)
# Timers
#       Elapsed Time: 0.846 (secs.)
#           CPU Time: 18.12 (secs.)
# Done at Mon Mar 21 02:49:41 2022
# novoalign (AVX2) (V3.09.00 - Build Jun 12 2018 @ 08:54:15) - A short read aligner with qualities.
# (C) 2008-2016 Novocraft Technologies Sdn Bhd.
# License file: /home/zhou/miniconda2/envs/kn/bin/novoalign.lic
# Licensed to Jian-Guo Zhou MD
#  novoalign -r A 1 -g 99 -x 99 -d /home/zhou/t12a/HRA000524/NCLscan/HRR179719.output/raw.JS.ndx -f /home/zhou/t12a/HRA000524/NCLscan/HRR179719.output/raw.main.unmapped_2.fastq -o SAM
# Starting at Mon Mar 21 02:49:41 2022
# Interpreting input files as Sanger FASTQ.
# Index Build Version: 3.9
#   Hash length:    9
#     Step size:    1
#     Read Sequences:   115527
#   Unique Alignment:        0 ( 0.0%)
#       Multi Mapped:        1 ( 0.0%)
#   No Mapping Found:   115269 (99.8%)
# QC Failures...
# Homopolymer Filter:      257 ( 0.2%)
# Timers
#       Elapsed Time: 0.816 (secs.)
#           CPU Time: 18.04 (secs.)
# Done at Mon Mar 21 02:49:42 2022
Start to split the input into 20 part ... 
Traceback (most recent call last):
  File "/home/zhou/soft/NCLscan/bin/mp_blat.py", line 152, in <module>
    mp_blat(args.reference, args.fasta, args.output, args.process, args.tmp_path, args.blat_bin, args.blat_opt)
  File "/home/zhou/soft/NCLscan/bin/mp_blat.py", line 72, in mp_blat
    edge_pos = [all_reads_pos[0]] + splice_positions + [fasta_file_size]
IndexError: list index out of range
cat: /home/zhou/t12a/HRA000524/NCLscan/HRR179719.output/raw.JS.GRCh37.psl: 没有那个文件或目录
Start to split the input into 20 part ... 
Traceback (most recent call last):
  File "/home/zhou/soft/NCLscan/bin/mp_blat.py", line 152, in <module>
    mp_blat(args.reference, args.fasta, args.output, args.process, args.tmp_path, args.blat_bin, args.blat_opt)
  File "/home/zhou/soft/NCLscan/bin/mp_blat.py", line 72, in mp_blat
    edge_pos = [all_reads_pos[0]] + splice_positions + [fasta_file_size]
IndexError: list index out of range
cat: /home/zhou/t12a/HRA000524/NCLscan/HRR179719.output/raw.2.info.GRCh37.psl: 没有那个文件或目录
PslChimeraFilter v0.4
@JianGuoZhou3
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JianGuoZhou3 commented Mar 21, 2022 •
edited
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Thanks for your support. Other datasets success, but this dataset did not work...

Whole-transcriptome RNA sequencing
Total RNA was extracted from unstained FFPE tumor samples by the All Prep-DNA/RNA-Micro Kit (Qiagen) following the
 standard manufacturer’s protocol. Reverse transcription and second-strand cDNA synthesis were subsequently performed. 
Barcoded RNA libraries were generated and captured by a customized whole-exome panel. All libraries were sequenced on 
the Illumina NovaSeq 6000 platform with 2 × 150 bp paired-end reads. The mean sequencing coverage across all samples 
was ∼100× (3.5 G). RNA-seq reads were mapped to the human reference genome GRCh37 using STAR[72]
(https://www.nature.com/articles/s41525-021-00169-w#ref-CR72), and gene expression was quantified using RSEM[73]
(https://www.nature.com/articles/s41525-021-00169-w#ref-CR73). Coding region reads were counted to calculate 
fragments per kilobase of transcript per million mapped reads (FPKM) values at the gene level and log2-transformed before
 analysis to avoid extremely skewed gene expression distributions.

Ref: https://www.nature.com/articles/s41525-021-00169-w#Sec9

@chiangtw
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Hi,

Please provide the output of the following command:

ls -ltr [/path/to/your/NCLscan/output/directory/]

Thanks,
tw

@JianGuoZhou3
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HI @chiangtw please check this file！
Best,
JG
nohup.out.txt

@JianGuoZhou3
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Hi @chiangtw @TreesLab @chenchiaying please check another cohort.
Best,
JG
nohup.out1.txt

@chiangtw
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chiangtw commented Apr 6, 2022

Hi,

For simplicity, is it possible to run NCLscan with only one sample at a time?
And it would be very helpful to provide both the log messages and the file sizes of all output files from NCLscan.

You can use the following command to get the file sizes:

ls -ltr [/path/to/your/NCLscan/output/directory/] > file_sizes.txt

Thanks,
tw

@JianGuoZhou3
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Hi,

For simplicity, is it possible to run NCLscan with only one sample at a time? And it would be very helpful to provide both the log messages and the file sizes of all output files from NCLscan.

You can use the following command to get the file sizes:

ls -ltr [/path/to/your/NCLscan/output/directory/] > file_sizes.txt

Thanks, tw

Hi @chiangtw Please check the file_sizes.txt of HRA000524 datasets' HRR179719.
file_sizes.txt
Thanks, JG.

@liu2005678
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Hi, i have met a similar problem

the filesizes are
total 11415056
-rw-rw-r-- 1 logen logen 7099414220 4月 6 18:34 cpsf30_0h.main.bwa.bam
-rw-rw-r-- 1 logen logen 833593837 4月 6 18:36 cpsf30_0h.main.bwa.unmapped.sam
-rw-rw-r-- 1 logen logen 27324653 4月 6 18:36 cpsf30_0h.main.bwa.unmapped.sam.id
-rw-rw-r-- 1 logen logen 243982013 4月 6 18:37 cpsf30_0h.main.bwa.unmapped_1.fastq
-rw-rw-r-- 1 logen logen 243982013 4月 6 18:38 cpsf30_0h.main.bwa.unmapped_2.fastq
-rw-rw-r-- 1 logen logen 301149143 4月 6 19:33 cpsf30_0h.main.sam
-rw-rw-r-- 1 logen logen 136498545 4月 6 19:33 cpsf30_0h.main.unmapped.sam
-rw-rw-r-- 1 logen logen 13700571 4月 6 19:33 cpsf30_0h.main.unmapped.sam.id
-rw-rw-r-- 1 logen logen 122336081 4月 6 19:33 cpsf30_0h.main.unmapped_1.fastq
-rw-rw-r-- 1 logen logen 122336081 4月 6 19:33 cpsf30_0h.main.unmapped_2.fastq
-rw-rw-r-- 1 logen logen 107499109 4月 6 19:34 cpsf30_0h.main.unmapped.fa
-rw-rw-r-- 1 logen logen 107499109 4月 6 19:34 cpsf30_0h.unmapped.fa
-rw-rw-r-- 1 logen logen 282143365 4月 6 19:45 cpsf30_0h.rG.psl
-rw-rw-r-- 1 logen logen 0 4月 6 19:45 cpsf30_0h.un.psl
-rw-rw-r-- 1 logen logen 282143365 4月 6 19:45 cpsf30_0h.rG.non_un.psl
-rw-rw-r-- 1 logen logen 21258825 4月 6 19:45 cpsf30_0h.chi0.bed
-rw-rw-r-- 1 logen logen 35733415 4月 6 19:45 cpsf30_0h.unmapped.2.fa
-rw-rw-r-- 1 logen logen 42764808 4月 6 19:49 cpsf30_0h.coding.2.psl
-rw-rw-r-- 1 logen logen 203472 4月 6 19:49 cpsf30_0h.lncRNA.2.psl
-rw-rw-r-- 1 logen logen 0 4月 6 19:50 cpsf30_0h.chrM.2.psl
-rw-rw-r-- 1 logen logen 16117 4月 6 19:50 cpsf30_0h.colinear.psl
-rw-rw-r-- 1 logen logen 21238911 4月 6 19:50 cpsf30_0h.chi.bed
-rw-rw-r-- 1 logen logen 1208387 4月 6 19:50 cpsf30_0h.preJS.bed
-rw-rw-r-- 1 logen logen 1146828 4月 6 19:50 cpsf30_0h.preJS.info
-rw-rw-r-- 1 logen logen 1144729 4月 6 19:50 cpsf30_0h.preJS.info2
-rw-rw-r-- 1 logen logen 488714 4月 6 19:50 cpsf30_0h.JS.info_1
-rw-rw-r-- 1 logen logen 705918 4月 6 19:50 cpsf30_0h.JS.info_2
-rw-rw-r-- 1 logen logen 60031 4月 6 19:50 cpsf30_0h.JS.info
-rw-rw-r-- 1 logen logen 51785 4月 6 19:50 cpsf30_0h.JS.cleaned.info
-rw-rw-r-- 1 logen logen 2880629 4月 6 19:50 cpsf30_0h.preJS.seq
-rw-rw-r-- 1 logen logen 2878530 4月 6 19:50 cpsf30_0h.preJS.seq2
-rw-rw-r-- 1 logen logen 1101790 4月 6 19:50 cpsf30_0h.JS.seq_1
-rw-rw-r-- 1 logen logen 1776738 4月 6 19:50 cpsf30_0h.JS.seq_2
-rw-rw-r-- 1 logen logen 182401 4月 6 19:50 cpsf30_0h.JS.seq12
-rw-rw-r-- 1 logen logen 157328 4月 6 19:50 cpsf30_0h.JS.seq
-rw-rw-r-- 1 logen logen 157786 4月 6 19:50 cpsf30_0h.JS.fa
-rwxr--r-- 1 logen logen 1683393 4月 6 19:50 cpsf30_0h.JS.ndx
-rw-rw-r-- 1 logen logen 135280811 4月 6 19:51 cpsf30_0h.main_1.JS.sam
-rw-rw-r-- 1 logen logen 135283178 4月 6 19:53 cpsf30_0h.main_2.JS.sam
-rw-rw-r-- 1 logen logen 270563989 4月 6 19:53 all.cpsf30_0h.JS.sam
-rw-rw-r-- 1 logen logen 9731 4月 6 19:53 all.cpsf30_0h.JS.Parsered.sam
-rw-rw-r-- 1 logen logen 343 4月 6 19:53 tmp.info
-rw-rw-r-- 1 logen logen 273 4月 6 19:53 cpsf30_0h.info
-rw-rw-r-- 1 logen logen 1048 4月 6 19:53 cpsf30_0h.JS.clear.fa
-rw-rw-r-- 1 logen logen 55491 4月 6 19:53 cpsf30_0h.JS.GRCh37.psl
-rw-rw-r-- 1 logen logen 205 4月 6 19:53 cpsf30_0h.JS.GRCh37.2.psl
-rw-rw-r-- 1 logen logen 38 4月 6 19:53 cpsf30_0h.linearJS
-rw-rw-r-- 1 logen logen 255 4月 6 19:53 cpsf30_0h.tmp.info
-rw-rw-r-- 1 logen logen 115 4月 6 19:53 cpsf30_0h.tmp2.info
-rw-rw-r-- 1 logen logen 77 4月 6 19:53 cpsf30_0h.2.info
-rw-rw-r-- 1 logen logen 688 4月 6 19:53 cpsf30_0h.2.info.fa
-rw-rw-r-- 1 logen logen 7122 4月 6 19:53 cpsf30_0h.2.info.GRCh37.psl
-rw-rw-r-- 1 logen logen 380 4月 6 19:53 cpsf30_0h.2.chi.bed
-rw-rw-r-- 1 logen logen 804 4月 6 19:53 temp.list
-rw-rw-r-- 1 logen logen 558 4月 6 19:53 cpsf30_0h.chi2.bed
-rw-rw-r-- 1 logen logen 378 4月 6 19:53 cpsf30_0h.chi3.bed
-rw-rw-r-- 1 logen logen 389 4月 6 19:53 cpsf30_0h.PreJS2.bed
-rw-rw-r-- 1 logen logen 384 4月 6 19:53 cpsf30_0h.PreJS2.info
-rw-rw-r-- 1 logen logen 342 4月 6 19:53 cpsf30_0h.PreJS2.info2
-rw-rw-r-- 1 logen logen 207 4月 6 19:53 cpsf30_0h.JS2.info_1
-rw-rw-r-- 1 logen logen 151 4月 6 19:53 cpsf30_0h.JS2.info_2
-rw-rw-r-- 1 logen logen 263 4月 6 19:53 cpsf30_0h.JS2.info
-rw-rw-r-- 1 logen logen 263 4月 6 19:53 cpsf30_0h.JS2.cleaned.info
-rw-rw-r-- 1 logen logen 180 4月 6 19:53 cpsf30_0h.JS2.preIdx
-rw-rw-r-- 1 logen logen 267 4月 6 19:53 cpsf30_0h.JS1.preIdx
-rw-rw-r-- 1 logen logen 261 4月 6 19:53 cpsf30_0h.JS1.Idx
-rw-rw-r-- 1 logen logen 180 4月 6 19:53 cpsf30_0h.JS2.Idx
-rw-rw-r-- 1 logen logen 3422 4月 6 19:53 cpsf30_0h.PreJS2.seq
-rw-rw-r-- 1 logen logen 3380 4月 6 19:53 cpsf30_0h.PreJS2.seq2
-rw-rw-r-- 1 logen logen 1689 4月 6 19:53 cpsf30_0h.JS2.seq_1
-rw-rw-r-- 1 logen logen 1689 4月 6 19:53 cpsf30_0h.JS2.seq_2
-rw-rw-r-- 1 logen logen 3283 4月 6 19:53 cpsf30_0h.JS2.seq
-rw-rw-r-- 1 logen logen 3285 4月 6 19:53 cpsf30_0h.JS2.prefa
-rw-rw-r-- 1 logen logen 3337 4月 6 19:53 cpsf30_0h.JS2.fa
-rwxr--r-- 1 logen logen 1063520 4月 6 19:53 cpsf30_0h.JS2.ndx
-rw-rw-r-- 1 logen logen 271518275 4月 6 19:55 cpsf30_0h.main.JS2.sam
-rw-rw-r-- 1 logen logen 0 4月 6 19:55 all.cpsf30_0h.1.sam
-rw-rw-r-- 1 logen logen 0 4月 6 19:55 all.cpsf30_0h.1.result
-rw-rw-r-- 1 logen logen 271518275 4月 6 19:55 all.cpsf30_0h.JS2.sam
-rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.ncl.sam
-rw-rw-r-- 1 logen logen 0 4月 6 19:55 all.cpsf30_0h.result
-rw-rw-r-- 1 logen logen 263 4月 6 19:55 cpsf30_0h.JS2.result.info
-rw-rw-r-- 1 logen logen 184 4月 6 19:55 cpsf30_0h.result.info
-rw-rw-r-- 1 logen logen 180 4月 6 19:55 cpsf30_0h.2b.info
-rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.4.info
-rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.3.info
-rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.preResult
-rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.main_1.um3.fastq
-rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.main_2.um3.fastq
-rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.main.um3.fa
-rw-rw-r-- 1 logen logen 0 4月 6 19:55 all.cpsf30_0h.um3.fa
-rw-rw-r-- 1 logen logen 0 4月 6 19:55 all.cpsf30_0h.um3.colinear.psl
-rw-rw-r-- 1 logen logen 271518275 4月 6 19:55 cpsf30_0h.main.JS2b.sam
-rw-rw-r-- 1 logen logen 0 4月 6 19:55 all.cpsf30_0h.1b.sam
-rw-rw-r-- 1 logen logen 0 4月 6 19:55 all.cpsf30_0h.1b.result
-rw-rw-r-- 1 logen logen 271518275 4月 6 19:55 all.cpsf30_0h.JS2b.sam
-rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.result.sam
-rw-rw-r-- 1 logen logen 0 4月 6 19:55 all.cpsf30_0h.b.result
-rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.3b.info
-rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.result.tmp
-rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.4b.info

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@chiangtw @JianGuoZhou3 @liu2005678