Job ID = 2002123 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T00:35:45 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T01:13:09 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 116,355,019 reads read : 116,355,019 reads written : 116,355,019 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:13:28 116355019 reads; of these: 116355019 (100.00%) were unpaired; of these: 2167038 (1.86%) aligned 0 times 101572529 (87.30%) aligned exactly 1 time 12615452 (10.84%) aligned >1 times 98.14% overall alignment rate Time searching: 01:13:31 Overall time: 01:13:31 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 48 files... [bam_rmdupse_core] 67763367 / 114187981 = 0.5934 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 12:41:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 12:41:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:41:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:41:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 12:41:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:41:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:41:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 12:41:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:41:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:41:23: 1000000 INFO @ Fri, 05 Jul 2019 12:41:23: 1000000 INFO @ Fri, 05 Jul 2019 12:41:23: 1000000 INFO @ Fri, 05 Jul 2019 12:41:32: 2000000 INFO @ Fri, 05 Jul 2019 12:41:32: 2000000 INFO @ Fri, 05 Jul 2019 12:41:32: 2000000 INFO @ Fri, 05 Jul 2019 12:41:40: 3000000 INFO @ Fri, 05 Jul 2019 12:41:41: 3000000 INFO @ Fri, 05 Jul 2019 12:41:41: 3000000 INFO @ Fri, 05 Jul 2019 12:41:49: 4000000 INFO @ Fri, 05 Jul 2019 12:41:50: 4000000 INFO @ Fri, 05 Jul 2019 12:41:50: 4000000 INFO @ Fri, 05 Jul 2019 12:41:58: 5000000 INFO @ Fri, 05 Jul 2019 12:41:58: 5000000 INFO @ Fri, 05 Jul 2019 12:41:59: 5000000 INFO @ Fri, 05 Jul 2019 12:42:06: 6000000 INFO @ Fri, 05 Jul 2019 12:42:07: 6000000 INFO @ Fri, 05 Jul 2019 12:42:07: 6000000 INFO @ Fri, 05 Jul 2019 12:42:15: 7000000 INFO @ Fri, 05 Jul 2019 12:42:16: 7000000 INFO @ Fri, 05 Jul 2019 12:42:16: 7000000 INFO @ Fri, 05 Jul 2019 12:42:23: 8000000 INFO @ Fri, 05 Jul 2019 12:42:25: 8000000 INFO @ Fri, 05 Jul 2019 12:42:25: 8000000 INFO @ Fri, 05 Jul 2019 12:42:31: 9000000 INFO @ Fri, 05 Jul 2019 12:42:33: 9000000 INFO @ Fri, 05 Jul 2019 12:42:33: 9000000 INFO @ Fri, 05 Jul 2019 12:42:39: 10000000 INFO @ Fri, 05 Jul 2019 12:42:42: 10000000 INFO @ Fri, 05 Jul 2019 12:42:42: 10000000 INFO @ Fri, 05 Jul 2019 12:42:48: 11000000 INFO @ Fri, 05 Jul 2019 12:42:50: 11000000 INFO @ Fri, 05 Jul 2019 12:42:50: 11000000 INFO @ Fri, 05 Jul 2019 12:42:56: 12000000 INFO @ Fri, 05 Jul 2019 12:42:59: 12000000 INFO @ Fri, 05 Jul 2019 12:42:59: 12000000 INFO @ Fri, 05 Jul 2019 12:43:04: 13000000 INFO @ Fri, 05 Jul 2019 12:43:07: 13000000 INFO @ Fri, 05 Jul 2019 12:43:07: 13000000 INFO @ Fri, 05 Jul 2019 12:43:11: 14000000 INFO @ Fri, 05 Jul 2019 12:43:15: 14000000 INFO @ Fri, 05 Jul 2019 12:43:15: 14000000 INFO @ Fri, 05 Jul 2019 12:43:19: 15000000 INFO @ Fri, 05 Jul 2019 12:43:23: 15000000 INFO @ Fri, 05 Jul 2019 12:43:23: 15000000 INFO @ Fri, 05 Jul 2019 12:43:27: 16000000 INFO @ Fri, 05 Jul 2019 12:43:32: 16000000 INFO @ Fri, 05 Jul 2019 12:43:32: 16000000 INFO @ Fri, 05 Jul 2019 12:43:35: 17000000 INFO @ Fri, 05 Jul 2019 12:43:40: 17000000 INFO @ Fri, 05 Jul 2019 12:43:40: 17000000 INFO @ Fri, 05 Jul 2019 12:43:43: 18000000 INFO @ Fri, 05 Jul 2019 12:43:49: 18000000 INFO @ Fri, 05 Jul 2019 12:43:49: 18000000 INFO @ Fri, 05 Jul 2019 12:43:51: 19000000 INFO @ Fri, 05 Jul 2019 12:43:57: 19000000 INFO @ Fri, 05 Jul 2019 12:43:57: 19000000 INFO @ Fri, 05 Jul 2019 12:44:00: 20000000 INFO @ Fri, 05 Jul 2019 12:44:06: 20000000 INFO @ Fri, 05 Jul 2019 12:44:06: 20000000 INFO @ Fri, 05 Jul 2019 12:44:08: 21000000 INFO @ Fri, 05 Jul 2019 12:44:15: 21000000 INFO @ Fri, 05 Jul 2019 12:44:15: 21000000 INFO @ Fri, 05 Jul 2019 12:44:16: 22000000 INFO @ Fri, 05 Jul 2019 12:44:24: 22000000 INFO @ Fri, 05 Jul 2019 12:44:24: 23000000 INFO @ Fri, 05 Jul 2019 12:44:24: 22000000 INFO @ Fri, 05 Jul 2019 12:44:32: 24000000 INFO @ Fri, 05 Jul 2019 12:44:33: 23000000 INFO @ Fri, 05 Jul 2019 12:44:33: 23000000 INFO @ Fri, 05 Jul 2019 12:44:40: 25000000 INFO @ Fri, 05 Jul 2019 12:44:41: 24000000 INFO @ Fri, 05 Jul 2019 12:44:41: 24000000 INFO @ Fri, 05 Jul 2019 12:44:48: 26000000 INFO @ Fri, 05 Jul 2019 12:44:50: 25000000 INFO @ Fri, 05 Jul 2019 12:44:50: 25000000 INFO @ Fri, 05 Jul 2019 12:44:56: 27000000 INFO @ Fri, 05 Jul 2019 12:44:58: 26000000 INFO @ Fri, 05 Jul 2019 12:44:58: 26000000 INFO @ Fri, 05 Jul 2019 12:45:04: 28000000 INFO @ Fri, 05 Jul 2019 12:45:07: 27000000 INFO @ Fri, 05 Jul 2019 12:45:07: 27000000 INFO @ Fri, 05 Jul 2019 12:45:12: 29000000 INFO @ Fri, 05 Jul 2019 12:45:15: 28000000 INFO @ Fri, 05 Jul 2019 12:45:15: 28000000 INFO @ Fri, 05 Jul 2019 12:45:20: 30000000 INFO @ Fri, 05 Jul 2019 12:45:24: 29000000 INFO @ Fri, 05 Jul 2019 12:45:24: 29000000 INFO @ Fri, 05 Jul 2019 12:45:28: 31000000 INFO @ Fri, 05 Jul 2019 12:45:32: 30000000 INFO @ Fri, 05 Jul 2019 12:45:32: 30000000 INFO @ Fri, 05 Jul 2019 12:45:37: 32000000 INFO @ Fri, 05 Jul 2019 12:45:41: 31000000 INFO @ Fri, 05 Jul 2019 12:45:41: 31000000 INFO @ Fri, 05 Jul 2019 12:45:46: 33000000 INFO @ Fri, 05 Jul 2019 12:45:49: 32000000 INFO @ Fri, 05 Jul 2019 12:45:49: 32000000 INFO @ Fri, 05 Jul 2019 12:45:54: 34000000 INFO @ Fri, 05 Jul 2019 12:45:58: 33000000 INFO @ Fri, 05 Jul 2019 12:45:58: 33000000 INFO @ Fri, 05 Jul 2019 12:46:03: 35000000 INFO @ Fri, 05 Jul 2019 12:46:06: 34000000 INFO @ Fri, 05 Jul 2019 12:46:06: 34000000 INFO @ Fri, 05 Jul 2019 12:46:11: 36000000 INFO @ Fri, 05 Jul 2019 12:46:15: 35000000 INFO @ Fri, 05 Jul 2019 12:46:15: 35000000 INFO @ Fri, 05 Jul 2019 12:46:19: 37000000 INFO @ Fri, 05 Jul 2019 12:46:23: 36000000 INFO @ Fri, 05 Jul 2019 12:46:23: 36000000 INFO @ Fri, 05 Jul 2019 12:46:27: 38000000 INFO @ Fri, 05 Jul 2019 12:46:31: 37000000 INFO @ Fri, 05 Jul 2019 12:46:32: 37000000 INFO @ Fri, 05 Jul 2019 12:46:36: 39000000 INFO @ Fri, 05 Jul 2019 12:46:39: 38000000 INFO @ Fri, 05 Jul 2019 12:46:40: 38000000 INFO @ Fri, 05 Jul 2019 12:46:44: 40000000 INFO @ Fri, 05 Jul 2019 12:46:48: 39000000 INFO @ Fri, 05 Jul 2019 12:46:48: 39000000 INFO @ Fri, 05 Jul 2019 12:46:54: 41000000 INFO @ Fri, 05 Jul 2019 12:46:57: 40000000 INFO @ Fri, 05 Jul 2019 12:46:57: 40000000 INFO @ Fri, 05 Jul 2019 12:47:02: 42000000 INFO @ Fri, 05 Jul 2019 12:47:06: 41000000 INFO @ Fri, 05 Jul 2019 12:47:06: 41000000 INFO @ Fri, 05 Jul 2019 12:47:10: 43000000 INFO @ Fri, 05 Jul 2019 12:47:15: 42000000 INFO @ Fri, 05 Jul 2019 12:47:16: 42000000 INFO @ Fri, 05 Jul 2019 12:47:18: 44000000 INFO @ Fri, 05 Jul 2019 12:47:24: 43000000 INFO @ Fri, 05 Jul 2019 12:47:24: 43000000 INFO @ Fri, 05 Jul 2019 12:47:26: 45000000 INFO @ Fri, 05 Jul 2019 12:47:32: 44000000 INFO @ Fri, 05 Jul 2019 12:47:32: 44000000 INFO @ Fri, 05 Jul 2019 12:47:34: 46000000 INFO @ Fri, 05 Jul 2019 12:47:38: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:47:38: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:47:38: #1 total tags in treatment: 46424614 INFO @ Fri, 05 Jul 2019 12:47:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:47:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:47:39: #1 tags after filtering in treatment: 46424434 INFO @ Fri, 05 Jul 2019 12:47:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:47:39: #1 finished! INFO @ Fri, 05 Jul 2019 12:47:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:47:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:47:40: 45000000 INFO @ Fri, 05 Jul 2019 12:47:41: 45000000 INFO @ Fri, 05 Jul 2019 12:47:49: 46000000 INFO @ Fri, 05 Jul 2019 12:47:49: 46000000 INFO @ Fri, 05 Jul 2019 12:47:51: #2 number of paired peaks: 101991 INFO @ Fri, 05 Jul 2019 12:47:51: start model_add_line... INFO @ Fri, 05 Jul 2019 12:47:52: start X-correlation... INFO @ Fri, 05 Jul 2019 12:47:52: end of X-cor INFO @ Fri, 05 Jul 2019 12:47:52: #2 finished! INFO @ Fri, 05 Jul 2019 12:47:52: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 12:47:52: #2 alternative fragment length(s) may be 2,136 bps INFO @ Fri, 05 Jul 2019 12:47:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.05_model.r INFO @ Fri, 05 Jul 2019 12:47:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:47:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:47:53: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:47:53: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:47:53: #1 total tags in treatment: 46424614 INFO @ Fri, 05 Jul 2019 12:47:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:47:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:47:53: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:47:53: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:47:53: #1 total tags in treatment: 46424614 INFO @ Fri, 05 Jul 2019 12:47:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:47:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:47:54: #1 tags after filtering in treatment: 46424434 INFO @ Fri, 05 Jul 2019 12:47:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:47:54: #1 finished! INFO @ Fri, 05 Jul 2019 12:47:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:47:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:47:54: #1 tags after filtering in treatment: 46424434 INFO @ Fri, 05 Jul 2019 12:47:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:47:54: #1 finished! INFO @ Fri, 05 Jul 2019 12:47:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:47:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:48:06: #2 number of paired peaks: 101991 INFO @ Fri, 05 Jul 2019 12:48:06: start model_add_line... INFO @ Fri, 05 Jul 2019 12:48:06: #2 number of paired peaks: 101991 INFO @ Fri, 05 Jul 2019 12:48:06: start model_add_line... INFO @ Fri, 05 Jul 2019 12:48:07: start X-correlation... INFO @ Fri, 05 Jul 2019 12:48:07: end of X-cor INFO @ Fri, 05 Jul 2019 12:48:07: #2 finished! INFO @ Fri, 05 Jul 2019 12:48:07: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 12:48:07: #2 alternative fragment length(s) may be 2,136 bps INFO @ Fri, 05 Jul 2019 12:48:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.10_model.r INFO @ Fri, 05 Jul 2019 12:48:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:48:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:48:07: start X-correlation... INFO @ Fri, 05 Jul 2019 12:48:07: end of X-cor INFO @ Fri, 05 Jul 2019 12:48:07: #2 finished! INFO @ Fri, 05 Jul 2019 12:48:07: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 12:48:07: #2 alternative fragment length(s) may be 2,136 bps INFO @ Fri, 05 Jul 2019 12:48:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.20_model.r INFO @ Fri, 05 Jul 2019 12:48:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:48:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:50:09: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:50:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:50:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:51:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:51:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:51:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.05_summits.bed INFO @ Fri, 05 Jul 2019 12:51:26: Done! pass1 - making usageList (191 chroms): 21 millis pass2 - checking and writing primary data (81430 records, 4 fields): 108 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:51:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:51:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:51:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.20_summits.bed INFO @ Fri, 05 Jul 2019 12:51:39: Done! INFO @ Fri, 05 Jul 2019 12:51:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.10_peaks.xls pass1 - making usageList (132 chroms): 13 millis pass2 - checking and writing primary data (42859 records, 4 fields): 60 millis INFO @ Fri, 05 Jul 2019 12:51:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:51:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102025/ERX102025.10_summits.bed INFO @ Fri, 05 Jul 2019 12:51:41: Done! pass1 - making usageList (159 chroms): 14 millis pass2 - checking and writing primary data (61638 records, 4 fields): 83 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。