Job ID = 2001666 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T22:43:10 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-04T22:44:47 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 : 58,108,391 reads read : 58,108,391 reads written : 58,108,391 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:20:33 58108391 reads; of these: 58108391 (100.00%) were unpaired; of these: 1371197 (2.36%) aligned 0 times 41406579 (71.26%) aligned exactly 1 time 15330615 (26.38%) aligned >1 times 97.64% overall alignment rate Time searching: 01:20:36 Overall time: 01:20:36 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 24 files... [bam_rmdupse_core] 4575293 / 56737194 = 0.0806 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 09:44:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.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 09:44:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:44:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:44:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.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 09:44:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:44:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:44:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.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 09:44:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:44:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:45:04: 1000000 INFO @ Fri, 05 Jul 2019 09:45:04: 1000000 INFO @ Fri, 05 Jul 2019 09:45:05: 1000000 INFO @ Fri, 05 Jul 2019 09:45:14: 2000000 INFO @ Fri, 05 Jul 2019 09:45:15: 2000000 INFO @ Fri, 05 Jul 2019 09:45:16: 2000000 INFO @ Fri, 05 Jul 2019 09:45:24: 3000000 INFO @ Fri, 05 Jul 2019 09:45:24: 3000000 INFO @ Fri, 05 Jul 2019 09:45:26: 3000000 INFO @ Fri, 05 Jul 2019 09:45:34: 4000000 INFO @ Fri, 05 Jul 2019 09:45:34: 4000000 INFO @ Fri, 05 Jul 2019 09:45:37: 4000000 INFO @ Fri, 05 Jul 2019 09:45:43: 5000000 INFO @ Fri, 05 Jul 2019 09:45:45: 5000000 INFO @ Fri, 05 Jul 2019 09:45:47: 5000000 INFO @ Fri, 05 Jul 2019 09:45:52: 6000000 INFO @ Fri, 05 Jul 2019 09:45:55: 6000000 INFO @ Fri, 05 Jul 2019 09:45:58: 6000000 INFO @ Fri, 05 Jul 2019 09:46:01: 7000000 INFO @ Fri, 05 Jul 2019 09:46:05: 7000000 INFO @ Fri, 05 Jul 2019 09:46:08: 7000000 INFO @ Fri, 05 Jul 2019 09:46:10: 8000000 INFO @ Fri, 05 Jul 2019 09:46:15: 8000000 INFO @ Fri, 05 Jul 2019 09:46:18: 8000000 INFO @ Fri, 05 Jul 2019 09:46:20: 9000000 INFO @ Fri, 05 Jul 2019 09:46:25: 9000000 INFO @ Fri, 05 Jul 2019 09:46:29: 10000000 INFO @ Fri, 05 Jul 2019 09:46:30: 9000000 INFO @ Fri, 05 Jul 2019 09:46:35: 10000000 INFO @ Fri, 05 Jul 2019 09:46:39: 11000000 INFO @ Fri, 05 Jul 2019 09:46:41: 10000000 INFO @ Fri, 05 Jul 2019 09:46:46: 11000000 INFO @ Fri, 05 Jul 2019 09:46:48: 12000000 INFO @ Fri, 05 Jul 2019 09:46:51: 11000000 INFO @ Fri, 05 Jul 2019 09:46:57: 12000000 INFO @ Fri, 05 Jul 2019 09:46:58: 13000000 INFO @ Fri, 05 Jul 2019 09:47:03: 12000000 INFO @ Fri, 05 Jul 2019 09:47:07: 14000000 INFO @ Fri, 05 Jul 2019 09:47:07: 13000000 INFO @ Fri, 05 Jul 2019 09:47:13: 13000000 INFO @ Fri, 05 Jul 2019 09:47:17: 15000000 INFO @ Fri, 05 Jul 2019 09:47:18: 14000000 INFO @ Fri, 05 Jul 2019 09:47:24: 14000000 INFO @ Fri, 05 Jul 2019 09:47:26: 16000000 INFO @ Fri, 05 Jul 2019 09:47:28: 15000000 INFO @ Fri, 05 Jul 2019 09:47:35: 15000000 INFO @ Fri, 05 Jul 2019 09:47:36: 17000000 INFO @ Fri, 05 Jul 2019 09:47:39: 16000000 INFO @ Fri, 05 Jul 2019 09:47:45: 16000000 INFO @ Fri, 05 Jul 2019 09:47:47: 18000000 INFO @ Fri, 05 Jul 2019 09:47:49: 17000000 INFO @ Fri, 05 Jul 2019 09:47:56: 17000000 INFO @ Fri, 05 Jul 2019 09:47:57: 19000000 INFO @ Fri, 05 Jul 2019 09:48:00: 18000000 INFO @ Fri, 05 Jul 2019 09:48:07: 18000000 INFO @ Fri, 05 Jul 2019 09:48:07: 20000000 INFO @ Fri, 05 Jul 2019 09:48:10: 19000000 INFO @ Fri, 05 Jul 2019 09:48:17: 21000000 INFO @ Fri, 05 Jul 2019 09:48:18: 19000000 INFO @ Fri, 05 Jul 2019 09:48:21: 20000000 INFO @ Fri, 05 Jul 2019 09:48:26: 22000000 INFO @ Fri, 05 Jul 2019 09:48:28: 20000000 INFO @ Fri, 05 Jul 2019 09:48:32: 21000000 INFO @ Fri, 05 Jul 2019 09:48:35: 23000000 INFO @ Fri, 05 Jul 2019 09:48:39: 21000000 INFO @ Fri, 05 Jul 2019 09:48:42: 22000000 INFO @ Fri, 05 Jul 2019 09:48:45: 24000000 INFO @ Fri, 05 Jul 2019 09:48:49: 22000000 INFO @ Fri, 05 Jul 2019 09:48:53: 23000000 INFO @ Fri, 05 Jul 2019 09:48:54: 25000000 INFO @ Fri, 05 Jul 2019 09:49:00: 23000000 INFO @ Fri, 05 Jul 2019 09:49:03: 26000000 INFO @ Fri, 05 Jul 2019 09:49:04: 24000000 INFO @ Fri, 05 Jul 2019 09:49:09: 24000000 INFO @ Fri, 05 Jul 2019 09:49:13: 27000000 INFO @ Fri, 05 Jul 2019 09:49:14: 25000000 INFO @ Fri, 05 Jul 2019 09:49:19: 25000000 INFO @ Fri, 05 Jul 2019 09:49:22: 28000000 INFO @ Fri, 05 Jul 2019 09:49:25: 26000000 INFO @ Fri, 05 Jul 2019 09:49:29: 26000000 INFO @ Fri, 05 Jul 2019 09:49:31: 29000000 INFO @ Fri, 05 Jul 2019 09:49:36: 27000000 INFO @ Fri, 05 Jul 2019 09:49:39: 27000000 INFO @ Fri, 05 Jul 2019 09:49:41: 30000000 INFO @ Fri, 05 Jul 2019 09:49:46: 28000000 INFO @ Fri, 05 Jul 2019 09:49:49: 28000000 INFO @ Fri, 05 Jul 2019 09:49:50: 31000000 INFO @ Fri, 05 Jul 2019 09:49:57: 29000000 INFO @ Fri, 05 Jul 2019 09:49:58: 29000000 INFO @ Fri, 05 Jul 2019 09:50:00: 32000000 INFO @ Fri, 05 Jul 2019 09:50:08: 30000000 INFO @ Fri, 05 Jul 2019 09:50:08: 30000000 INFO @ Fri, 05 Jul 2019 09:50:09: 33000000 INFO @ Fri, 05 Jul 2019 09:50:18: 31000000 INFO @ Fri, 05 Jul 2019 09:50:18: 34000000 INFO @ Fri, 05 Jul 2019 09:50:19: 31000000 INFO @ Fri, 05 Jul 2019 09:50:28: 35000000 INFO @ Fri, 05 Jul 2019 09:50:28: 32000000 INFO @ Fri, 05 Jul 2019 09:50:29: 32000000 INFO @ Fri, 05 Jul 2019 09:50:38: 36000000 INFO @ Fri, 05 Jul 2019 09:50:38: 33000000 INFO @ Fri, 05 Jul 2019 09:50:39: 33000000 INFO @ Fri, 05 Jul 2019 09:50:48: 37000000 INFO @ Fri, 05 Jul 2019 09:50:49: 34000000 INFO @ Fri, 05 Jul 2019 09:50:49: 34000000 INFO @ Fri, 05 Jul 2019 09:50:59: 35000000 INFO @ Fri, 05 Jul 2019 09:50:59: 38000000 INFO @ Fri, 05 Jul 2019 09:51:00: 35000000 INFO @ Fri, 05 Jul 2019 09:51:09: 36000000 INFO @ Fri, 05 Jul 2019 09:51:09: 39000000 INFO @ Fri, 05 Jul 2019 09:51:10: 36000000 INFO @ Fri, 05 Jul 2019 09:51:19: 40000000 INFO @ Fri, 05 Jul 2019 09:51:19: 37000000 INFO @ Fri, 05 Jul 2019 09:51:21: 37000000 INFO @ Fri, 05 Jul 2019 09:51:28: 41000000 INFO @ Fri, 05 Jul 2019 09:51:30: 38000000 INFO @ Fri, 05 Jul 2019 09:51:31: 38000000 INFO @ Fri, 05 Jul 2019 09:51:38: 42000000 INFO @ Fri, 05 Jul 2019 09:51:40: 39000000 INFO @ Fri, 05 Jul 2019 09:51:42: 39000000 INFO @ Fri, 05 Jul 2019 09:51:47: 43000000 INFO @ Fri, 05 Jul 2019 09:51:51: 40000000 INFO @ Fri, 05 Jul 2019 09:51:52: 40000000 INFO @ Fri, 05 Jul 2019 09:51:57: 44000000 INFO @ Fri, 05 Jul 2019 09:52:01: 41000000 INFO @ Fri, 05 Jul 2019 09:52:02: 41000000 INFO @ Fri, 05 Jul 2019 09:52:06: 45000000 INFO @ Fri, 05 Jul 2019 09:52:10: 42000000 INFO @ Fri, 05 Jul 2019 09:52:12: 42000000 INFO @ Fri, 05 Jul 2019 09:52:15: 46000000 INFO @ Fri, 05 Jul 2019 09:52:20: 43000000 INFO @ Fri, 05 Jul 2019 09:52:23: 43000000 INFO @ Fri, 05 Jul 2019 09:52:24: 47000000 INFO @ Fri, 05 Jul 2019 09:52:30: 44000000 INFO @ Fri, 05 Jul 2019 09:52:33: 44000000 INFO @ Fri, 05 Jul 2019 09:52:34: 48000000 INFO @ Fri, 05 Jul 2019 09:52:40: 45000000 INFO @ Fri, 05 Jul 2019 09:52:43: 49000000 INFO @ Fri, 05 Jul 2019 09:52:44: 45000000 INFO @ Fri, 05 Jul 2019 09:52:50: 46000000 INFO @ Fri, 05 Jul 2019 09:52:52: 50000000 INFO @ Fri, 05 Jul 2019 09:52:55: 46000000 INFO @ Fri, 05 Jul 2019 09:53:00: 47000000 INFO @ Fri, 05 Jul 2019 09:53:02: 51000000 INFO @ Fri, 05 Jul 2019 09:53:06: 47000000 INFO @ Fri, 05 Jul 2019 09:53:10: 48000000 INFO @ Fri, 05 Jul 2019 09:53:11: 52000000 INFO @ Fri, 05 Jul 2019 09:53:13: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 09:53:13: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 09:53:13: #1 total tags in treatment: 52161901 INFO @ Fri, 05 Jul 2019 09:53:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:53:13: #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 09:53:14: #1 tags after filtering in treatment: 52161821 INFO @ Fri, 05 Jul 2019 09:53:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:53:14: #1 finished! INFO @ Fri, 05 Jul 2019 09:53:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:53:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:53:16: 48000000 INFO @ Fri, 05 Jul 2019 09:53:19: 49000000 INFO @ Fri, 05 Jul 2019 09:53:21: #2 number of paired peaks: 18309 INFO @ Fri, 05 Jul 2019 09:53:21: start model_add_line... INFO @ Fri, 05 Jul 2019 09:53:22: start X-correlation... INFO @ Fri, 05 Jul 2019 09:53:22: end of X-cor INFO @ Fri, 05 Jul 2019 09:53:22: #2 finished! INFO @ Fri, 05 Jul 2019 09:53:22: #2 predicted fragment length is 106 bps INFO @ Fri, 05 Jul 2019 09:53:22: #2 alternative fragment length(s) may be 4,106,486 bps INFO @ Fri, 05 Jul 2019 09:53:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.10_model.r INFO @ Fri, 05 Jul 2019 09:53:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:53:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:53:27: 49000000 INFO @ Fri, 05 Jul 2019 09:53:29: 50000000 INFO @ Fri, 05 Jul 2019 09:53:37: 50000000 INFO @ Fri, 05 Jul 2019 09:53:39: 51000000 INFO @ Fri, 05 Jul 2019 09:53:47: 51000000 INFO @ Fri, 05 Jul 2019 09:53:48: 52000000 INFO @ Fri, 05 Jul 2019 09:53:50: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 09:53:50: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 09:53:50: #1 total tags in treatment: 52161901 INFO @ Fri, 05 Jul 2019 09:53:50: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:53:50: #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 09:53:52: #1 tags after filtering in treatment: 52161821 INFO @ Fri, 05 Jul 2019 09:53:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:53:52: #1 finished! INFO @ Fri, 05 Jul 2019 09:53:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:53:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:53:57: 52000000 INFO @ Fri, 05 Jul 2019 09:53:58: #2 number of paired peaks: 18309 INFO @ Fri, 05 Jul 2019 09:53:58: start model_add_line... INFO @ Fri, 05 Jul 2019 09:53:59: start X-correlation... INFO @ Fri, 05 Jul 2019 09:53:59: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 09:53:59: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 09:53:59: #1 total tags in treatment: 52161901 INFO @ Fri, 05 Jul 2019 09:53:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:53:59: #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 09:53:59: end of X-cor INFO @ Fri, 05 Jul 2019 09:53:59: #2 finished! INFO @ Fri, 05 Jul 2019 09:53:59: #2 predicted fragment length is 106 bps INFO @ Fri, 05 Jul 2019 09:53:59: #2 alternative fragment length(s) may be 4,106,486 bps INFO @ Fri, 05 Jul 2019 09:53:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.20_model.r INFO @ Fri, 05 Jul 2019 09:53:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:53:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:54:00: #1 tags after filtering in treatment: 52161821 INFO @ Fri, 05 Jul 2019 09:54:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:54:00: #1 finished! INFO @ Fri, 05 Jul 2019 09:54:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:54:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:54:06: #2 number of paired peaks: 18309 INFO @ Fri, 05 Jul 2019 09:54:06: start model_add_line... INFO @ Fri, 05 Jul 2019 09:54:07: start X-correlation... INFO @ Fri, 05 Jul 2019 09:54:07: end of X-cor INFO @ Fri, 05 Jul 2019 09:54:07: #2 finished! INFO @ Fri, 05 Jul 2019 09:54:07: #2 predicted fragment length is 106 bps INFO @ Fri, 05 Jul 2019 09:54:07: #2 alternative fragment length(s) may be 4,106,486 bps INFO @ Fri, 05 Jul 2019 09:54:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.05_model.r INFO @ Fri, 05 Jul 2019 09:54:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:54:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:56:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:56:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:56:56: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:57:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:57:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:57:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.10_summits.bed INFO @ Fri, 05 Jul 2019 09:57:48: Done! pass1 - making usageList (50 chroms): 3 millis pass2 - checking and writing primary data (1848 records, 4 fields): 62 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:58:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.05_peaks.xls INFO @ Fri, 05 Jul 2019 09:58:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:58:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.05_summits.bed INFO @ Fri, 05 Jul 2019 09:58:22: Done! pass1 - making usageList (88 chroms): 2 millis pass2 - checking and writing primary data (7257 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:58:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.20_peaks.xls INFO @ Fri, 05 Jul 2019 09:58:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:58:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101981/ERX101981.20_summits.bed INFO @ Fri, 05 Jul 2019 09:58:30: Done! pass1 - making usageList (34 chroms): 2 millis pass2 - checking and writing primary data (375 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。