Job ID = 2001669 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T23:04:14 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 ) 2019-07-04T23:09:38 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 ) 2019-07-04T23:33:13 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 : 122,404,581 reads read : 122,404,581 reads written : 122,404,581 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: 01:08:42 122404581 reads; of these: 122404581 (100.00%) were unpaired; of these: 2088041 (1.71%) aligned 0 times 107834213 (88.10%) aligned exactly 1 time 12482327 (10.20%) aligned >1 times 98.29% overall alignment rate Time searching: 01:08:45 Overall time: 01:08:45 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 52 files... [bam_rmdupse_core] 76405652 / 120316540 = 0.6350 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 10:34:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.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 10:34:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:34:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:35:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.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 10:35:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:35:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:35:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.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 10:35:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:35:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:35:12: 1000000 INFO @ Fri, 05 Jul 2019 10:35:12: 1000000 INFO @ Fri, 05 Jul 2019 10:35:12: 1000000 INFO @ Fri, 05 Jul 2019 10:35:23: 2000000 INFO @ Fri, 05 Jul 2019 10:35:23: 2000000 INFO @ Fri, 05 Jul 2019 10:35:25: 2000000 INFO @ Fri, 05 Jul 2019 10:35:34: 3000000 INFO @ Fri, 05 Jul 2019 10:35:34: 3000000 INFO @ Fri, 05 Jul 2019 10:35:38: 3000000 INFO @ Fri, 05 Jul 2019 10:35:43: 4000000 INFO @ Fri, 05 Jul 2019 10:35:45: 4000000 INFO @ Fri, 05 Jul 2019 10:35:51: 4000000 INFO @ Fri, 05 Jul 2019 10:35:53: 5000000 INFO @ Fri, 05 Jul 2019 10:35:56: 5000000 INFO @ Fri, 05 Jul 2019 10:36:04: 5000000 INFO @ Fri, 05 Jul 2019 10:36:04: 6000000 INFO @ Fri, 05 Jul 2019 10:36:08: 6000000 INFO @ Fri, 05 Jul 2019 10:36:14: 7000000 INFO @ Fri, 05 Jul 2019 10:36:17: 6000000 INFO @ Fri, 05 Jul 2019 10:36:19: 7000000 INFO @ Fri, 05 Jul 2019 10:36:24: 8000000 INFO @ Fri, 05 Jul 2019 10:36:29: 7000000 INFO @ Fri, 05 Jul 2019 10:36:30: 8000000 INFO @ Fri, 05 Jul 2019 10:36:35: 9000000 INFO @ Fri, 05 Jul 2019 10:36:41: 9000000 INFO @ Fri, 05 Jul 2019 10:36:42: 8000000 INFO @ Fri, 05 Jul 2019 10:36:45: 10000000 INFO @ Fri, 05 Jul 2019 10:36:53: 10000000 INFO @ Fri, 05 Jul 2019 10:36:55: 11000000 INFO @ Fri, 05 Jul 2019 10:36:55: 9000000 INFO @ Fri, 05 Jul 2019 10:37:03: 11000000 INFO @ Fri, 05 Jul 2019 10:37:05: 12000000 INFO @ Fri, 05 Jul 2019 10:37:07: 10000000 INFO @ Fri, 05 Jul 2019 10:37:15: 12000000 INFO @ Fri, 05 Jul 2019 10:37:15: 13000000 INFO @ Fri, 05 Jul 2019 10:37:20: 11000000 INFO @ Fri, 05 Jul 2019 10:37:26: 13000000 INFO @ Fri, 05 Jul 2019 10:37:26: 14000000 INFO @ Fri, 05 Jul 2019 10:37:34: 12000000 INFO @ Fri, 05 Jul 2019 10:37:36: 14000000 INFO @ Fri, 05 Jul 2019 10:37:36: 15000000 INFO @ Fri, 05 Jul 2019 10:37:47: 13000000 INFO @ Fri, 05 Jul 2019 10:37:47: 15000000 INFO @ Fri, 05 Jul 2019 10:37:47: 16000000 INFO @ Fri, 05 Jul 2019 10:37:58: 16000000 INFO @ Fri, 05 Jul 2019 10:37:59: 17000000 INFO @ Fri, 05 Jul 2019 10:38:01: 14000000 INFO @ Fri, 05 Jul 2019 10:38:09: 17000000 INFO @ Fri, 05 Jul 2019 10:38:10: 18000000 INFO @ Fri, 05 Jul 2019 10:38:15: 15000000 INFO @ Fri, 05 Jul 2019 10:38:20: 18000000 INFO @ Fri, 05 Jul 2019 10:38:21: 19000000 INFO @ Fri, 05 Jul 2019 10:38:28: 16000000 INFO @ Fri, 05 Jul 2019 10:38:31: 20000000 INFO @ Fri, 05 Jul 2019 10:38:31: 19000000 INFO @ Fri, 05 Jul 2019 10:38:39: 17000000 INFO @ Fri, 05 Jul 2019 10:38:41: 21000000 INFO @ Fri, 05 Jul 2019 10:38:42: 20000000 INFO @ Fri, 05 Jul 2019 10:38:51: 18000000 INFO @ Fri, 05 Jul 2019 10:38:51: 22000000 INFO @ Fri, 05 Jul 2019 10:38:52: 21000000 INFO @ Fri, 05 Jul 2019 10:39:01: 23000000 INFO @ Fri, 05 Jul 2019 10:39:02: 19000000 INFO @ Fri, 05 Jul 2019 10:39:03: 22000000 INFO @ Fri, 05 Jul 2019 10:39:11: 24000000 INFO @ Fri, 05 Jul 2019 10:39:14: 23000000 INFO @ Fri, 05 Jul 2019 10:39:14: 20000000 INFO @ Fri, 05 Jul 2019 10:39:22: 25000000 INFO @ Fri, 05 Jul 2019 10:39:24: 24000000 INFO @ Fri, 05 Jul 2019 10:39:26: 21000000 INFO @ Fri, 05 Jul 2019 10:39:32: 26000000 INFO @ Fri, 05 Jul 2019 10:39:35: 25000000 INFO @ Fri, 05 Jul 2019 10:39:37: 22000000 INFO @ Fri, 05 Jul 2019 10:39:41: 27000000 INFO @ Fri, 05 Jul 2019 10:39:45: 26000000 INFO @ Fri, 05 Jul 2019 10:39:49: 23000000 INFO @ Fri, 05 Jul 2019 10:39:51: 28000000 INFO @ Fri, 05 Jul 2019 10:39:56: 27000000 INFO @ Fri, 05 Jul 2019 10:40:00: 24000000 INFO @ Fri, 05 Jul 2019 10:40:01: 29000000 INFO @ Fri, 05 Jul 2019 10:40:06: 28000000 INFO @ Fri, 05 Jul 2019 10:40:10: 30000000 INFO @ Fri, 05 Jul 2019 10:40:11: 25000000 INFO @ Fri, 05 Jul 2019 10:40:17: 29000000 INFO @ Fri, 05 Jul 2019 10:40:19: 31000000 INFO @ Fri, 05 Jul 2019 10:40:23: 26000000 INFO @ Fri, 05 Jul 2019 10:40:28: 30000000 INFO @ Fri, 05 Jul 2019 10:40:29: 32000000 INFO @ Fri, 05 Jul 2019 10:40:34: 27000000 INFO @ Fri, 05 Jul 2019 10:40:38: 33000000 INFO @ Fri, 05 Jul 2019 10:40:39: 31000000 INFO @ Fri, 05 Jul 2019 10:40:45: 28000000 INFO @ Fri, 05 Jul 2019 10:40:47: 34000000 INFO @ Fri, 05 Jul 2019 10:40:49: 32000000 INFO @ Fri, 05 Jul 2019 10:40:55: 29000000 INFO @ Fri, 05 Jul 2019 10:40:56: 35000000 INFO @ Fri, 05 Jul 2019 10:40:59: 33000000 INFO @ Fri, 05 Jul 2019 10:41:05: 36000000 INFO @ Fri, 05 Jul 2019 10:41:06: 30000000 INFO @ Fri, 05 Jul 2019 10:41:09: 34000000 INFO @ Fri, 05 Jul 2019 10:41:14: 37000000 INFO @ Fri, 05 Jul 2019 10:41:17: 31000000 INFO @ Fri, 05 Jul 2019 10:41:20: 35000000 INFO @ Fri, 05 Jul 2019 10:41:23: 38000000 INFO @ Fri, 05 Jul 2019 10:41:28: 32000000 INFO @ Fri, 05 Jul 2019 10:41:30: 36000000 INFO @ Fri, 05 Jul 2019 10:41:32: 39000000 INFO @ Fri, 05 Jul 2019 10:41:38: 33000000 INFO @ Fri, 05 Jul 2019 10:41:40: 37000000 INFO @ Fri, 05 Jul 2019 10:41:41: 40000000 INFO @ Fri, 05 Jul 2019 10:41:49: 34000000 INFO @ Fri, 05 Jul 2019 10:41:50: 41000000 INFO @ Fri, 05 Jul 2019 10:41:50: 38000000 INFO @ Fri, 05 Jul 2019 10:41:59: 42000000 INFO @ Fri, 05 Jul 2019 10:42:00: 35000000 INFO @ Fri, 05 Jul 2019 10:42:00: 39000000 INFO @ Fri, 05 Jul 2019 10:42:09: 43000000 INFO @ Fri, 05 Jul 2019 10:42:11: 36000000 INFO @ Fri, 05 Jul 2019 10:42:11: 40000000 INFO @ Fri, 05 Jul 2019 10:42:18: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 10:42:18: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 10:42:18: #1 total tags in treatment: 43910888 INFO @ Fri, 05 Jul 2019 10:42:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:42:18: #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 10:42:19: #1 tags after filtering in treatment: 43910705 INFO @ Fri, 05 Jul 2019 10:42:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:42:19: #1 finished! INFO @ Fri, 05 Jul 2019 10:42:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:42:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:42:21: 41000000 INFO @ Fri, 05 Jul 2019 10:42:22: 37000000 INFO @ Fri, 05 Jul 2019 10:42:31: 42000000 INFO @ Fri, 05 Jul 2019 10:42:31: #2 number of paired peaks: 100212 INFO @ Fri, 05 Jul 2019 10:42:31: start model_add_line... INFO @ Fri, 05 Jul 2019 10:42:33: 38000000 INFO @ Fri, 05 Jul 2019 10:42:33: start X-correlation... INFO @ Fri, 05 Jul 2019 10:42:33: end of X-cor INFO @ Fri, 05 Jul 2019 10:42:33: #2 finished! INFO @ Fri, 05 Jul 2019 10:42:33: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 10:42:33: #2 alternative fragment length(s) may be 3,135 bps INFO @ Fri, 05 Jul 2019 10:42:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.20_model.r INFO @ Fri, 05 Jul 2019 10:42:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:42:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:42:41: 43000000 INFO @ Fri, 05 Jul 2019 10:42:44: 39000000 INFO @ Fri, 05 Jul 2019 10:42:51: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 10:42:51: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 10:42:51: #1 total tags in treatment: 43910888 INFO @ Fri, 05 Jul 2019 10:42:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:42:51: #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 10:42:52: #1 tags after filtering in treatment: 43910705 INFO @ Fri, 05 Jul 2019 10:42:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:42:52: #1 finished! INFO @ Fri, 05 Jul 2019 10:42:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:42:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:42:55: 40000000 INFO @ Fri, 05 Jul 2019 10:43:05: #2 number of paired peaks: 100212 INFO @ Fri, 05 Jul 2019 10:43:05: start model_add_line... INFO @ Fri, 05 Jul 2019 10:43:06: start X-correlation... INFO @ Fri, 05 Jul 2019 10:43:06: end of X-cor INFO @ Fri, 05 Jul 2019 10:43:06: #2 finished! INFO @ Fri, 05 Jul 2019 10:43:06: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 10:43:06: #2 alternative fragment length(s) may be 3,135 bps INFO @ Fri, 05 Jul 2019 10:43:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.10_model.r INFO @ Fri, 05 Jul 2019 10:43:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:43:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:43:06: 41000000 INFO @ Fri, 05 Jul 2019 10:43:17: 42000000 INFO @ Fri, 05 Jul 2019 10:43:29: 43000000 INFO @ Fri, 05 Jul 2019 10:43:39: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 10:43:39: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 10:43:39: #1 total tags in treatment: 43910888 INFO @ Fri, 05 Jul 2019 10:43:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:43:39: #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 10:43:40: #1 tags after filtering in treatment: 43910705 INFO @ Fri, 05 Jul 2019 10:43:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:43:40: #1 finished! INFO @ Fri, 05 Jul 2019 10:43:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:43:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:43:52: #2 number of paired peaks: 100212 INFO @ Fri, 05 Jul 2019 10:43:52: start model_add_line... INFO @ Fri, 05 Jul 2019 10:43:54: start X-correlation... INFO @ Fri, 05 Jul 2019 10:43:54: end of X-cor INFO @ Fri, 05 Jul 2019 10:43:54: #2 finished! INFO @ Fri, 05 Jul 2019 10:43:54: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 10:43:54: #2 alternative fragment length(s) may be 3,135 bps INFO @ Fri, 05 Jul 2019 10:43:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.05_model.r INFO @ Fri, 05 Jul 2019 10:43:54: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:43:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:44:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:45:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:46:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:46:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.20_peaks.xls INFO @ Fri, 05 Jul 2019 10:46:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:46:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.20_summits.bed INFO @ Fri, 05 Jul 2019 10:46:19: Done! pass1 - making usageList (130 chroms): 15 millis pass2 - checking and writing primary data (43699 records, 4 fields): 70 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:46:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.10_peaks.xls INFO @ Fri, 05 Jul 2019 10:46:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:46:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.10_summits.bed INFO @ Fri, 05 Jul 2019 10:46:56: Done! pass1 - making usageList (156 chroms): 16 millis pass2 - checking and writing primary data (62966 records, 4 fields): 93 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:47:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.05_peaks.xls INFO @ Fri, 05 Jul 2019 10:47:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:47:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101984/ERX101984.05_summits.bed INFO @ Fri, 05 Jul 2019 10:47:32: Done! pass1 - making usageList (183 chroms): 19 millis pass2 - checking and writing primary data (81493 records, 4 fields): 119 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。