Job ID = 2002124 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T00:41:41 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 ) 2019-07-05T00:41:41 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 ) 2019-07-05T00:41:41 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 ) 2019-07-05T00:41:41 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 ) 2019-07-05T00:43:07 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 ) 2019-07-05T00:56:30 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 ) 2019-07-05T01:29:42 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 ) 2019-07-05T01:29:43 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 ) 2019-07-05T01:41:45 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 ) spots read : 118,593,179 reads read : 118,593,179 reads written : 118,593,179 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: 01:13:08 118593179 reads; of these: 118593179 (100.00%) were unpaired; of these: 2039515 (1.72%) aligned 0 times 103573156 (87.33%) aligned exactly 1 time 12980508 (10.95%) aligned >1 times 98.28% overall alignment rate Time searching: 01:13:11 Overall time: 01:13:11 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] 69766034 / 116553664 = 0.5986 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 12:37:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.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 12:37:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:37:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:37:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.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 12:37:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:37:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:37:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.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 12:37:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:37:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:37:47: 1000000 INFO @ Fri, 05 Jul 2019 12:37:48: 1000000 INFO @ Fri, 05 Jul 2019 12:37:48: 1000000 INFO @ Fri, 05 Jul 2019 12:37:58: 2000000 INFO @ Fri, 05 Jul 2019 12:37:58: 2000000 INFO @ Fri, 05 Jul 2019 12:37:59: 2000000 INFO @ Fri, 05 Jul 2019 12:38:08: 3000000 INFO @ Fri, 05 Jul 2019 12:38:08: 3000000 INFO @ Fri, 05 Jul 2019 12:38:09: 3000000 INFO @ Fri, 05 Jul 2019 12:38:19: 4000000 INFO @ Fri, 05 Jul 2019 12:38:19: 4000000 INFO @ Fri, 05 Jul 2019 12:38:21: 4000000 INFO @ Fri, 05 Jul 2019 12:38:30: 5000000 INFO @ Fri, 05 Jul 2019 12:38:31: 5000000 INFO @ Fri, 05 Jul 2019 12:38:32: 5000000 INFO @ Fri, 05 Jul 2019 12:38:41: 6000000 INFO @ Fri, 05 Jul 2019 12:38:43: 6000000 INFO @ Fri, 05 Jul 2019 12:38:43: 6000000 INFO @ Fri, 05 Jul 2019 12:38:51: 7000000 INFO @ Fri, 05 Jul 2019 12:38:54: 7000000 INFO @ Fri, 05 Jul 2019 12:38:54: 7000000 INFO @ Fri, 05 Jul 2019 12:39:02: 8000000 INFO @ Fri, 05 Jul 2019 12:39:06: 8000000 INFO @ Fri, 05 Jul 2019 12:39:06: 8000000 INFO @ Fri, 05 Jul 2019 12:39:13: 9000000 INFO @ Fri, 05 Jul 2019 12:39:18: 9000000 INFO @ Fri, 05 Jul 2019 12:39:18: 9000000 INFO @ Fri, 05 Jul 2019 12:39:23: 10000000 INFO @ Fri, 05 Jul 2019 12:39:29: 10000000 INFO @ Fri, 05 Jul 2019 12:39:29: 10000000 INFO @ Fri, 05 Jul 2019 12:39:33: 11000000 INFO @ Fri, 05 Jul 2019 12:39:40: 11000000 INFO @ Fri, 05 Jul 2019 12:39:40: 11000000 INFO @ Fri, 05 Jul 2019 12:39:43: 12000000 INFO @ Fri, 05 Jul 2019 12:39:51: 12000000 INFO @ Fri, 05 Jul 2019 12:39:51: 12000000 INFO @ Fri, 05 Jul 2019 12:39:54: 13000000 INFO @ Fri, 05 Jul 2019 12:40:02: 13000000 INFO @ Fri, 05 Jul 2019 12:40:02: 13000000 INFO @ Fri, 05 Jul 2019 12:40:04: 14000000 INFO @ Fri, 05 Jul 2019 12:40:12: 14000000 INFO @ Fri, 05 Jul 2019 12:40:13: 14000000 INFO @ Fri, 05 Jul 2019 12:40:14: 15000000 INFO @ Fri, 05 Jul 2019 12:40:23: 15000000 INFO @ Fri, 05 Jul 2019 12:40:23: 15000000 INFO @ Fri, 05 Jul 2019 12:40:25: 16000000 INFO @ Fri, 05 Jul 2019 12:40:33: 16000000 INFO @ Fri, 05 Jul 2019 12:40:34: 17000000 INFO @ Fri, 05 Jul 2019 12:40:35: 16000000 INFO @ Fri, 05 Jul 2019 12:40:43: 17000000 INFO @ Fri, 05 Jul 2019 12:40:45: 18000000 INFO @ Fri, 05 Jul 2019 12:40:47: 17000000 INFO @ Fri, 05 Jul 2019 12:40:54: 18000000 INFO @ Fri, 05 Jul 2019 12:40:55: 19000000 INFO @ Fri, 05 Jul 2019 12:40:58: 18000000 INFO @ Fri, 05 Jul 2019 12:41:05: 19000000 INFO @ Fri, 05 Jul 2019 12:41:06: 20000000 INFO @ Fri, 05 Jul 2019 12:41:09: 19000000 INFO @ Fri, 05 Jul 2019 12:41:15: 20000000 INFO @ Fri, 05 Jul 2019 12:41:17: 21000000 INFO @ Fri, 05 Jul 2019 12:41:20: 20000000 INFO @ Fri, 05 Jul 2019 12:41:26: 21000000 INFO @ Fri, 05 Jul 2019 12:41:28: 22000000 INFO @ Fri, 05 Jul 2019 12:41:31: 21000000 INFO @ Fri, 05 Jul 2019 12:41:36: 22000000 INFO @ Fri, 05 Jul 2019 12:41:38: 23000000 INFO @ Fri, 05 Jul 2019 12:41:41: 22000000 INFO @ Fri, 05 Jul 2019 12:41:46: 23000000 INFO @ Fri, 05 Jul 2019 12:41:48: 24000000 INFO @ Fri, 05 Jul 2019 12:41:52: 23000000 INFO @ Fri, 05 Jul 2019 12:41:56: 24000000 INFO @ Fri, 05 Jul 2019 12:41:58: 25000000 INFO @ Fri, 05 Jul 2019 12:42:03: 24000000 INFO @ Fri, 05 Jul 2019 12:42:06: 25000000 INFO @ Fri, 05 Jul 2019 12:42:08: 26000000 INFO @ Fri, 05 Jul 2019 12:42:13: 25000000 INFO @ Fri, 05 Jul 2019 12:42:16: 26000000 INFO @ Fri, 05 Jul 2019 12:42:19: 27000000 INFO @ Fri, 05 Jul 2019 12:42:23: 26000000 INFO @ Fri, 05 Jul 2019 12:42:26: 27000000 INFO @ Fri, 05 Jul 2019 12:42:29: 28000000 INFO @ Fri, 05 Jul 2019 12:42:34: 27000000 INFO @ Fri, 05 Jul 2019 12:42:36: 28000000 INFO @ Fri, 05 Jul 2019 12:42:39: 29000000 INFO @ Fri, 05 Jul 2019 12:42:44: 28000000 INFO @ Fri, 05 Jul 2019 12:42:46: 29000000 INFO @ Fri, 05 Jul 2019 12:42:49: 30000000 INFO @ Fri, 05 Jul 2019 12:42:54: 29000000 INFO @ Fri, 05 Jul 2019 12:42:57: 30000000 INFO @ Fri, 05 Jul 2019 12:42:58: 31000000 INFO @ Fri, 05 Jul 2019 12:43:05: 30000000 INFO @ Fri, 05 Jul 2019 12:43:07: 31000000 INFO @ Fri, 05 Jul 2019 12:43:09: 32000000 INFO @ Fri, 05 Jul 2019 12:43:15: 31000000 INFO @ Fri, 05 Jul 2019 12:43:18: 32000000 INFO @ Fri, 05 Jul 2019 12:43:18: 33000000 INFO @ Fri, 05 Jul 2019 12:43:26: 32000000 INFO @ Fri, 05 Jul 2019 12:43:28: 34000000 INFO @ Fri, 05 Jul 2019 12:43:28: 33000000 INFO @ Fri, 05 Jul 2019 12:43:37: 33000000 INFO @ Fri, 05 Jul 2019 12:43:38: 35000000 INFO @ Fri, 05 Jul 2019 12:43:39: 34000000 INFO @ Fri, 05 Jul 2019 12:43:47: 34000000 INFO @ Fri, 05 Jul 2019 12:43:48: 36000000 INFO @ Fri, 05 Jul 2019 12:43:50: 35000000 INFO @ Fri, 05 Jul 2019 12:43:58: 35000000 INFO @ Fri, 05 Jul 2019 12:43:58: 37000000 INFO @ Fri, 05 Jul 2019 12:44:00: 36000000 INFO @ Fri, 05 Jul 2019 12:44:08: 38000000 INFO @ Fri, 05 Jul 2019 12:44:08: 36000000 INFO @ Fri, 05 Jul 2019 12:44:10: 37000000 INFO @ Fri, 05 Jul 2019 12:44:17: 39000000 INFO @ Fri, 05 Jul 2019 12:44:19: 37000000 INFO @ Fri, 05 Jul 2019 12:44:20: 38000000 INFO @ Fri, 05 Jul 2019 12:44:27: 40000000 INFO @ Fri, 05 Jul 2019 12:44:29: 38000000 INFO @ Fri, 05 Jul 2019 12:44:31: 39000000 INFO @ Fri, 05 Jul 2019 12:44:37: 41000000 INFO @ Fri, 05 Jul 2019 12:44:39: 39000000 INFO @ Fri, 05 Jul 2019 12:44:41: 40000000 INFO @ Fri, 05 Jul 2019 12:44:47: 42000000 INFO @ Fri, 05 Jul 2019 12:44:49: 40000000 INFO @ Fri, 05 Jul 2019 12:44:52: 41000000 INFO @ Fri, 05 Jul 2019 12:44:57: 43000000 INFO @ Fri, 05 Jul 2019 12:45:00: 41000000 INFO @ Fri, 05 Jul 2019 12:45:03: 42000000 INFO @ Fri, 05 Jul 2019 12:45:07: 44000000 INFO @ Fri, 05 Jul 2019 12:45:10: 42000000 INFO @ Fri, 05 Jul 2019 12:45:13: 43000000 INFO @ Fri, 05 Jul 2019 12:45:17: 45000000 INFO @ Fri, 05 Jul 2019 12:45:20: 43000000 INFO @ Fri, 05 Jul 2019 12:45:24: 44000000 INFO @ Fri, 05 Jul 2019 12:45:26: 46000000 INFO @ Fri, 05 Jul 2019 12:45:30: 44000000 INFO @ Fri, 05 Jul 2019 12:45:34: 45000000 INFO @ Fri, 05 Jul 2019 12:45:35: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:45:35: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:45:35: #1 total tags in treatment: 46787630 INFO @ Fri, 05 Jul 2019 12:45:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:45:35: #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 12:45:36: #1 tags after filtering in treatment: 46787459 INFO @ Fri, 05 Jul 2019 12:45:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:45:36: #1 finished! INFO @ Fri, 05 Jul 2019 12:45:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:45:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:45:40: 45000000 INFO @ Fri, 05 Jul 2019 12:45:45: 46000000 INFO @ Fri, 05 Jul 2019 12:45:48: #2 number of paired peaks: 109940 INFO @ Fri, 05 Jul 2019 12:45:48: start model_add_line... INFO @ Fri, 05 Jul 2019 12:45:50: 46000000 INFO @ Fri, 05 Jul 2019 12:45:50: start X-correlation... INFO @ Fri, 05 Jul 2019 12:45:50: end of X-cor INFO @ Fri, 05 Jul 2019 12:45:50: #2 finished! INFO @ Fri, 05 Jul 2019 12:45:50: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 12:45:50: #2 alternative fragment length(s) may be 3,129 bps INFO @ Fri, 05 Jul 2019 12:45:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.20_model.r INFO @ Fri, 05 Jul 2019 12:45:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:45:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:45:53: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:45:53: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:45:53: #1 total tags in treatment: 46787630 INFO @ Fri, 05 Jul 2019 12:45:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:45:53: #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 12:45:54: #1 tags after filtering in treatment: 46787459 INFO @ Fri, 05 Jul 2019 12:45:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:45:54: #1 finished! INFO @ Fri, 05 Jul 2019 12:45:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:45:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:45:58: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:45:58: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:45:58: #1 total tags in treatment: 46787630 INFO @ Fri, 05 Jul 2019 12:45:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:45:58: #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 12:45:59: #1 tags after filtering in treatment: 46787459 INFO @ Fri, 05 Jul 2019 12:45:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:45:59: #1 finished! INFO @ Fri, 05 Jul 2019 12:45:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:45:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:46:07: #2 number of paired peaks: 109940 INFO @ Fri, 05 Jul 2019 12:46:07: start model_add_line... INFO @ Fri, 05 Jul 2019 12:46:08: start X-correlation... INFO @ Fri, 05 Jul 2019 12:46:09: end of X-cor INFO @ Fri, 05 Jul 2019 12:46:09: #2 finished! INFO @ Fri, 05 Jul 2019 12:46:09: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 12:46:09: #2 alternative fragment length(s) may be 3,129 bps INFO @ Fri, 05 Jul 2019 12:46:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.10_model.r INFO @ Fri, 05 Jul 2019 12:46:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:46:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:46:12: #2 number of paired peaks: 109940 INFO @ Fri, 05 Jul 2019 12:46:12: start model_add_line... INFO @ Fri, 05 Jul 2019 12:46:14: start X-correlation... INFO @ Fri, 05 Jul 2019 12:46:14: end of X-cor INFO @ Fri, 05 Jul 2019 12:46:14: #2 finished! INFO @ Fri, 05 Jul 2019 12:46:14: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 12:46:14: #2 alternative fragment length(s) may be 3,129 bps INFO @ Fri, 05 Jul 2019 12:46:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.05_model.r INFO @ Fri, 05 Jul 2019 12:46:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:46:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:48:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:48:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:48:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:49:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:49:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:49:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.20_summits.bed INFO @ Fri, 05 Jul 2019 12:49:38: Done! pass1 - making usageList (138 chroms): 11 millis pass2 - checking and writing primary data (44476 records, 4 fields): 66 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:49:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:49:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:49:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.10_summits.bed INFO @ Fri, 05 Jul 2019 12:49:51: Done! pass1 - making usageList (167 chroms): 14 millis pass2 - checking and writing primary data (67810 records, 4 fields): 89 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:49:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:50:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:50:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102026/ERX102026.05_summits.bed INFO @ Fri, 05 Jul 2019 12:50:01: Done! pass1 - making usageList (189 chroms): 18 millis pass2 - checking and writing primary data (90346 records, 4 fields): 117 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。