Job ID = 2001619 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T21:29:49 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 ) 2019-07-04T21:36:31 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 ) 2019-07-04T21:43:20 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 ) 2019-07-04T21:53:43 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 ) spots read : 116,840,675 reads read : 116,840,675 reads written : 116,840,675 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:51:06 116840675 reads; of these: 116840675 (100.00%) were unpaired; of these: 1996620 (1.71%) aligned 0 times 103317857 (88.43%) aligned exactly 1 time 11526198 (9.86%) aligned >1 times 98.29% overall alignment rate Time searching: 00:51:09 Overall time: 00:51:09 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] 79118204 / 114844055 = 0.6889 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 08:23:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.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 08:23:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:23:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:23:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.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 08:23:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:23:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:23:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.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 08:23:51: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:23:51: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:23:57: 1000000 INFO @ Fri, 05 Jul 2019 08:23:58: 1000000 INFO @ Fri, 05 Jul 2019 08:23:59: 1000000 INFO @ Fri, 05 Jul 2019 08:24:05: 2000000 INFO @ Fri, 05 Jul 2019 08:24:05: 2000000 INFO @ Fri, 05 Jul 2019 08:24:07: 2000000 INFO @ Fri, 05 Jul 2019 08:24:12: 3000000 INFO @ Fri, 05 Jul 2019 08:24:13: 3000000 INFO @ Fri, 05 Jul 2019 08:24:15: 3000000 INFO @ Fri, 05 Jul 2019 08:24:20: 4000000 INFO @ Fri, 05 Jul 2019 08:24:20: 4000000 INFO @ Fri, 05 Jul 2019 08:24:23: 4000000 INFO @ Fri, 05 Jul 2019 08:24:27: 5000000 INFO @ Fri, 05 Jul 2019 08:24:27: 5000000 INFO @ Fri, 05 Jul 2019 08:24:31: 5000000 INFO @ Fri, 05 Jul 2019 08:24:34: 6000000 INFO @ Fri, 05 Jul 2019 08:24:35: 6000000 INFO @ Fri, 05 Jul 2019 08:24:39: 6000000 INFO @ Fri, 05 Jul 2019 08:24:42: 7000000 INFO @ Fri, 05 Jul 2019 08:24:42: 7000000 INFO @ Fri, 05 Jul 2019 08:24:47: 7000000 INFO @ Fri, 05 Jul 2019 08:24:49: 8000000 INFO @ Fri, 05 Jul 2019 08:24:50: 8000000 INFO @ Fri, 05 Jul 2019 08:24:56: 8000000 INFO @ Fri, 05 Jul 2019 08:24:57: 9000000 INFO @ Fri, 05 Jul 2019 08:24:57: 9000000 INFO @ Fri, 05 Jul 2019 08:25:04: 9000000 INFO @ Fri, 05 Jul 2019 08:25:04: 10000000 INFO @ Fri, 05 Jul 2019 08:25:04: 10000000 INFO @ Fri, 05 Jul 2019 08:25:11: 11000000 INFO @ Fri, 05 Jul 2019 08:25:11: 11000000 INFO @ Fri, 05 Jul 2019 08:25:12: 10000000 INFO @ Fri, 05 Jul 2019 08:25:18: 12000000 INFO @ Fri, 05 Jul 2019 08:25:19: 12000000 INFO @ Fri, 05 Jul 2019 08:25:21: 11000000 INFO @ Fri, 05 Jul 2019 08:25:26: 13000000 INFO @ Fri, 05 Jul 2019 08:25:26: 13000000 INFO @ Fri, 05 Jul 2019 08:25:29: 12000000 INFO @ Fri, 05 Jul 2019 08:25:33: 14000000 INFO @ Fri, 05 Jul 2019 08:25:33: 14000000 INFO @ Fri, 05 Jul 2019 08:25:37: 13000000 INFO @ Fri, 05 Jul 2019 08:25:41: 15000000 INFO @ Fri, 05 Jul 2019 08:25:41: 15000000 INFO @ Fri, 05 Jul 2019 08:25:46: 14000000 INFO @ Fri, 05 Jul 2019 08:25:48: 16000000 INFO @ Fri, 05 Jul 2019 08:25:48: 16000000 INFO @ Fri, 05 Jul 2019 08:25:54: 15000000 INFO @ Fri, 05 Jul 2019 08:25:55: 17000000 INFO @ Fri, 05 Jul 2019 08:25:55: 17000000 INFO @ Fri, 05 Jul 2019 08:26:02: 16000000 INFO @ Fri, 05 Jul 2019 08:26:03: 18000000 INFO @ Fri, 05 Jul 2019 08:26:04: 18000000 INFO @ Fri, 05 Jul 2019 08:26:10: 17000000 INFO @ Fri, 05 Jul 2019 08:26:11: 19000000 INFO @ Fri, 05 Jul 2019 08:26:12: 19000000 INFO @ Fri, 05 Jul 2019 08:26:18: 18000000 INFO @ Fri, 05 Jul 2019 08:26:19: 20000000 INFO @ Fri, 05 Jul 2019 08:26:20: 20000000 INFO @ Fri, 05 Jul 2019 08:26:26: 19000000 INFO @ Fri, 05 Jul 2019 08:26:28: 21000000 INFO @ Fri, 05 Jul 2019 08:26:28: 21000000 INFO @ Fri, 05 Jul 2019 08:26:34: 20000000 INFO @ Fri, 05 Jul 2019 08:26:36: 22000000 INFO @ Fri, 05 Jul 2019 08:26:36: 22000000 INFO @ Fri, 05 Jul 2019 08:26:42: 21000000 INFO @ Fri, 05 Jul 2019 08:26:44: 23000000 INFO @ Fri, 05 Jul 2019 08:26:44: 23000000 INFO @ Fri, 05 Jul 2019 08:26:50: 22000000 INFO @ Fri, 05 Jul 2019 08:26:52: 24000000 INFO @ Fri, 05 Jul 2019 08:26:52: 24000000 INFO @ Fri, 05 Jul 2019 08:26:58: 23000000 INFO @ Fri, 05 Jul 2019 08:27:00: 25000000 INFO @ Fri, 05 Jul 2019 08:27:00: 25000000 INFO @ Fri, 05 Jul 2019 08:27:06: 24000000 INFO @ Fri, 05 Jul 2019 08:27:08: 26000000 INFO @ Fri, 05 Jul 2019 08:27:08: 26000000 INFO @ Fri, 05 Jul 2019 08:27:14: 25000000 INFO @ Fri, 05 Jul 2019 08:27:16: 27000000 INFO @ Fri, 05 Jul 2019 08:27:17: 27000000 INFO @ Fri, 05 Jul 2019 08:27:22: 26000000 INFO @ Fri, 05 Jul 2019 08:27:24: 28000000 INFO @ Fri, 05 Jul 2019 08:27:25: 28000000 INFO @ Fri, 05 Jul 2019 08:27:30: 27000000 INFO @ Fri, 05 Jul 2019 08:27:32: 29000000 INFO @ Fri, 05 Jul 2019 08:27:33: 29000000 INFO @ Fri, 05 Jul 2019 08:27:38: 28000000 INFO @ Fri, 05 Jul 2019 08:27:39: 30000000 INFO @ Fri, 05 Jul 2019 08:27:40: 30000000 INFO @ Fri, 05 Jul 2019 08:27:45: 29000000 INFO @ Fri, 05 Jul 2019 08:27:46: 31000000 INFO @ Fri, 05 Jul 2019 08:27:47: 31000000 INFO @ Fri, 05 Jul 2019 08:27:53: 30000000 INFO @ Fri, 05 Jul 2019 08:27:53: 32000000 INFO @ Fri, 05 Jul 2019 08:27:54: 32000000 INFO @ Fri, 05 Jul 2019 08:28:01: 33000000 INFO @ Fri, 05 Jul 2019 08:28:01: 31000000 INFO @ Fri, 05 Jul 2019 08:28:01: 33000000 INFO @ Fri, 05 Jul 2019 08:28:08: 34000000 INFO @ Fri, 05 Jul 2019 08:28:08: 34000000 INFO @ Fri, 05 Jul 2019 08:28:08: 32000000 INFO @ Fri, 05 Jul 2019 08:28:15: 35000000 INFO @ Fri, 05 Jul 2019 08:28:16: 35000000 INFO @ Fri, 05 Jul 2019 08:28:16: 33000000 INFO @ Fri, 05 Jul 2019 08:28:21: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 08:28:21: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 08:28:21: #1 total tags in treatment: 35725851 INFO @ Fri, 05 Jul 2019 08:28:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:28:21: #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 08:28:21: #1 tags after filtering in treatment: 35725647 INFO @ Fri, 05 Jul 2019 08:28:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:28:21: #1 finished! INFO @ Fri, 05 Jul 2019 08:28:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:28:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:28:22: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 08:28:22: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 08:28:22: #1 total tags in treatment: 35725851 INFO @ Fri, 05 Jul 2019 08:28:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:28:22: #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 08:28:23: #1 tags after filtering in treatment: 35725647 INFO @ Fri, 05 Jul 2019 08:28:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:28:23: #1 finished! INFO @ Fri, 05 Jul 2019 08:28:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:28:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:28:24: 34000000 INFO @ Fri, 05 Jul 2019 08:28:30: #2 number of paired peaks: 68640 INFO @ Fri, 05 Jul 2019 08:28:30: start model_add_line... INFO @ Fri, 05 Jul 2019 08:28:31: start X-correlation... INFO @ Fri, 05 Jul 2019 08:28:31: end of X-cor INFO @ Fri, 05 Jul 2019 08:28:31: #2 finished! INFO @ Fri, 05 Jul 2019 08:28:31: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 08:28:31: #2 alternative fragment length(s) may be 4,136 bps INFO @ Fri, 05 Jul 2019 08:28:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.10_model.r INFO @ Fri, 05 Jul 2019 08:28:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:28:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:28:31: #2 number of paired peaks: 68640 INFO @ Fri, 05 Jul 2019 08:28:31: start model_add_line... INFO @ Fri, 05 Jul 2019 08:28:32: 35000000 INFO @ Fri, 05 Jul 2019 08:28:32: start X-correlation... INFO @ Fri, 05 Jul 2019 08:28:32: end of X-cor INFO @ Fri, 05 Jul 2019 08:28:32: #2 finished! INFO @ Fri, 05 Jul 2019 08:28:32: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 08:28:32: #2 alternative fragment length(s) may be 4,136 bps INFO @ Fri, 05 Jul 2019 08:28:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.05_model.r INFO @ Fri, 05 Jul 2019 08:28:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:28:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:28:37: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 08:28:37: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 08:28:37: #1 total tags in treatment: 35725851 INFO @ Fri, 05 Jul 2019 08:28:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:28:37: #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 08:28:38: #1 tags after filtering in treatment: 35725647 INFO @ Fri, 05 Jul 2019 08:28:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:28:38: #1 finished! INFO @ Fri, 05 Jul 2019 08:28:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:28:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:28:46: #2 number of paired peaks: 68640 INFO @ Fri, 05 Jul 2019 08:28:46: start model_add_line... INFO @ Fri, 05 Jul 2019 08:28:47: start X-correlation... INFO @ Fri, 05 Jul 2019 08:28:47: end of X-cor INFO @ Fri, 05 Jul 2019 08:28:47: #2 finished! INFO @ Fri, 05 Jul 2019 08:28:47: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 08:28:47: #2 alternative fragment length(s) may be 4,136 bps INFO @ Fri, 05 Jul 2019 08:28:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.20_model.r INFO @ Fri, 05 Jul 2019 08:28:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:28:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:30:12: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:30:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:30:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:31:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.10_peaks.xls INFO @ Fri, 05 Jul 2019 08:31:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:31:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.10_summits.bed INFO @ Fri, 05 Jul 2019 08:31:08: Done! pass1 - making usageList (151 chroms): 17 millis pass2 - checking and writing primary data (50517 records, 4 fields): 76 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:31:17: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.05_peaks.xls INFO @ Fri, 05 Jul 2019 08:31:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:31:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.05_summits.bed INFO @ Fri, 05 Jul 2019 08:31:19: Done! pass1 - making usageList (167 chroms): 12 millis pass2 - checking and writing primary data (60653 records, 4 fields): 82 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:31:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.20_peaks.xls INFO @ Fri, 05 Jul 2019 08:31:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:31:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101941/ERX101941.20_summits.bed INFO @ Fri, 05 Jul 2019 08:31:23: Done! pass1 - making usageList (126 chroms): 7 millis pass2 - checking and writing primary data (37921 records, 4 fields): 53 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。