Job ID = 2001573 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T20:19:39 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 ) 2019-07-04T21:18:53 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 : 192,024,642 reads read : 192,024,642 reads written : 192,024,642 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: 00:00:02 Multiseed full-index search: 03:09:35 192024642 reads; of these: 192024642 (100.00%) were unpaired; of these: 4794165 (2.50%) aligned 0 times 136299160 (70.98%) aligned exactly 1 time 50931317 (26.52%) aligned >1 times 97.50% overall alignment rate Time searching: 03:09:40 Overall time: 03:09:40 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 80 files... [bam_rmdupse_core] 29407730 / 187230477 = 0.1571 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 11:20:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.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 11:20:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:20:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:20:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.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 11:20:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:20:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:20:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.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 11:20:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:20:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:20:23: 1000000 INFO @ Fri, 05 Jul 2019 11:20:24: 1000000 INFO @ Fri, 05 Jul 2019 11:20:25: 1000000 INFO @ Fri, 05 Jul 2019 11:20:30: 2000000 INFO @ Fri, 05 Jul 2019 11:20:32: 2000000 INFO @ Fri, 05 Jul 2019 11:20:33: 2000000 INFO @ Fri, 05 Jul 2019 11:20:37: 3000000 INFO @ Fri, 05 Jul 2019 11:20:39: 3000000 INFO @ Fri, 05 Jul 2019 11:20:40: 3000000 INFO @ Fri, 05 Jul 2019 11:20:45: 4000000 INFO @ Fri, 05 Jul 2019 11:20:47: 4000000 INFO @ Fri, 05 Jul 2019 11:20:48: 4000000 INFO @ Fri, 05 Jul 2019 11:20:53: 5000000 INFO @ Fri, 05 Jul 2019 11:20:55: 5000000 INFO @ Fri, 05 Jul 2019 11:20:56: 5000000 INFO @ Fri, 05 Jul 2019 11:21:01: 6000000 INFO @ Fri, 05 Jul 2019 11:21:02: 6000000 INFO @ Fri, 05 Jul 2019 11:21:04: 6000000 INFO @ Fri, 05 Jul 2019 11:21:08: 7000000 INFO @ Fri, 05 Jul 2019 11:21:10: 7000000 INFO @ Fri, 05 Jul 2019 11:21:11: 7000000 INFO @ Fri, 05 Jul 2019 11:21:16: 8000000 INFO @ Fri, 05 Jul 2019 11:21:18: 8000000 INFO @ Fri, 05 Jul 2019 11:21:19: 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05 Jul 2019 11:36:58: 128000000 INFO @ Fri, 05 Jul 2019 11:37:05: 138000000 INFO @ Fri, 05 Jul 2019 11:37:05: 130000000 INFO @ Fri, 05 Jul 2019 11:37:06: 129000000 INFO @ Fri, 05 Jul 2019 11:37:12: 139000000 INFO @ Fri, 05 Jul 2019 11:37:12: 131000000 INFO @ Fri, 05 Jul 2019 11:37:13: 130000000 INFO @ Fri, 05 Jul 2019 11:37:19: 140000000 INFO @ Fri, 05 Jul 2019 11:37:19: 132000000 INFO @ Fri, 05 Jul 2019 11:37:20: 131000000 INFO @ Fri, 05 Jul 2019 11:37:26: 141000000 INFO @ Fri, 05 Jul 2019 11:37:26: 133000000 INFO @ Fri, 05 Jul 2019 11:37:27: 132000000 INFO @ Fri, 05 Jul 2019 11:37:33: 142000000 INFO @ Fri, 05 Jul 2019 11:37:33: 134000000 INFO @ Fri, 05 Jul 2019 11:37:34: 133000000 INFO @ Fri, 05 Jul 2019 11:37:40: 143000000 INFO @ Fri, 05 Jul 2019 11:37:40: 135000000 INFO @ Fri, 05 Jul 2019 11:37:41: 134000000 INFO @ Fri, 05 Jul 2019 11:37:47: 144000000 INFO @ Fri, 05 Jul 2019 11:37:47: 136000000 INFO @ Fri, 05 Jul 2019 11:37:48: 135000000 INFO @ Fri, 05 Jul 2019 11:37:54: 145000000 INFO @ Fri, 05 Jul 2019 11:37:54: 137000000 INFO @ Fri, 05 Jul 2019 11:37:55: 136000000 INFO @ Fri, 05 Jul 2019 11:38:01: 138000000 INFO @ Fri, 05 Jul 2019 11:38:01: 146000000 INFO @ Fri, 05 Jul 2019 11:38:02: 137000000 INFO @ Fri, 05 Jul 2019 11:38:08: 139000000 INFO @ Fri, 05 Jul 2019 11:38:08: 147000000 INFO @ Fri, 05 Jul 2019 11:38:10: 138000000 INFO @ Fri, 05 Jul 2019 11:38:15: 140000000 INFO @ Fri, 05 Jul 2019 11:38:15: 148000000 INFO @ Fri, 05 Jul 2019 11:38:16: 139000000 INFO @ Fri, 05 Jul 2019 11:38:22: 149000000 INFO @ Fri, 05 Jul 2019 11:38:22: 141000000 INFO @ Fri, 05 Jul 2019 11:38:23: 140000000 INFO @ Fri, 05 Jul 2019 11:38:29: 150000000 INFO @ Fri, 05 Jul 2019 11:38:29: 142000000 INFO @ Fri, 05 Jul 2019 11:38:30: 141000000 INFO @ Fri, 05 Jul 2019 11:38:36: 143000000 INFO @ Fri, 05 Jul 2019 11:38:36: 151000000 INFO @ Fri, 05 Jul 2019 11:38:37: 142000000 INFO @ Fri, 05 Jul 2019 11:38:43: 144000000 INFO @ Fri, 05 Jul 2019 11:38:44: 152000000 INFO @ Fri, 05 Jul 2019 11:38:44: 143000000 INFO @ Fri, 05 Jul 2019 11:38:50: 145000000 INFO @ Fri, 05 Jul 2019 11:38:51: 153000000 INFO @ Fri, 05 Jul 2019 11:38:51: 144000000 INFO @ Fri, 05 Jul 2019 11:38:57: 146000000 INFO @ Fri, 05 Jul 2019 11:38:58: 154000000 INFO @ Fri, 05 Jul 2019 11:38:58: 145000000 INFO @ Fri, 05 Jul 2019 11:39:05: 147000000 INFO @ Fri, 05 Jul 2019 11:39:05: 155000000 INFO @ Fri, 05 Jul 2019 11:39:06: 146000000 INFO @ Fri, 05 Jul 2019 11:39:12: 148000000 INFO @ Fri, 05 Jul 2019 11:39:12: 156000000 INFO @ Fri, 05 Jul 2019 11:39:13: 147000000 INFO @ Fri, 05 Jul 2019 11:39:19: 149000000 INFO @ Fri, 05 Jul 2019 11:39:20: 157000000 INFO @ Fri, 05 Jul 2019 11:39:20: 148000000 INFO @ Fri, 05 Jul 2019 11:39:26: 150000000 INFO @ Fri, 05 Jul 2019 11:39:27: 149000000 INFO @ Fri, 05 Jul 2019 11:39:28: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:39:28: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:39:28: #1 total tags in treatment: 157822747 INFO @ Fri, 05 Jul 2019 11:39:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:39:28: #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 11:39:31: #1 tags after filtering in treatment: 157822712 INFO @ Fri, 05 Jul 2019 11:39:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:39:31: #1 finished! INFO @ Fri, 05 Jul 2019 11:39:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:39:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:39:33: 151000000 INFO @ Fri, 05 Jul 2019 11:39:34: 150000000 INFO @ Fri, 05 Jul 2019 11:39:40: 152000000 INFO @ Fri, 05 Jul 2019 11:39:41: 151000000 INFO @ Fri, 05 Jul 2019 11:39:46: #2 number of paired peaks: 10814 INFO @ Fri, 05 Jul 2019 11:39:46: start model_add_line... INFO @ Fri, 05 Jul 2019 11:39:47: 153000000 INFO @ Fri, 05 Jul 2019 11:39:48: start X-correlation... INFO @ Fri, 05 Jul 2019 11:39:48: end of X-cor INFO @ Fri, 05 Jul 2019 11:39:48: #2 finished! INFO @ Fri, 05 Jul 2019 11:39:48: #2 predicted fragment length is 111 bps INFO @ Fri, 05 Jul 2019 11:39:48: #2 alternative fragment length(s) may be 2,111 bps INFO @ Fri, 05 Jul 2019 11:39:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.05_model.r INFO @ Fri, 05 Jul 2019 11:39:48: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:39:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:39:48: 152000000 INFO @ Fri, 05 Jul 2019 11:39:54: 154000000 INFO @ Fri, 05 Jul 2019 11:39:55: 153000000 INFO @ Fri, 05 Jul 2019 11:40:01: 155000000 INFO @ Fri, 05 Jul 2019 11:40:02: 154000000 INFO @ Fri, 05 Jul 2019 11:40:08: 156000000 INFO @ Fri, 05 Jul 2019 11:40:09: 155000000 INFO @ Fri, 05 Jul 2019 11:40:15: 157000000 INFO @ Fri, 05 Jul 2019 11:40:16: 156000000 INFO @ Fri, 05 Jul 2019 11:40:23: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:40:23: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:40:23: #1 total tags in treatment: 157822747 INFO @ Fri, 05 Jul 2019 11:40:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:40:23: #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 11:40:23: 157000000 INFO @ Fri, 05 Jul 2019 11:40:26: #1 tags after filtering in treatment: 157822712 INFO @ Fri, 05 Jul 2019 11:40:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:40:26: #1 finished! INFO @ Fri, 05 Jul 2019 11:40:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:40:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:40:32: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:40:32: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:40:32: #1 total tags in treatment: 157822747 INFO @ Fri, 05 Jul 2019 11:40:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:40:32: #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 11:40:35: #1 tags after filtering in treatment: 157822712 INFO @ Fri, 05 Jul 2019 11:40:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:40:35: #1 finished! INFO @ Fri, 05 Jul 2019 11:40:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:40:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:40:42: #2 number of paired peaks: 10814 INFO @ Fri, 05 Jul 2019 11:40:42: start model_add_line... INFO @ Fri, 05 Jul 2019 11:40:43: start X-correlation... INFO @ Fri, 05 Jul 2019 11:40:43: end of X-cor INFO @ Fri, 05 Jul 2019 11:40:43: #2 finished! INFO @ Fri, 05 Jul 2019 11:40:43: #2 predicted fragment length is 111 bps INFO @ Fri, 05 Jul 2019 11:40:43: #2 alternative fragment length(s) may be 2,111 bps INFO @ Fri, 05 Jul 2019 11:40:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.10_model.r INFO @ Fri, 05 Jul 2019 11:40:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:40:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:40:50: #2 number of paired peaks: 10814 INFO @ Fri, 05 Jul 2019 11:40:50: start model_add_line... INFO @ Fri, 05 Jul 2019 11:40:52: start X-correlation... INFO @ Fri, 05 Jul 2019 11:40:52: end of X-cor INFO @ Fri, 05 Jul 2019 11:40:52: #2 finished! INFO @ Fri, 05 Jul 2019 11:40:52: #2 predicted fragment length is 111 bps INFO @ Fri, 05 Jul 2019 11:40:52: #2 alternative fragment length(s) may be 2,111 bps INFO @ Fri, 05 Jul 2019 11:40:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.20_model.r INFO @ Fri, 05 Jul 2019 11:40:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:40:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:47:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:48:42: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:48:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:52:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:52:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:52:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.05_summits.bed INFO @ Fri, 05 Jul 2019 11:52:46: Done! pass1 - making usageList (167 chroms): 6 millis pass2 - checking and writing primary data (25325 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:53:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:53:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:53:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.10_summits.bed INFO @ Fri, 05 Jul 2019 11:53:01: Done! pass1 - making usageList (91 chroms): 3 millis pass2 - checking and writing primary data (4937 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:53:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:53:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:53:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101916/ERX101916.20_summits.bed INFO @ Fri, 05 Jul 2019 11:53:05: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (1017 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。