Job ID = 2001716 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T00:40:34 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 ) 2019-07-05T00:43:46 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 ) 2019-07-05T00:48:52 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 : 111,627,368 reads read : 111,627,368 reads written : 111,627,368 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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:04:45 111627368 reads; of these: 111627368 (100.00%) were unpaired; of these: 1963396 (1.76%) aligned 0 times 98278751 (88.04%) aligned exactly 1 time 11385221 (10.20%) aligned >1 times 98.24% overall alignment rate Time searching: 01:04:46 Overall time: 01:04:46 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] 74776588 / 109663972 = 0.6819 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 12:18:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.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 12:18:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:18:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:18:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.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 12:18:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:18:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:18:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.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 12:18:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:18:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:18:36: 1000000 INFO @ Fri, 05 Jul 2019 12:18:36: 1000000 INFO @ Fri, 05 Jul 2019 12:18:38: 1000000 INFO @ Fri, 05 Jul 2019 12:18:44: 2000000 INFO @ Fri, 05 Jul 2019 12:18:45: 2000000 INFO @ Fri, 05 Jul 2019 12:18:46: 2000000 INFO @ Fri, 05 Jul 2019 12:18:52: 3000000 INFO @ Fri, 05 Jul 2019 12:18:54: 3000000 INFO @ Fri, 05 Jul 2019 12:18:55: 3000000 INFO @ Fri, 05 Jul 2019 12:19:00: 4000000 INFO @ Fri, 05 Jul 2019 12:19:03: 4000000 INFO @ Fri, 05 Jul 2019 12:19:03: 4000000 INFO @ Fri, 05 Jul 2019 12:19:08: 5000000 INFO @ Fri, 05 Jul 2019 12:19:12: 5000000 INFO @ Fri, 05 Jul 2019 12:19:12: 5000000 INFO @ Fri, 05 Jul 2019 12:19:16: 6000000 INFO @ Fri, 05 Jul 2019 12:19:21: 6000000 INFO @ Fri, 05 Jul 2019 12:19:21: 6000000 INFO @ Fri, 05 Jul 2019 12:19:24: 7000000 INFO @ Fri, 05 Jul 2019 12:19:29: 7000000 INFO @ Fri, 05 Jul 2019 12:19:30: 7000000 INFO @ Fri, 05 Jul 2019 12:19:32: 8000000 INFO @ Fri, 05 Jul 2019 12:19:38: 8000000 INFO @ Fri, 05 Jul 2019 12:19:40: 8000000 INFO @ Fri, 05 Jul 2019 12:19:40: 9000000 INFO @ Fri, 05 Jul 2019 12:19:47: 9000000 INFO @ Fri, 05 Jul 2019 12:19:48: 10000000 INFO @ Fri, 05 Jul 2019 12:19:50: 9000000 INFO @ Fri, 05 Jul 2019 12:19:56: 10000000 INFO @ Fri, 05 Jul 2019 12:19:56: 11000000 INFO @ Fri, 05 Jul 2019 12:19:59: 10000000 INFO @ Fri, 05 Jul 2019 12:20:04: 12000000 INFO @ Fri, 05 Jul 2019 12:20:04: 11000000 INFO @ Fri, 05 Jul 2019 12:20:09: 11000000 INFO @ Fri, 05 Jul 2019 12:20:13: 12000000 INFO @ Fri, 05 Jul 2019 12:20:14: 13000000 INFO @ Fri, 05 Jul 2019 12:20:20: 12000000 INFO @ Fri, 05 Jul 2019 12:20:21: 13000000 INFO @ Fri, 05 Jul 2019 12:20:21: 14000000 INFO @ Fri, 05 Jul 2019 12:20:29: 15000000 INFO @ Fri, 05 Jul 2019 12:20:29: 13000000 INFO @ Fri, 05 Jul 2019 12:20:29: 14000000 INFO @ Fri, 05 Jul 2019 12:20:37: 16000000 INFO @ Fri, 05 Jul 2019 12:20:38: 15000000 INFO @ Fri, 05 Jul 2019 12:20:39: 14000000 INFO @ Fri, 05 Jul 2019 12:20:45: 17000000 INFO @ Fri, 05 Jul 2019 12:20:46: 16000000 INFO @ Fri, 05 Jul 2019 12:20:49: 15000000 INFO @ Fri, 05 Jul 2019 12:20:53: 18000000 INFO @ Fri, 05 Jul 2019 12:20:54: 17000000 INFO @ Fri, 05 Jul 2019 12:20:59: 16000000 INFO @ Fri, 05 Jul 2019 12:21:00: 19000000 INFO @ Fri, 05 Jul 2019 12:21:03: 18000000 INFO @ Fri, 05 Jul 2019 12:21:08: 20000000 INFO @ Fri, 05 Jul 2019 12:21:09: 17000000 INFO @ Fri, 05 Jul 2019 12:21:11: 19000000 INFO @ Fri, 05 Jul 2019 12:21:15: 21000000 INFO @ Fri, 05 Jul 2019 12:21:19: 18000000 INFO @ Fri, 05 Jul 2019 12:21:19: 20000000 INFO @ Fri, 05 Jul 2019 12:21:23: 22000000 INFO @ Fri, 05 Jul 2019 12:21:27: 21000000 INFO @ Fri, 05 Jul 2019 12:21:28: 19000000 INFO @ Fri, 05 Jul 2019 12:21:30: 23000000 INFO @ Fri, 05 Jul 2019 12:21:35: 22000000 INFO @ Fri, 05 Jul 2019 12:21:38: 24000000 INFO @ Fri, 05 Jul 2019 12:21:38: 20000000 INFO @ Fri, 05 Jul 2019 12:21:43: 23000000 INFO @ Fri, 05 Jul 2019 12:21:45: 25000000 INFO @ Fri, 05 Jul 2019 12:21:47: 21000000 INFO @ Fri, 05 Jul 2019 12:21:51: 24000000 INFO @ Fri, 05 Jul 2019 12:21:53: 26000000 INFO @ Fri, 05 Jul 2019 12:21:57: 22000000 INFO @ Fri, 05 Jul 2019 12:22:00: 25000000 INFO @ Fri, 05 Jul 2019 12:22:00: 27000000 INFO @ Fri, 05 Jul 2019 12:22:07: 23000000 INFO @ Fri, 05 Jul 2019 12:22:08: 28000000 INFO @ Fri, 05 Jul 2019 12:22:08: 26000000 INFO @ Fri, 05 Jul 2019 12:22:15: 29000000 INFO @ Fri, 05 Jul 2019 12:22:17: 27000000 INFO @ Fri, 05 Jul 2019 12:22:17: 24000000 INFO @ Fri, 05 Jul 2019 12:22:23: 30000000 INFO @ Fri, 05 Jul 2019 12:22:25: 28000000 INFO @ Fri, 05 Jul 2019 12:22:27: 25000000 INFO @ Fri, 05 Jul 2019 12:22:33: 31000000 INFO @ Fri, 05 Jul 2019 12:22:34: 29000000 INFO @ Fri, 05 Jul 2019 12:22:37: 26000000 INFO @ Fri, 05 Jul 2019 12:22:42: 30000000 INFO @ Fri, 05 Jul 2019 12:22:43: 32000000 INFO @ Fri, 05 Jul 2019 12:22:47: 27000000 INFO @ Fri, 05 Jul 2019 12:22:50: 31000000 INFO @ Fri, 05 Jul 2019 12:22:52: 33000000 INFO @ Fri, 05 Jul 2019 12:22:57: 28000000 INFO @ Fri, 05 Jul 2019 12:22:59: 32000000 INFO @ Fri, 05 Jul 2019 12:23:02: 34000000 INFO @ Fri, 05 Jul 2019 12:23:07: 33000000 INFO @ Fri, 05 Jul 2019 12:23:07: 29000000 INFO @ Fri, 05 Jul 2019 12:23:12: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 12:23:12: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 12:23:12: #1 total tags in treatment: 34887384 INFO @ Fri, 05 Jul 2019 12:23:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:23:12: #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 12:23:13: #1 tags after filtering in treatment: 34887171 INFO @ Fri, 05 Jul 2019 12:23:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:23:13: #1 finished! INFO @ Fri, 05 Jul 2019 12:23:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:23:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:23:16: 34000000 INFO @ Fri, 05 Jul 2019 12:23:18: 30000000 INFO @ Fri, 05 Jul 2019 12:23:22: #2 number of paired peaks: 76222 INFO @ Fri, 05 Jul 2019 12:23:22: start model_add_line... INFO @ Fri, 05 Jul 2019 12:23:23: start X-correlation... INFO @ Fri, 05 Jul 2019 12:23:23: end of X-cor INFO @ Fri, 05 Jul 2019 12:23:23: #2 finished! INFO @ Fri, 05 Jul 2019 12:23:23: #2 predicted fragment length is 137 bps INFO @ Fri, 05 Jul 2019 12:23:23: #2 alternative fragment length(s) may be 4,137 bps INFO @ Fri, 05 Jul 2019 12:23:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.10_model.r INFO @ Fri, 05 Jul 2019 12:23:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:23:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:23:24: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 12:23:24: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 12:23:24: #1 total tags in treatment: 34887384 INFO @ Fri, 05 Jul 2019 12:23:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:23:24: #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 12:23:25: #1 tags after filtering in treatment: 34887171 INFO @ Fri, 05 Jul 2019 12:23:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:23:25: #1 finished! INFO @ Fri, 05 Jul 2019 12:23:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:23:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:23:27: 31000000 INFO @ Fri, 05 Jul 2019 12:23:34: #2 number of paired peaks: 76222 INFO @ Fri, 05 Jul 2019 12:23:34: start model_add_line... INFO @ Fri, 05 Jul 2019 12:23:35: start X-correlation... INFO @ Fri, 05 Jul 2019 12:23:35: end of X-cor INFO @ Fri, 05 Jul 2019 12:23:35: #2 finished! INFO @ Fri, 05 Jul 2019 12:23:35: #2 predicted fragment length is 137 bps INFO @ Fri, 05 Jul 2019 12:23:35: #2 alternative fragment length(s) may be 4,137 bps INFO @ Fri, 05 Jul 2019 12:23:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.20_model.r INFO @ Fri, 05 Jul 2019 12:23:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:23:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:23:38: 32000000 INFO @ Fri, 05 Jul 2019 12:23:48: 33000000 INFO @ Fri, 05 Jul 2019 12:23:58: 34000000 INFO @ Fri, 05 Jul 2019 12:24:07: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 12:24:07: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 12:24:07: #1 total tags in treatment: 34887384 INFO @ Fri, 05 Jul 2019 12:24:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:24:07: #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 12:24:08: #1 tags after filtering in treatment: 34887171 INFO @ Fri, 05 Jul 2019 12:24:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:24:08: #1 finished! INFO @ Fri, 05 Jul 2019 12:24:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:24:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:24:17: #2 number of paired peaks: 76222 INFO @ Fri, 05 Jul 2019 12:24:17: start model_add_line... INFO @ Fri, 05 Jul 2019 12:24:18: start X-correlation... INFO @ Fri, 05 Jul 2019 12:24:18: end of X-cor INFO @ Fri, 05 Jul 2019 12:24:18: #2 finished! INFO @ Fri, 05 Jul 2019 12:24:18: #2 predicted fragment length is 137 bps INFO @ Fri, 05 Jul 2019 12:24:18: #2 alternative fragment length(s) may be 4,137 bps INFO @ Fri, 05 Jul 2019 12:24:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.05_model.r INFO @ Fri, 05 Jul 2019 12:24:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:24:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:25:12: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:25:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:26:09: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:26:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:26:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:26:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.10_summits.bed INFO @ Fri, 05 Jul 2019 12:26:16: Done! pass1 - making usageList (154 chroms): 13 millis pass2 - checking and writing primary data (51657 records, 4 fields): 80 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:26:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:26:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:26:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.20_summits.bed INFO @ Fri, 05 Jul 2019 12:26:33: Done! pass1 - making usageList (120 chroms): 8 millis pass2 - checking and writing primary data (37406 records, 4 fields): 108 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:27:17: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:27:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:27:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102021/ERX102021.05_summits.bed INFO @ Fri, 05 Jul 2019 12:27:19: Done! pass1 - making usageList (176 chroms): 14 millis pass2 - checking and writing primary data (65711 records, 4 fields): 116 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。