Job ID = 2001567 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T20:06:03 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 ) 2019-07-04T20:06:03 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 ) 2019-07-04T20:06:03 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 ) 2019-07-04T20:07:18 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 ) 2019-07-04T20:07:18 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 ) 2019-07-04T20:10:23 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 ) 2019-07-04T20:12:49 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 ) 2019-07-04T20:18:25 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 : 119,636,098 reads read : 119,636,098 reads written : 119,636,098 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: 00:59:55 119636098 reads; of these: 119636098 (100.00%) were unpaired; of these: 2038826 (1.70%) aligned 0 times 105591110 (88.26%) aligned exactly 1 time 12006162 (10.04%) aligned >1 times 98.30% overall alignment rate Time searching: 00:59:58 Overall time: 00:59:58 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] 73185421 / 117597272 = 0.6223 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 07:23:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.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 07:23:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:23:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:23:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.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 07:23:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:23:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:23:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.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 07:23:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:23:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:23:27: 1000000 INFO @ Fri, 05 Jul 2019 07:23:28: 1000000 INFO @ Fri, 05 Jul 2019 07:23:29: 1000000 INFO @ Fri, 05 Jul 2019 07:23:37: 2000000 INFO @ Fri, 05 Jul 2019 07:23:37: 2000000 INFO @ Fri, 05 Jul 2019 07:23:38: 2000000 INFO @ Fri, 05 Jul 2019 07:23:45: 3000000 INFO @ Fri, 05 Jul 2019 07:23:47: 3000000 INFO @ Fri, 05 Jul 2019 07:23:47: 3000000 INFO @ Fri, 05 Jul 2019 07:23:54: 4000000 INFO @ Fri, 05 Jul 2019 07:23:56: 4000000 INFO @ Fri, 05 Jul 2019 07:23:56: 4000000 INFO @ Fri, 05 Jul 2019 07:24:03: 5000000 INFO @ Fri, 05 Jul 2019 07:24:05: 5000000 INFO @ Fri, 05 Jul 2019 07:24:06: 5000000 INFO @ Fri, 05 Jul 2019 07:24:11: 6000000 INFO @ Fri, 05 Jul 2019 07:24:14: 6000000 INFO @ Fri, 05 Jul 2019 07:24:14: 6000000 INFO @ Fri, 05 Jul 2019 07:24:20: 7000000 INFO @ Fri, 05 Jul 2019 07:24:22: 7000000 INFO @ Fri, 05 Jul 2019 07:24:23: 7000000 INFO @ Fri, 05 Jul 2019 07:24:29: 8000000 INFO @ Fri, 05 Jul 2019 07:24:31: 8000000 INFO @ Fri, 05 Jul 2019 07:24:32: 8000000 INFO @ Fri, 05 Jul 2019 07:24:38: 9000000 INFO @ Fri, 05 Jul 2019 07:24:39: 9000000 INFO @ Fri, 05 Jul 2019 07:24:41: 9000000 INFO @ Fri, 05 Jul 2019 07:24:47: 10000000 INFO @ Fri, 05 Jul 2019 07:24:48: 10000000 INFO @ Fri, 05 Jul 2019 07:24:50: 10000000 INFO @ Fri, 05 Jul 2019 07:24:56: 11000000 INFO @ Fri, 05 Jul 2019 07:24:56: 11000000 INFO @ Fri, 05 Jul 2019 07:24:59: 11000000 INFO @ Fri, 05 Jul 2019 07:25:04: 12000000 INFO @ Fri, 05 Jul 2019 07:25:05: 12000000 INFO @ Fri, 05 Jul 2019 07:25:08: 12000000 INFO @ Fri, 05 Jul 2019 07:25:13: 13000000 INFO @ Fri, 05 Jul 2019 07:25:14: 13000000 INFO @ Fri, 05 Jul 2019 07:25:17: 13000000 INFO @ Fri, 05 Jul 2019 07:25:22: 14000000 INFO @ Fri, 05 Jul 2019 07:25:23: 14000000 INFO @ Fri, 05 Jul 2019 07:25:25: 14000000 INFO @ Fri, 05 Jul 2019 07:25:31: 15000000 INFO @ Fri, 05 Jul 2019 07:25:32: 15000000 INFO @ Fri, 05 Jul 2019 07:25:34: 15000000 INFO @ Fri, 05 Jul 2019 07:25:41: 16000000 INFO @ Fri, 05 Jul 2019 07:25:42: 16000000 INFO @ Fri, 05 Jul 2019 07:25:44: 16000000 INFO @ Fri, 05 Jul 2019 07:25:50: 17000000 INFO @ Fri, 05 Jul 2019 07:25:51: 17000000 INFO @ Fri, 05 Jul 2019 07:25:52: 17000000 INFO @ Fri, 05 Jul 2019 07:25:59: 18000000 INFO @ Fri, 05 Jul 2019 07:26:00: 18000000 INFO @ Fri, 05 Jul 2019 07:26:01: 18000000 INFO @ Fri, 05 Jul 2019 07:26:08: 19000000 INFO @ Fri, 05 Jul 2019 07:26:09: 19000000 INFO @ Fri, 05 Jul 2019 07:26:09: 19000000 INFO @ Fri, 05 Jul 2019 07:26:18: 20000000 INFO @ Fri, 05 Jul 2019 07:26:18: 20000000 INFO @ Fri, 05 Jul 2019 07:26:19: 20000000 INFO @ Fri, 05 Jul 2019 07:26:26: 21000000 INFO @ Fri, 05 Jul 2019 07:26:27: 21000000 INFO @ Fri, 05 Jul 2019 07:26:29: 21000000 INFO @ Fri, 05 Jul 2019 07:26:35: 22000000 INFO @ Fri, 05 Jul 2019 07:26:37: 22000000 INFO @ Fri, 05 Jul 2019 07:26:38: 22000000 INFO @ Fri, 05 Jul 2019 07:26:43: 23000000 INFO @ Fri, 05 Jul 2019 07:26:46: 23000000 INFO @ Fri, 05 Jul 2019 07:26:47: 23000000 INFO @ Fri, 05 Jul 2019 07:26:52: 24000000 INFO @ Fri, 05 Jul 2019 07:26:55: 24000000 INFO @ Fri, 05 Jul 2019 07:26:57: 24000000 INFO @ Fri, 05 Jul 2019 07:27:00: 25000000 INFO @ Fri, 05 Jul 2019 07:27:04: 25000000 INFO @ Fri, 05 Jul 2019 07:27:06: 25000000 INFO @ Fri, 05 Jul 2019 07:27:09: 26000000 INFO @ Fri, 05 Jul 2019 07:27:13: 26000000 INFO @ Fri, 05 Jul 2019 07:27:15: 26000000 INFO @ Fri, 05 Jul 2019 07:27:17: 27000000 INFO @ Fri, 05 Jul 2019 07:27:22: 27000000 INFO @ Fri, 05 Jul 2019 07:27:24: 27000000 INFO @ Fri, 05 Jul 2019 07:27:25: 28000000 INFO @ Fri, 05 Jul 2019 07:27:31: 28000000 INFO @ Fri, 05 Jul 2019 07:27:33: 28000000 INFO @ Fri, 05 Jul 2019 07:27:34: 29000000 INFO @ Fri, 05 Jul 2019 07:27:41: 29000000 INFO @ Fri, 05 Jul 2019 07:27:42: 30000000 INFO @ Fri, 05 Jul 2019 07:27:43: 29000000 INFO @ Fri, 05 Jul 2019 07:27:51: 30000000 INFO @ Fri, 05 Jul 2019 07:27:51: 31000000 INFO @ Fri, 05 Jul 2019 07:27:52: 30000000 INFO @ Fri, 05 Jul 2019 07:28:00: 32000000 INFO @ Fri, 05 Jul 2019 07:28:00: 31000000 INFO @ Fri, 05 Jul 2019 07:28:02: 31000000 INFO @ Fri, 05 Jul 2019 07:28:08: 33000000 INFO @ Fri, 05 Jul 2019 07:28:10: 32000000 INFO @ Fri, 05 Jul 2019 07:28:11: 32000000 INFO @ Fri, 05 Jul 2019 07:28:17: 34000000 INFO @ Fri, 05 Jul 2019 07:28:19: 33000000 INFO @ Fri, 05 Jul 2019 07:28:21: 33000000 INFO @ Fri, 05 Jul 2019 07:28:26: 35000000 INFO @ Fri, 05 Jul 2019 07:28:29: 34000000 INFO @ Fri, 05 Jul 2019 07:28:31: 34000000 INFO @ Fri, 05 Jul 2019 07:28:34: 36000000 INFO @ Fri, 05 Jul 2019 07:28:38: 35000000 INFO @ Fri, 05 Jul 2019 07:28:40: 35000000 INFO @ Fri, 05 Jul 2019 07:28:43: 37000000 INFO @ Fri, 05 Jul 2019 07:28:47: 36000000 INFO @ Fri, 05 Jul 2019 07:28:50: 36000000 INFO @ Fri, 05 Jul 2019 07:28:52: 38000000 INFO @ Fri, 05 Jul 2019 07:28:56: 37000000 INFO @ Fri, 05 Jul 2019 07:28:59: 37000000 INFO @ Fri, 05 Jul 2019 07:29:01: 39000000 INFO @ Fri, 05 Jul 2019 07:29:05: 38000000 INFO @ Fri, 05 Jul 2019 07:29:08: 38000000 INFO @ Fri, 05 Jul 2019 07:29:10: 40000000 INFO @ Fri, 05 Jul 2019 07:29:15: 39000000 INFO @ Fri, 05 Jul 2019 07:29:18: 39000000 INFO @ Fri, 05 Jul 2019 07:29:18: 41000000 INFO @ Fri, 05 Jul 2019 07:29:24: 40000000 INFO @ Fri, 05 Jul 2019 07:29:26: 42000000 INFO @ Fri, 05 Jul 2019 07:29:27: 40000000 INFO @ Fri, 05 Jul 2019 07:29:34: 41000000 INFO @ Fri, 05 Jul 2019 07:29:35: 43000000 INFO @ Fri, 05 Jul 2019 07:29:37: 41000000 INFO @ Fri, 05 Jul 2019 07:29:43: 44000000 INFO @ Fri, 05 Jul 2019 07:29:43: 42000000 INFO @ Fri, 05 Jul 2019 07:29:46: 42000000 INFO @ Fri, 05 Jul 2019 07:29:47: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:29:47: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:29:47: #1 total tags in treatment: 44411851 INFO @ Fri, 05 Jul 2019 07:29:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:29:47: #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 07:29:48: #1 tags after filtering in treatment: 44411668 INFO @ Fri, 05 Jul 2019 07:29:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:29:48: #1 finished! INFO @ Fri, 05 Jul 2019 07:29:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:29:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:29:52: 43000000 INFO @ Fri, 05 Jul 2019 07:29:55: 43000000 INFO @ Fri, 05 Jul 2019 07:30:00: #2 number of paired peaks: 105115 INFO @ Fri, 05 Jul 2019 07:30:00: start model_add_line... INFO @ Fri, 05 Jul 2019 07:30:01: 44000000 INFO @ Fri, 05 Jul 2019 07:30:01: start X-correlation... INFO @ Fri, 05 Jul 2019 07:30:01: end of X-cor INFO @ Fri, 05 Jul 2019 07:30:01: #2 finished! INFO @ Fri, 05 Jul 2019 07:30:01: #2 predicted fragment length is 139 bps INFO @ Fri, 05 Jul 2019 07:30:01: #2 alternative fragment length(s) may be 2,139 bps INFO @ Fri, 05 Jul 2019 07:30:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.05_model.r INFO @ Fri, 05 Jul 2019 07:30:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:30:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:30:03: 44000000 INFO @ Fri, 05 Jul 2019 07:30:05: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:30:05: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:30:05: #1 total tags in treatment: 44411851 INFO @ Fri, 05 Jul 2019 07:30:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:30:05: #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 07:30:06: #1 tags after filtering in treatment: 44411668 INFO @ Fri, 05 Jul 2019 07:30:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:30:06: #1 finished! INFO @ Fri, 05 Jul 2019 07:30:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:30:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:30:08: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:30:08: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:30:08: #1 total tags in treatment: 44411851 INFO @ Fri, 05 Jul 2019 07:30:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:30:08: #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 07:30:09: #1 tags after filtering in treatment: 44411668 INFO @ Fri, 05 Jul 2019 07:30:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:30:09: #1 finished! INFO @ Fri, 05 Jul 2019 07:30:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:30:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:30:18: #2 number of paired peaks: 105115 INFO @ Fri, 05 Jul 2019 07:30:18: start model_add_line... INFO @ Fri, 05 Jul 2019 07:30:20: start X-correlation... INFO @ Fri, 05 Jul 2019 07:30:20: end of X-cor INFO @ Fri, 05 Jul 2019 07:30:20: #2 finished! INFO @ Fri, 05 Jul 2019 07:30:20: #2 predicted fragment length is 139 bps INFO @ Fri, 05 Jul 2019 07:30:20: #2 alternative fragment length(s) may be 2,139 bps INFO @ Fri, 05 Jul 2019 07:30:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.10_model.r INFO @ Fri, 05 Jul 2019 07:30:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:30:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:30:20: #2 number of paired peaks: 105115 INFO @ Fri, 05 Jul 2019 07:30:20: start model_add_line... INFO @ Fri, 05 Jul 2019 07:30:22: start X-correlation... INFO @ Fri, 05 Jul 2019 07:30:22: end of X-cor INFO @ Fri, 05 Jul 2019 07:30:22: #2 finished! INFO @ Fri, 05 Jul 2019 07:30:22: #2 predicted fragment length is 139 bps INFO @ Fri, 05 Jul 2019 07:30:22: #2 alternative fragment length(s) may be 2,139 bps INFO @ Fri, 05 Jul 2019 07:30:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.20_model.r INFO @ Fri, 05 Jul 2019 07:30:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:30:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:32:21: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:32:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:32:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:33:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.05_peaks.xls INFO @ Fri, 05 Jul 2019 07:33:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:33:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.05_summits.bed INFO @ Fri, 05 Jul 2019 07:33:38: Done! pass1 - making usageList (187 chroms): 23 millis pass2 - checking and writing primary data (84561 records, 4 fields): 136 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 07:33:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.20_peaks.xls INFO @ Fri, 05 Jul 2019 07:33:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:33:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.20_summits.bed INFO @ Fri, 05 Jul 2019 07:33:51: Done! INFO @ Fri, 05 Jul 2019 07:33:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.10_peaks.xls pass1 - making usageList (138 chroms): 11 millis pass2 - checking and writing primary data (45374 records, 4 fields): 63 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:33:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:33:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101910/ERX101910.10_summits.bed INFO @ Fri, 05 Jul 2019 07:33:53: Done! pass1 - making usageList (157 chroms): 16 millis pass2 - checking and writing primary data (65392 records, 4 fields): 94 millis CompletedMACS2peakCalling BigWig に変換しました。