Job ID = 2001565 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T20:04:55 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 ) 2019-07-04T20:18:38 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 ) 2019-07-04T20:18:38 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 ) 2019-07-04T20:18:38 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 ) 2019-07-04T20:24:41 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-04T20:33:22 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 ) 2019-07-04T20:33:22 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 ) 2019-07-04T20:33:22 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 : 118,818,421 reads read : 118,818,421 reads written : 118,818,421 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: 00:00:00 Multiseed full-index search: 01:09:43 118818421 reads; of these: 118818421 (100.00%) were unpaired; of these: 2098563 (1.77%) aligned 0 times 104046525 (87.57%) aligned exactly 1 time 12673333 (10.67%) aligned >1 times 98.23% overall alignment rate Time searching: 01:09:46 Overall time: 01:09:46 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] 72123006 / 116719858 = 0.6179 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 07:33:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.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 07:33:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:33:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:33:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.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 07:33:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:33:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:33:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.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 07:33:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:33:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:33:15: 1000000 INFO @ Fri, 05 Jul 2019 07:33:15: 1000000 INFO @ Fri, 05 Jul 2019 07:33:17: 1000000 INFO @ Fri, 05 Jul 2019 07:33:24: 2000000 INFO @ Fri, 05 Jul 2019 07:33:26: 2000000 INFO @ Fri, 05 Jul 2019 07:33:28: 2000000 INFO @ Fri, 05 Jul 2019 07:33:34: 3000000 INFO @ Fri, 05 Jul 2019 07:33:36: 3000000 INFO @ Fri, 05 Jul 2019 07:33:39: 3000000 INFO @ Fri, 05 Jul 2019 07:33:44: 4000000 INFO @ Fri, 05 Jul 2019 07:33:47: 4000000 INFO @ Fri, 05 Jul 2019 07:33:50: 4000000 INFO @ Fri, 05 Jul 2019 07:33:54: 5000000 INFO @ Fri, 05 Jul 2019 07:33:57: 5000000 INFO @ Fri, 05 Jul 2019 07:34:00: 5000000 INFO @ Fri, 05 Jul 2019 07:34:03: 6000000 INFO @ Fri, 05 Jul 2019 07:34:08: 6000000 INFO @ Fri, 05 Jul 2019 07:34:10: 6000000 INFO @ Fri, 05 Jul 2019 07:34:13: 7000000 INFO @ Fri, 05 Jul 2019 07:34:19: 7000000 INFO @ Fri, 05 Jul 2019 07:34:21: 7000000 INFO @ Fri, 05 Jul 2019 07:34:23: 8000000 INFO @ Fri, 05 Jul 2019 07:34:30: 8000000 INFO @ Fri, 05 Jul 2019 07:34:32: 8000000 INFO @ Fri, 05 Jul 2019 07:34:32: 9000000 INFO @ Fri, 05 Jul 2019 07:34:40: 9000000 INFO @ Fri, 05 Jul 2019 07:34:41: 10000000 INFO @ Fri, 05 Jul 2019 07:34:42: 9000000 INFO @ Fri, 05 Jul 2019 07:34:49: 10000000 INFO @ Fri, 05 Jul 2019 07:34:49: 11000000 INFO @ Fri, 05 Jul 2019 07:34:52: 10000000 INFO @ Fri, 05 Jul 2019 07:34:58: 12000000 INFO @ Fri, 05 Jul 2019 07:34:59: 11000000 INFO @ Fri, 05 Jul 2019 07:35:02: 11000000 INFO @ Fri, 05 Jul 2019 07:35:07: 13000000 INFO @ Fri, 05 Jul 2019 07:35:09: 12000000 INFO @ Fri, 05 Jul 2019 07:35:13: 12000000 INFO @ Fri, 05 Jul 2019 07:35:15: 14000000 INFO @ Fri, 05 Jul 2019 07:35:19: 13000000 INFO @ Fri, 05 Jul 2019 07:35:23: 13000000 INFO @ Fri, 05 Jul 2019 07:35:25: 15000000 INFO @ Fri, 05 Jul 2019 07:35:29: 14000000 INFO @ Fri, 05 Jul 2019 07:35:34: 14000000 INFO @ Fri, 05 Jul 2019 07:35:35: 16000000 INFO @ Fri, 05 Jul 2019 07:35:40: 15000000 INFO @ Fri, 05 Jul 2019 07:35:44: 15000000 INFO @ Fri, 05 Jul 2019 07:35:45: 17000000 INFO @ Fri, 05 Jul 2019 07:35:51: 16000000 INFO @ Fri, 05 Jul 2019 07:35:55: 16000000 INFO @ Fri, 05 Jul 2019 07:35:56: 18000000 INFO @ Fri, 05 Jul 2019 07:36:01: 17000000 INFO @ Fri, 05 Jul 2019 07:36:05: 17000000 INFO @ Fri, 05 Jul 2019 07:36:05: 19000000 INFO @ Fri, 05 Jul 2019 07:36:12: 18000000 INFO @ Fri, 05 Jul 2019 07:36:15: 18000000 INFO @ Fri, 05 Jul 2019 07:36:16: 20000000 INFO @ Fri, 05 Jul 2019 07:36:21: 19000000 INFO @ Fri, 05 Jul 2019 07:36:26: 19000000 INFO @ Fri, 05 Jul 2019 07:36:26: 21000000 INFO @ Fri, 05 Jul 2019 07:36:31: 20000000 INFO @ Fri, 05 Jul 2019 07:36:37: 20000000 INFO @ Fri, 05 Jul 2019 07:36:37: 22000000 INFO @ Fri, 05 Jul 2019 07:36:41: 21000000 INFO @ Fri, 05 Jul 2019 07:36:47: 21000000 INFO @ Fri, 05 Jul 2019 07:36:49: 23000000 INFO @ Fri, 05 Jul 2019 07:36:52: 22000000 INFO @ Fri, 05 Jul 2019 07:36:58: 22000000 INFO @ Fri, 05 Jul 2019 07:37:00: 24000000 INFO @ Fri, 05 Jul 2019 07:37:03: 23000000 INFO @ Fri, 05 Jul 2019 07:37:09: 23000000 INFO @ Fri, 05 Jul 2019 07:37:11: 25000000 INFO @ Fri, 05 Jul 2019 07:37:14: 24000000 INFO @ Fri, 05 Jul 2019 07:37:20: 24000000 INFO @ Fri, 05 Jul 2019 07:37:23: 26000000 INFO @ Fri, 05 Jul 2019 07:37:25: 25000000 INFO @ Fri, 05 Jul 2019 07:37:32: 25000000 INFO @ Fri, 05 Jul 2019 07:37:34: 27000000 INFO @ Fri, 05 Jul 2019 07:37:37: 26000000 INFO @ Fri, 05 Jul 2019 07:37:43: 26000000 INFO @ Fri, 05 Jul 2019 07:37:46: 28000000 INFO @ Fri, 05 Jul 2019 07:37:48: 27000000 INFO @ Fri, 05 Jul 2019 07:37:55: 27000000 INFO @ Fri, 05 Jul 2019 07:37:57: 29000000 INFO @ Fri, 05 Jul 2019 07:37:59: 28000000 INFO @ Fri, 05 Jul 2019 07:38:06: 28000000 INFO @ Fri, 05 Jul 2019 07:38:09: 30000000 INFO @ Fri, 05 Jul 2019 07:38:10: 29000000 INFO @ Fri, 05 Jul 2019 07:38:18: 29000000 INFO @ Fri, 05 Jul 2019 07:38:20: 31000000 INFO @ Fri, 05 Jul 2019 07:38:22: 30000000 INFO @ Fri, 05 Jul 2019 07:38:29: 30000000 INFO @ Fri, 05 Jul 2019 07:38:31: 32000000 INFO @ Fri, 05 Jul 2019 07:38:33: 31000000 INFO @ Fri, 05 Jul 2019 07:38:40: 31000000 INFO @ Fri, 05 Jul 2019 07:38:42: 33000000 INFO @ Fri, 05 Jul 2019 07:38:44: 32000000 INFO @ Fri, 05 Jul 2019 07:38:51: 32000000 INFO @ Fri, 05 Jul 2019 07:38:53: 34000000 INFO @ Fri, 05 Jul 2019 07:38:54: 33000000 INFO @ Fri, 05 Jul 2019 07:39:01: 33000000 INFO @ Fri, 05 Jul 2019 07:39:03: 35000000 INFO @ Fri, 05 Jul 2019 07:39:05: 34000000 INFO @ Fri, 05 Jul 2019 07:39:11: 34000000 INFO @ Fri, 05 Jul 2019 07:39:14: 36000000 INFO @ Fri, 05 Jul 2019 07:39:15: 35000000 INFO @ Fri, 05 Jul 2019 07:39:21: 35000000 INFO @ Fri, 05 Jul 2019 07:39:25: 37000000 INFO @ Fri, 05 Jul 2019 07:39:26: 36000000 INFO @ Fri, 05 Jul 2019 07:39:31: 36000000 INFO @ Fri, 05 Jul 2019 07:39:35: 38000000 INFO @ Fri, 05 Jul 2019 07:39:36: 37000000 INFO @ Fri, 05 Jul 2019 07:39:41: 37000000 INFO @ Fri, 05 Jul 2019 07:39:46: 39000000 INFO @ Fri, 05 Jul 2019 07:39:47: 38000000 INFO @ Fri, 05 Jul 2019 07:39:51: 38000000 INFO @ Fri, 05 Jul 2019 07:39:56: 40000000 INFO @ Fri, 05 Jul 2019 07:39:58: 39000000 INFO @ Fri, 05 Jul 2019 07:40:01: 39000000 INFO @ Fri, 05 Jul 2019 07:40:07: 41000000 INFO @ Fri, 05 Jul 2019 07:40:09: 40000000 INFO @ Fri, 05 Jul 2019 07:40:11: 40000000 INFO @ Fri, 05 Jul 2019 07:40:17: 42000000 INFO @ Fri, 05 Jul 2019 07:40:20: 41000000 INFO @ Fri, 05 Jul 2019 07:40:21: 41000000 INFO @ Fri, 05 Jul 2019 07:40:28: 43000000 INFO @ Fri, 05 Jul 2019 07:40:31: 42000000 INFO @ Fri, 05 Jul 2019 07:40:31: 42000000 INFO @ Fri, 05 Jul 2019 07:40:39: 44000000 INFO @ Fri, 05 Jul 2019 07:40:41: 43000000 INFO @ Fri, 05 Jul 2019 07:40:42: 43000000 INFO @ Fri, 05 Jul 2019 07:40:46: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:40:46: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:40:46: #1 total tags in treatment: 44596852 INFO @ Fri, 05 Jul 2019 07:40:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:40:46: #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 07:40:47: #1 tags after filtering in treatment: 44596685 INFO @ Fri, 05 Jul 2019 07:40:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:40:47: #1 finished! INFO @ Fri, 05 Jul 2019 07:40:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:40:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:40:52: 44000000 INFO @ Fri, 05 Jul 2019 07:40:53: 44000000 INFO @ Fri, 05 Jul 2019 07:40:59: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:40:59: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:40:59: #1 total tags in treatment: 44596852 INFO @ Fri, 05 Jul 2019 07:40:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:40:59: #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 07:41:00: #2 number of paired peaks: 99745 INFO @ Fri, 05 Jul 2019 07:41:00: start model_add_line... INFO @ Fri, 05 Jul 2019 07:41:00: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:41:00: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:41:00: #1 total tags in treatment: 44596852 INFO @ Fri, 05 Jul 2019 07:41:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:41:00: #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 07:41:00: #1 tags after filtering in treatment: 44596685 INFO @ Fri, 05 Jul 2019 07:41:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:41:00: #1 finished! INFO @ Fri, 05 Jul 2019 07:41:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:41:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:41:02: start X-correlation... INFO @ Fri, 05 Jul 2019 07:41:02: #1 tags after filtering in treatment: 44596685 INFO @ Fri, 05 Jul 2019 07:41:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:41:02: #1 finished! INFO @ Fri, 05 Jul 2019 07:41:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:41:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:41:02: end of X-cor INFO @ Fri, 05 Jul 2019 07:41:02: #2 finished! INFO @ Fri, 05 Jul 2019 07:41:02: #2 predicted fragment length is 144 bps INFO @ Fri, 05 Jul 2019 07:41:02: #2 alternative fragment length(s) may be 4,144 bps INFO @ Fri, 05 Jul 2019 07:41:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.10_model.r INFO @ Fri, 05 Jul 2019 07:41:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:41:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:41:14: #2 number of paired peaks: 99745 INFO @ Fri, 05 Jul 2019 07:41:14: start model_add_line... INFO @ Fri, 05 Jul 2019 07:41:16: start X-correlation... INFO @ Fri, 05 Jul 2019 07:41:16: end of X-cor INFO @ Fri, 05 Jul 2019 07:41:16: #2 finished! INFO @ Fri, 05 Jul 2019 07:41:16: #2 predicted fragment length is 144 bps INFO @ Fri, 05 Jul 2019 07:41:16: #2 alternative fragment length(s) may be 4,144 bps INFO @ Fri, 05 Jul 2019 07:41:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.20_model.r INFO @ Fri, 05 Jul 2019 07:41:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:41:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:41:16: #2 number of paired peaks: 99745 INFO @ Fri, 05 Jul 2019 07:41:16: start model_add_line... INFO @ Fri, 05 Jul 2019 07:41:17: start X-correlation... INFO @ Fri, 05 Jul 2019 07:41:17: end of X-cor INFO @ Fri, 05 Jul 2019 07:41:17: #2 finished! INFO @ Fri, 05 Jul 2019 07:41:17: #2 predicted fragment length is 144 bps INFO @ Fri, 05 Jul 2019 07:41:17: #2 alternative fragment length(s) may be 4,144 bps INFO @ Fri, 05 Jul 2019 07:41:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.05_model.r INFO @ Fri, 05 Jul 2019 07:41:17: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:41:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:43:56: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:44:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:44:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:45:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.10_peaks.xls INFO @ Fri, 05 Jul 2019 07:45:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:45:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.10_summits.bed INFO @ Fri, 05 Jul 2019 07:45:33: Done! pass1 - making usageList (165 chroms): 13 millis pass2 - checking and writing primary data (60151 records, 4 fields): 148 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:45:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.20_peaks.xls INFO @ Fri, 05 Jul 2019 07:45:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:45:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.20_summits.bed INFO @ Fri, 05 Jul 2019 07:45:37: Done! pass1 - making usageList (131 chroms): 9 millis pass2 - checking and writing primary data (42415 records, 4 fields): 126 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:45:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.05_peaks.xls INFO @ Fri, 05 Jul 2019 07:45:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:45:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101908/ERX101908.05_summits.bed INFO @ Fri, 05 Jul 2019 07:45:44: Done! pass1 - making usageList (189 chroms): 19 millis pass2 - checking and writing primary data (78493 records, 4 fields): 119 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。