Job ID = 2001550 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:53:51 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 ) 2019-07-04T19:59:37 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 ) 2019-07-04T20:03:22 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 : 80,050,600 reads read : 80,050,600 reads written : 80,050,600 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: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:53:02 80050600 reads; of these: 80050600 (100.00%) were unpaired; of these: 2509327 (3.13%) aligned 0 times 69261491 (86.52%) aligned exactly 1 time 8279782 (10.34%) aligned >1 times 96.87% overall alignment rate Time searching: 00:53:06 Overall time: 00:53:06 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 32 files... [bam_rmdupse_core] 39931927 / 77541273 = 0.5150 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 06:25:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.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 06:25:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:25:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:25:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.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 06:25:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:25:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:25:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.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 06:25:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:25:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:25:32: 1000000 INFO @ Fri, 05 Jul 2019 06:25:33: 1000000 INFO @ Fri, 05 Jul 2019 06:25:35: 1000000 INFO @ Fri, 05 Jul 2019 06:25:41: 2000000 INFO @ Fri, 05 Jul 2019 06:25:45: 2000000 INFO @ Fri, 05 Jul 2019 06:25:47: 2000000 INFO @ Fri, 05 Jul 2019 06:25:51: 3000000 INFO @ Fri, 05 Jul 2019 06:25:57: 3000000 INFO @ Fri, 05 Jul 2019 06:25:59: 3000000 INFO @ Fri, 05 Jul 2019 06:26:00: 4000000 INFO @ Fri, 05 Jul 2019 06:26:08: 4000000 INFO @ Fri, 05 Jul 2019 06:26:09: 5000000 INFO @ Fri, 05 Jul 2019 06:26:11: 4000000 INFO @ Fri, 05 Jul 2019 06:26:18: 6000000 INFO @ Fri, 05 Jul 2019 06:26:20: 5000000 INFO @ Fri, 05 Jul 2019 06:26:23: 5000000 INFO @ Fri, 05 Jul 2019 06:26:28: 7000000 INFO @ Fri, 05 Jul 2019 06:26:31: 6000000 INFO @ Fri, 05 Jul 2019 06:26:33: 6000000 INFO @ Fri, 05 Jul 2019 06:26:38: 8000000 INFO @ Fri, 05 Jul 2019 06:26:42: 7000000 INFO @ Fri, 05 Jul 2019 06:26:44: 7000000 INFO @ Fri, 05 Jul 2019 06:26:47: 9000000 INFO @ Fri, 05 Jul 2019 06:26:52: 8000000 INFO @ Fri, 05 Jul 2019 06:26:55: 8000000 INFO @ Fri, 05 Jul 2019 06:26:56: 10000000 INFO @ Fri, 05 Jul 2019 06:27:04: 9000000 INFO @ Fri, 05 Jul 2019 06:27:05: 11000000 INFO @ Fri, 05 Jul 2019 06:27:07: 9000000 INFO @ Fri, 05 Jul 2019 06:27:14: 12000000 INFO @ Fri, 05 Jul 2019 06:27:16: 10000000 INFO @ Fri, 05 Jul 2019 06:27:19: 10000000 INFO @ Fri, 05 Jul 2019 06:27:24: 13000000 INFO @ Fri, 05 Jul 2019 06:27:28: 11000000 INFO @ Fri, 05 Jul 2019 06:27:31: 11000000 INFO @ Fri, 05 Jul 2019 06:27:33: 14000000 INFO @ Fri, 05 Jul 2019 06:27:40: 12000000 INFO @ Fri, 05 Jul 2019 06:27:43: 12000000 INFO @ Fri, 05 Jul 2019 06:27:43: 15000000 INFO @ Fri, 05 Jul 2019 06:27:51: 13000000 INFO @ Fri, 05 Jul 2019 06:27:53: 16000000 INFO @ Fri, 05 Jul 2019 06:27:55: 13000000 INFO @ Fri, 05 Jul 2019 06:28:02: 14000000 INFO @ Fri, 05 Jul 2019 06:28:03: 17000000 INFO @ Fri, 05 Jul 2019 06:28:07: 14000000 INFO @ Fri, 05 Jul 2019 06:28:13: 18000000 INFO @ Fri, 05 Jul 2019 06:28:14: 15000000 INFO @ Fri, 05 Jul 2019 06:28:20: 15000000 INFO @ Fri, 05 Jul 2019 06:28:24: 19000000 INFO @ Fri, 05 Jul 2019 06:28:26: 16000000 INFO @ Fri, 05 Jul 2019 06:28:33: 16000000 INFO @ Fri, 05 Jul 2019 06:28:34: 20000000 INFO @ Fri, 05 Jul 2019 06:28:38: 17000000 INFO @ Fri, 05 Jul 2019 06:28:44: 21000000 INFO @ Fri, 05 Jul 2019 06:28:45: 17000000 INFO @ Fri, 05 Jul 2019 06:28:51: 18000000 INFO @ Fri, 05 Jul 2019 06:28:55: 22000000 INFO @ Fri, 05 Jul 2019 06:28:58: 18000000 INFO @ Fri, 05 Jul 2019 06:29:03: 19000000 INFO @ Fri, 05 Jul 2019 06:29:05: 23000000 INFO @ Fri, 05 Jul 2019 06:29:11: 19000000 INFO @ Fri, 05 Jul 2019 06:29:15: 20000000 INFO @ Fri, 05 Jul 2019 06:29:15: 24000000 INFO @ Fri, 05 Jul 2019 06:29:23: 20000000 INFO @ Fri, 05 Jul 2019 06:29:26: 25000000 INFO @ Fri, 05 Jul 2019 06:29:27: 21000000 INFO @ Fri, 05 Jul 2019 06:29:36: 21000000 INFO @ Fri, 05 Jul 2019 06:29:36: 26000000 INFO @ Fri, 05 Jul 2019 06:29:40: 22000000 INFO @ Fri, 05 Jul 2019 06:29:47: 27000000 INFO @ Fri, 05 Jul 2019 06:29:48: 22000000 INFO @ Fri, 05 Jul 2019 06:29:52: 23000000 INFO @ Fri, 05 Jul 2019 06:29:57: 28000000 INFO @ Fri, 05 Jul 2019 06:30:01: 23000000 INFO @ Fri, 05 Jul 2019 06:30:05: 24000000 INFO @ Fri, 05 Jul 2019 06:30:07: 29000000 INFO @ Fri, 05 Jul 2019 06:30:13: 24000000 INFO @ Fri, 05 Jul 2019 06:30:17: 30000000 INFO @ Fri, 05 Jul 2019 06:30:18: 25000000 INFO @ Fri, 05 Jul 2019 06:30:26: 25000000 INFO @ Fri, 05 Jul 2019 06:30:28: 31000000 INFO @ Fri, 05 Jul 2019 06:30:31: 26000000 INFO @ Fri, 05 Jul 2019 06:30:38: 32000000 INFO @ Fri, 05 Jul 2019 06:30:39: 26000000 INFO @ Fri, 05 Jul 2019 06:30:43: 27000000 INFO @ Fri, 05 Jul 2019 06:30:48: 33000000 INFO @ Fri, 05 Jul 2019 06:30:52: 27000000 INFO @ Fri, 05 Jul 2019 06:30:56: 28000000 INFO @ Fri, 05 Jul 2019 06:30:58: 34000000 INFO @ Fri, 05 Jul 2019 06:31:05: 28000000 INFO @ Fri, 05 Jul 2019 06:31:08: 35000000 INFO @ Fri, 05 Jul 2019 06:31:09: 29000000 INFO @ Fri, 05 Jul 2019 06:31:18: 29000000 INFO @ Fri, 05 Jul 2019 06:31:18: 36000000 INFO @ Fri, 05 Jul 2019 06:31:22: 30000000 INFO @ Fri, 05 Jul 2019 06:31:29: 37000000 INFO @ Fri, 05 Jul 2019 06:31:31: 30000000 INFO @ Fri, 05 Jul 2019 06:31:35: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 06:31:35: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 06:31:35: #1 total tags in treatment: 37609346 INFO @ Fri, 05 Jul 2019 06:31:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:31:35: #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 06:31:36: 31000000 INFO @ Fri, 05 Jul 2019 06:31:36: #1 tags after filtering in treatment: 37609134 INFO @ Fri, 05 Jul 2019 06:31:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:31:36: #1 finished! INFO @ Fri, 05 Jul 2019 06:31:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:31:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:31:44: 31000000 INFO @ Fri, 05 Jul 2019 06:31:47: #2 number of paired peaks: 92533 INFO @ Fri, 05 Jul 2019 06:31:47: start model_add_line... INFO @ Fri, 05 Jul 2019 06:31:48: start X-correlation... INFO @ Fri, 05 Jul 2019 06:31:48: end of X-cor INFO @ Fri, 05 Jul 2019 06:31:48: #2 finished! INFO @ Fri, 05 Jul 2019 06:31:48: #2 predicted fragment length is 113 bps INFO @ Fri, 05 Jul 2019 06:31:48: #2 alternative fragment length(s) may be 3,113 bps INFO @ Fri, 05 Jul 2019 06:31:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.10_model.r INFO @ Fri, 05 Jul 2019 06:31:48: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:31:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:31:48: 32000000 INFO @ Fri, 05 Jul 2019 06:31:57: 32000000 INFO @ Fri, 05 Jul 2019 06:32:01: 33000000 INFO @ Fri, 05 Jul 2019 06:32:09: 33000000 INFO @ Fri, 05 Jul 2019 06:32:13: 34000000 INFO @ Fri, 05 Jul 2019 06:32:21: 34000000 INFO @ Fri, 05 Jul 2019 06:32:25: 35000000 INFO @ Fri, 05 Jul 2019 06:32:34: 35000000 INFO @ Fri, 05 Jul 2019 06:32:38: 36000000 INFO @ Fri, 05 Jul 2019 06:32:46: 36000000 INFO @ Fri, 05 Jul 2019 06:32:52: 37000000 INFO @ Fri, 05 Jul 2019 06:33:00: 37000000 INFO @ Fri, 05 Jul 2019 06:33:01: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 06:33:01: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 06:33:01: #1 total tags in treatment: 37609346 INFO @ Fri, 05 Jul 2019 06:33:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:33:01: #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 06:33:02: #1 tags after filtering in treatment: 37609134 INFO @ Fri, 05 Jul 2019 06:33:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:33:02: #1 finished! INFO @ Fri, 05 Jul 2019 06:33:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:33:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:33:08: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 06:33:08: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 06:33:08: #1 total tags in treatment: 37609346 INFO @ Fri, 05 Jul 2019 06:33:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:33:08: #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 06:33:09: #1 tags after filtering in treatment: 37609134 INFO @ Fri, 05 Jul 2019 06:33:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:33:09: #1 finished! INFO @ Fri, 05 Jul 2019 06:33:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:33:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:33:13: #2 number of paired peaks: 92533 INFO @ Fri, 05 Jul 2019 06:33:13: start model_add_line... INFO @ Fri, 05 Jul 2019 06:33:14: start X-correlation... INFO @ Fri, 05 Jul 2019 06:33:14: end of X-cor INFO @ Fri, 05 Jul 2019 06:33:14: #2 finished! INFO @ Fri, 05 Jul 2019 06:33:14: #2 predicted fragment length is 113 bps INFO @ Fri, 05 Jul 2019 06:33:14: #2 alternative fragment length(s) may be 3,113 bps INFO @ Fri, 05 Jul 2019 06:33:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.05_model.r INFO @ Fri, 05 Jul 2019 06:33:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:33:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:33:20: #2 number of paired peaks: 92533 INFO @ Fri, 05 Jul 2019 06:33:20: start model_add_line... INFO @ Fri, 05 Jul 2019 06:33:21: start X-correlation... INFO @ Fri, 05 Jul 2019 06:33:21: end of X-cor INFO @ Fri, 05 Jul 2019 06:33:21: #2 finished! INFO @ Fri, 05 Jul 2019 06:33:21: #2 predicted fragment length is 113 bps INFO @ Fri, 05 Jul 2019 06:33:21: #2 alternative fragment length(s) may be 3,113 bps INFO @ Fri, 05 Jul 2019 06:33:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.20_model.r INFO @ Fri, 05 Jul 2019 06:33:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:33:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:33:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:34:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.10_peaks.xls INFO @ Fri, 05 Jul 2019 06:34:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:34:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.10_summits.bed INFO @ Fri, 05 Jul 2019 06:34:58: Done! pass1 - making usageList (137 chroms): 19 millis pass2 - checking and writing primary data (52185 records, 4 fields): 75 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:35:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:35:42: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:37:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.05_peaks.xls INFO @ Fri, 05 Jul 2019 06:37:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:37:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.05_summits.bed INFO @ Fri, 05 Jul 2019 06:37:04: Done! pass1 - making usageList (164 chroms): 31 millis pass2 - checking and writing primary data (67301 records, 4 fields): 149 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:37:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.20_peaks.xls INFO @ Fri, 05 Jul 2019 06:37:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:37:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101893/ERX101893.20_summits.bed INFO @ Fri, 05 Jul 2019 06:37:21: Done! pass1 - making usageList (114 chroms): 8 millis pass2 - checking and writing primary data (36515 records, 4 fields): 105 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。