Job ID = 2001146 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:26:59 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 ) 2019-07-04T19:50:02 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 ) spots read : 111,411,407 reads read : 111,411,407 reads written : 111,411,407 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: 01:04:27 111411407 reads; of these: 111411407 (100.00%) were unpaired; of these: 1958331 (1.76%) aligned 0 times 97398669 (87.42%) aligned exactly 1 time 12054407 (10.82%) aligned >1 times 98.24% overall alignment rate Time searching: 01:04:28 Overall time: 01:04:28 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] 65554544 / 109453076 = 0.5989 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 06:26:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.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 06:26:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:26:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:26:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.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 06:26:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:26:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:26:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.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 06:26:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:26:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:26:43: 1000000 INFO @ Fri, 05 Jul 2019 06:26:44: 1000000 INFO @ Fri, 05 Jul 2019 06:26:45: 1000000 INFO @ Fri, 05 Jul 2019 06:26:53: 2000000 INFO @ Fri, 05 Jul 2019 06:26:53: 2000000 INFO @ Fri, 05 Jul 2019 06:26:55: 2000000 INFO @ Fri, 05 Jul 2019 06:27:03: 3000000 INFO @ Fri, 05 Jul 2019 06:27:03: 3000000 INFO @ Fri, 05 Jul 2019 06:27:05: 3000000 INFO @ Fri, 05 Jul 2019 06:27:12: 4000000 INFO @ Fri, 05 Jul 2019 06:27:13: 4000000 INFO @ Fri, 05 Jul 2019 06:27:14: 4000000 INFO @ Fri, 05 Jul 2019 06:27:22: 5000000 INFO @ Fri, 05 Jul 2019 06:27:22: 5000000 INFO @ Fri, 05 Jul 2019 06:27:24: 5000000 INFO @ Fri, 05 Jul 2019 06:27:31: 6000000 INFO @ Fri, 05 Jul 2019 06:27:32: 6000000 INFO @ Fri, 05 Jul 2019 06:27:33: 6000000 INFO @ Fri, 05 Jul 2019 06:27:39: 7000000 INFO @ Fri, 05 Jul 2019 06:27:41: 7000000 INFO @ Fri, 05 Jul 2019 06:27:43: 7000000 INFO @ Fri, 05 Jul 2019 06:27:48: 8000000 INFO @ Fri, 05 Jul 2019 06:27:50: 8000000 INFO @ Fri, 05 Jul 2019 06:27:52: 8000000 INFO @ Fri, 05 Jul 2019 06:27:57: 9000000 INFO @ Fri, 05 Jul 2019 06:27:59: 9000000 INFO @ Fri, 05 Jul 2019 06:28:02: 9000000 INFO @ Fri, 05 Jul 2019 06:28:05: 10000000 INFO @ Fri, 05 Jul 2019 06:28:07: 10000000 INFO @ Fri, 05 Jul 2019 06:28:11: 10000000 INFO @ Fri, 05 Jul 2019 06:28:14: 11000000 INFO @ Fri, 05 Jul 2019 06:28:16: 11000000 INFO @ Fri, 05 Jul 2019 06:28:20: 11000000 INFO @ Fri, 05 Jul 2019 06:28:22: 12000000 INFO @ Fri, 05 Jul 2019 06:28:26: 12000000 INFO @ Fri, 05 Jul 2019 06:28:29: 12000000 INFO @ Fri, 05 Jul 2019 06:28:31: 13000000 INFO @ Fri, 05 Jul 2019 06:28:35: 13000000 INFO @ Fri, 05 Jul 2019 06:28:38: 13000000 INFO @ Fri, 05 Jul 2019 06:28:40: 14000000 INFO @ Fri, 05 Jul 2019 06:28:44: 14000000 INFO @ Fri, 05 Jul 2019 06:28:47: 14000000 INFO @ Fri, 05 Jul 2019 06:28:48: 15000000 INFO @ Fri, 05 Jul 2019 06:28:54: 15000000 INFO @ Fri, 05 Jul 2019 06:28:56: 15000000 INFO @ Fri, 05 Jul 2019 06:28:57: 16000000 INFO @ Fri, 05 Jul 2019 06:29:03: 16000000 INFO @ Fri, 05 Jul 2019 06:29:06: 17000000 INFO @ Fri, 05 Jul 2019 06:29:06: 16000000 INFO @ Fri, 05 Jul 2019 06:29:13: 17000000 INFO @ Fri, 05 Jul 2019 06:29:14: 18000000 INFO @ Fri, 05 Jul 2019 06:29:16: 17000000 INFO @ Fri, 05 Jul 2019 06:29:22: 18000000 INFO @ Fri, 05 Jul 2019 06:29:23: 19000000 INFO @ Fri, 05 Jul 2019 06:29:25: 18000000 INFO @ Fri, 05 Jul 2019 06:29:31: 19000000 INFO @ Fri, 05 Jul 2019 06:29:32: 20000000 INFO @ Fri, 05 Jul 2019 06:29:34: 19000000 INFO @ Fri, 05 Jul 2019 06:29:41: 21000000 INFO @ Fri, 05 Jul 2019 06:29:41: 20000000 INFO @ Fri, 05 Jul 2019 06:29:44: 20000000 INFO @ Fri, 05 Jul 2019 06:29:50: 22000000 INFO @ Fri, 05 Jul 2019 06:29:51: 21000000 INFO @ Fri, 05 Jul 2019 06:29:54: 21000000 INFO @ Fri, 05 Jul 2019 06:29:58: 23000000 INFO @ Fri, 05 Jul 2019 06:30:01: 22000000 INFO @ Fri, 05 Jul 2019 06:30:04: 22000000 INFO @ Fri, 05 Jul 2019 06:30:07: 24000000 INFO @ Fri, 05 Jul 2019 06:30:10: 23000000 INFO @ Fri, 05 Jul 2019 06:30:13: 23000000 INFO @ Fri, 05 Jul 2019 06:30:16: 25000000 INFO @ Fri, 05 Jul 2019 06:30:19: 24000000 INFO @ Fri, 05 Jul 2019 06:30:22: 24000000 INFO @ Fri, 05 Jul 2019 06:30:25: 26000000 INFO @ Fri, 05 Jul 2019 06:30:28: 25000000 INFO @ Fri, 05 Jul 2019 06:30:32: 25000000 INFO @ Fri, 05 Jul 2019 06:30:34: 27000000 INFO @ Fri, 05 Jul 2019 06:30:38: 26000000 INFO @ Fri, 05 Jul 2019 06:30:42: 26000000 INFO @ Fri, 05 Jul 2019 06:30:43: 28000000 INFO @ Fri, 05 Jul 2019 06:30:48: 27000000 INFO @ Fri, 05 Jul 2019 06:30:52: 29000000 INFO @ Fri, 05 Jul 2019 06:30:52: 27000000 INFO @ Fri, 05 Jul 2019 06:30:58: 28000000 INFO @ Fri, 05 Jul 2019 06:31:00: 30000000 INFO @ Fri, 05 Jul 2019 06:31:02: 28000000 INFO @ Fri, 05 Jul 2019 06:31:08: 29000000 INFO @ Fri, 05 Jul 2019 06:31:09: 31000000 INFO @ Fri, 05 Jul 2019 06:31:12: 29000000 INFO @ Fri, 05 Jul 2019 06:31:18: 30000000 INFO @ Fri, 05 Jul 2019 06:31:18: 32000000 INFO @ Fri, 05 Jul 2019 06:31:22: 30000000 INFO @ Fri, 05 Jul 2019 06:31:27: 33000000 INFO @ Fri, 05 Jul 2019 06:31:28: 31000000 INFO @ Fri, 05 Jul 2019 06:31:31: 31000000 INFO @ Fri, 05 Jul 2019 06:31:36: 34000000 INFO @ Fri, 05 Jul 2019 06:31:37: 32000000 INFO @ Fri, 05 Jul 2019 06:31:40: 32000000 INFO @ Fri, 05 Jul 2019 06:31:44: 35000000 INFO @ Fri, 05 Jul 2019 06:31:46: 33000000 INFO @ Fri, 05 Jul 2019 06:31:49: 33000000 INFO @ Fri, 05 Jul 2019 06:31:53: 36000000 INFO @ Fri, 05 Jul 2019 06:31:55: 34000000 INFO @ Fri, 05 Jul 2019 06:31:58: 34000000 INFO @ Fri, 05 Jul 2019 06:32:02: 37000000 INFO @ Fri, 05 Jul 2019 06:32:05: 35000000 INFO @ Fri, 05 Jul 2019 06:32:07: 35000000 INFO @ Fri, 05 Jul 2019 06:32:11: 38000000 INFO @ Fri, 05 Jul 2019 06:32:14: 36000000 INFO @ Fri, 05 Jul 2019 06:32:16: 36000000 INFO @ Fri, 05 Jul 2019 06:32:19: 39000000 INFO @ Fri, 05 Jul 2019 06:32:23: 37000000 INFO @ Fri, 05 Jul 2019 06:32:25: 37000000 INFO @ Fri, 05 Jul 2019 06:32:28: 40000000 INFO @ Fri, 05 Jul 2019 06:32:32: 38000000 INFO @ Fri, 05 Jul 2019 06:32:34: 38000000 INFO @ Fri, 05 Jul 2019 06:32:37: 41000000 INFO @ Fri, 05 Jul 2019 06:32:41: 39000000 INFO @ Fri, 05 Jul 2019 06:32:42: 39000000 INFO @ Fri, 05 Jul 2019 06:32:46: 42000000 INFO @ Fri, 05 Jul 2019 06:32:50: 40000000 INFO @ Fri, 05 Jul 2019 06:32:50: 40000000 INFO @ Fri, 05 Jul 2019 06:32:55: 43000000 INFO @ Fri, 05 Jul 2019 06:32:58: 41000000 INFO @ Fri, 05 Jul 2019 06:32:59: 41000000 INFO @ Fri, 05 Jul 2019 06:33:04: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 06:33:04: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 06:33:04: #1 total tags in treatment: 43898532 INFO @ Fri, 05 Jul 2019 06:33:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:33:04: #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 06:33:05: #1 tags after filtering in treatment: 43898344 INFO @ Fri, 05 Jul 2019 06:33:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:33:05: #1 finished! INFO @ Fri, 05 Jul 2019 06:33:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:33:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:33:06: 42000000 INFO @ Fri, 05 Jul 2019 06:33:08: 42000000 INFO @ Fri, 05 Jul 2019 06:33:14: 43000000 INFO @ Fri, 05 Jul 2019 06:33:17: #2 number of paired peaks: 114227 INFO @ Fri, 05 Jul 2019 06:33:17: start model_add_line... INFO @ Fri, 05 Jul 2019 06:33:17: 43000000 INFO @ Fri, 05 Jul 2019 06:33:18: start X-correlation... INFO @ Fri, 05 Jul 2019 06:33:18: end of X-cor INFO @ Fri, 05 Jul 2019 06:33:18: #2 finished! INFO @ Fri, 05 Jul 2019 06:33:18: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 06:33:18: #2 alternative fragment length(s) may be 3,134 bps INFO @ Fri, 05 Jul 2019 06:33:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.10_model.r INFO @ Fri, 05 Jul 2019 06:33:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:33:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:33:21: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 06:33:21: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 06:33:21: #1 total tags in treatment: 43898532 INFO @ Fri, 05 Jul 2019 06:33:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:33:21: #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 06:33:22: #1 tags after filtering in treatment: 43898344 INFO @ Fri, 05 Jul 2019 06:33:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:33:22: #1 finished! INFO @ Fri, 05 Jul 2019 06:33:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:33:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:33:25: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 06:33:25: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 06:33:25: #1 total tags in treatment: 43898532 INFO @ Fri, 05 Jul 2019 06:33:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:33:25: #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 06:33:26: #1 tags after filtering in treatment: 43898344 INFO @ Fri, 05 Jul 2019 06:33:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:33:26: #1 finished! INFO @ Fri, 05 Jul 2019 06:33:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:33:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:33:34: #2 number of paired peaks: 114227 INFO @ Fri, 05 Jul 2019 06:33:34: start model_add_line... INFO @ Fri, 05 Jul 2019 06:33:36: start X-correlation... INFO @ Fri, 05 Jul 2019 06:33:36: end of X-cor INFO @ Fri, 05 Jul 2019 06:33:36: #2 finished! INFO @ Fri, 05 Jul 2019 06:33:36: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 06:33:36: #2 alternative fragment length(s) may be 3,134 bps INFO @ Fri, 05 Jul 2019 06:33:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.20_model.r INFO @ Fri, 05 Jul 2019 06:33:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:33:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:33:38: #2 number of paired peaks: 114227 INFO @ Fri, 05 Jul 2019 06:33:38: start model_add_line... INFO @ Fri, 05 Jul 2019 06:33:40: start X-correlation... INFO @ Fri, 05 Jul 2019 06:33:40: end of X-cor INFO @ Fri, 05 Jul 2019 06:33:40: #2 finished! INFO @ Fri, 05 Jul 2019 06:33:40: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 06:33:40: #2 alternative fragment length(s) may be 3,134 bps INFO @ Fri, 05 Jul 2019 06:33:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.05_model.r INFO @ Fri, 05 Jul 2019 06:33:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:33:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:35:31: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:35:50: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:36:02: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:36:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.10_peaks.xls INFO @ Fri, 05 Jul 2019 06:36:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:36:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.10_summits.bed INFO @ Fri, 05 Jul 2019 06:36:47: Done! pass1 - making usageList (159 chroms): 18 millis pass2 - checking and writing primary data (68544 records, 4 fields): 91 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:37:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.20_peaks.xls INFO @ Fri, 05 Jul 2019 06:37:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:37:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.20_summits.bed INFO @ Fri, 05 Jul 2019 06:37:06: Done! pass1 - making usageList (133 chroms): 16 millis pass2 - checking and writing primary data (45178 records, 4 fields): 61 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 06:37:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.05_peaks.xls INFO @ Fri, 05 Jul 2019 06:37:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:37:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101836/ERX101836.05_summits.bed INFO @ Fri, 05 Jul 2019 06:37:25: Done! pass1 - making usageList (191 chroms): 17 millis pass2 - checking and writing primary data (90817 records, 4 fields): 118 millis CompletedMACS2peakCalling BigWig に変換しました。