Job ID = 2001709 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T00:35:45 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 ) 2019-07-05T00:35:45 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 ) spots read : 111,345,267 reads read : 111,345,267 reads written : 111,345,267 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:12:58 111345267 reads; of these: 111345267 (100.00%) were unpaired; of these: 1986086 (1.78%) aligned 0 times 97127238 (87.23%) aligned exactly 1 time 12231943 (10.99%) aligned >1 times 98.22% overall alignment rate Time searching: 01:13:00 Overall time: 01:13:00 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] 63904187 / 109359181 = 0.5844 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 12:23:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.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 12:23:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:23:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:23:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.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 12:23:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:23:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:23:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.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 12:23:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:23:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:24:03: 1000000 INFO @ Fri, 05 Jul 2019 12:24:05: 1000000 INFO @ Fri, 05 Jul 2019 12:24:08: 1000000 INFO @ Fri, 05 Jul 2019 12:24:14: 2000000 INFO @ Fri, 05 Jul 2019 12:24:19: 2000000 INFO @ Fri, 05 Jul 2019 12:24:19: 2000000 INFO @ Fri, 05 Jul 2019 12:24:27: 3000000 INFO @ Fri, 05 Jul 2019 12:24:31: 3000000 INFO @ Fri, 05 Jul 2019 12:24:32: 3000000 INFO @ Fri, 05 Jul 2019 12:24:38: 4000000 INFO @ Fri, 05 Jul 2019 12:24:44: 4000000 INFO @ Fri, 05 Jul 2019 12:24:46: 4000000 INFO @ Fri, 05 Jul 2019 12:24:48: 5000000 INFO @ Fri, 05 Jul 2019 12:24:55: 5000000 INFO @ Fri, 05 Jul 2019 12:24:59: 6000000 INFO @ Fri, 05 Jul 2019 12:24:59: 5000000 INFO @ Fri, 05 Jul 2019 12:25:08: 6000000 INFO @ Fri, 05 Jul 2019 12:25:09: 7000000 INFO @ Fri, 05 Jul 2019 12:25:11: 6000000 INFO @ Fri, 05 Jul 2019 12:25:19: 7000000 INFO @ Fri, 05 Jul 2019 12:25:20: 8000000 INFO @ Fri, 05 Jul 2019 12:25:25: 7000000 INFO @ Fri, 05 Jul 2019 12:25:31: 9000000 INFO @ Fri, 05 Jul 2019 12:25:31: 8000000 INFO @ Fri, 05 Jul 2019 12:25:37: 8000000 INFO @ Fri, 05 Jul 2019 12:25:43: 9000000 INFO @ Fri, 05 Jul 2019 12:25:44: 10000000 INFO @ Fri, 05 Jul 2019 12:25:50: 9000000 INFO @ Fri, 05 Jul 2019 12:25:54: 10000000 INFO @ Fri, 05 Jul 2019 12:25:55: 11000000 INFO @ Fri, 05 Jul 2019 12:26:02: 10000000 INFO @ Fri, 05 Jul 2019 12:26:05: 11000000 INFO @ Fri, 05 Jul 2019 12:26:05: 12000000 INFO @ Fri, 05 Jul 2019 12:26:14: 11000000 INFO @ Fri, 05 Jul 2019 12:26:15: 12000000 INFO @ Fri, 05 Jul 2019 12:26:17: 13000000 INFO @ Fri, 05 Jul 2019 12:26:26: 13000000 INFO @ Fri, 05 Jul 2019 12:26:26: 12000000 INFO @ Fri, 05 Jul 2019 12:26:29: 14000000 INFO @ Fri, 05 Jul 2019 12:26:38: 14000000 INFO @ Fri, 05 Jul 2019 12:26:38: 13000000 INFO @ Fri, 05 Jul 2019 12:26:40: 15000000 INFO @ Fri, 05 Jul 2019 12:26:48: 15000000 INFO @ Fri, 05 Jul 2019 12:26:52: 14000000 INFO @ Fri, 05 Jul 2019 12:26:53: 16000000 INFO @ Fri, 05 Jul 2019 12:26:59: 16000000 INFO @ Fri, 05 Jul 2019 12:27:04: 15000000 INFO @ Fri, 05 Jul 2019 12:27:06: 17000000 INFO @ Fri, 05 Jul 2019 12:27:11: 17000000 INFO @ Fri, 05 Jul 2019 12:27:17: 18000000 INFO @ Fri, 05 Jul 2019 12:27:17: 16000000 INFO @ Fri, 05 Jul 2019 12:27:22: 18000000 INFO @ Fri, 05 Jul 2019 12:27:28: 19000000 INFO @ Fri, 05 Jul 2019 12:27:31: 17000000 INFO @ Fri, 05 Jul 2019 12:27:34: 19000000 INFO @ Fri, 05 Jul 2019 12:27:40: 20000000 INFO @ Fri, 05 Jul 2019 12:27:44: 18000000 INFO @ Fri, 05 Jul 2019 12:27:46: 20000000 INFO @ Fri, 05 Jul 2019 12:27:51: 21000000 INFO @ Fri, 05 Jul 2019 12:27:57: 21000000 INFO @ Fri, 05 Jul 2019 12:27:57: 19000000 INFO @ Fri, 05 Jul 2019 12:28:02: 22000000 INFO @ Fri, 05 Jul 2019 12:28:09: 22000000 INFO @ Fri, 05 Jul 2019 12:28:10: 20000000 INFO @ Fri, 05 Jul 2019 12:28:12: 23000000 INFO @ Fri, 05 Jul 2019 12:28:21: 23000000 INFO @ Fri, 05 Jul 2019 12:28:23: 21000000 INFO @ Fri, 05 Jul 2019 12:28:24: 24000000 INFO @ Fri, 05 Jul 2019 12:28:33: 24000000 INFO @ Fri, 05 Jul 2019 12:28:35: 22000000 INFO @ Fri, 05 Jul 2019 12:28:39: 25000000 INFO @ Fri, 05 Jul 2019 12:28:44: 25000000 INFO @ Fri, 05 Jul 2019 12:28:50: 23000000 INFO @ Fri, 05 Jul 2019 12:28:51: 26000000 INFO @ Fri, 05 Jul 2019 12:28:55: 26000000 INFO @ Fri, 05 Jul 2019 12:29:02: 27000000 INFO @ Fri, 05 Jul 2019 12:29:05: 24000000 INFO @ Fri, 05 Jul 2019 12:29:07: 27000000 INFO @ Fri, 05 Jul 2019 12:29:13: 28000000 INFO @ Fri, 05 Jul 2019 12:29:17: 28000000 INFO @ Fri, 05 Jul 2019 12:29:19: 25000000 INFO @ Fri, 05 Jul 2019 12:29:24: 29000000 INFO @ Fri, 05 Jul 2019 12:29:29: 29000000 INFO @ Fri, 05 Jul 2019 12:29:31: 26000000 INFO @ Fri, 05 Jul 2019 12:29:36: 30000000 INFO @ Fri, 05 Jul 2019 12:29:40: 30000000 INFO @ Fri, 05 Jul 2019 12:29:45: 27000000 INFO @ Fri, 05 Jul 2019 12:29:46: 31000000 INFO @ Fri, 05 Jul 2019 12:29:51: 31000000 INFO @ Fri, 05 Jul 2019 12:29:57: 32000000 INFO @ Fri, 05 Jul 2019 12:29:58: 28000000 INFO @ Fri, 05 Jul 2019 12:30:01: 32000000 INFO @ Fri, 05 Jul 2019 12:30:09: 33000000 INFO @ Fri, 05 Jul 2019 12:30:10: 29000000 INFO @ Fri, 05 Jul 2019 12:30:12: 33000000 INFO @ Fri, 05 Jul 2019 12:30:21: 34000000 INFO @ Fri, 05 Jul 2019 12:30:21: 30000000 INFO @ Fri, 05 Jul 2019 12:30:23: 34000000 INFO @ Fri, 05 Jul 2019 12:30:33: 35000000 INFO @ Fri, 05 Jul 2019 12:30:34: 35000000 INFO @ Fri, 05 Jul 2019 12:30:35: 31000000 INFO @ Fri, 05 Jul 2019 12:30:44: 36000000 INFO @ Fri, 05 Jul 2019 12:30:45: 36000000 INFO @ Fri, 05 Jul 2019 12:30:49: 32000000 INFO @ Fri, 05 Jul 2019 12:30:57: 37000000 INFO @ Fri, 05 Jul 2019 12:30:58: 37000000 INFO @ Fri, 05 Jul 2019 12:31:04: 33000000 INFO @ Fri, 05 Jul 2019 12:31:09: 38000000 INFO @ Fri, 05 Jul 2019 12:31:10: 38000000 INFO @ Fri, 05 Jul 2019 12:31:17: 34000000 INFO @ Fri, 05 Jul 2019 12:31:20: 39000000 INFO @ Fri, 05 Jul 2019 12:31:21: 39000000 INFO @ Fri, 05 Jul 2019 12:31:31: 35000000 INFO @ Fri, 05 Jul 2019 12:31:32: 40000000 INFO @ Fri, 05 Jul 2019 12:31:33: 40000000 INFO @ Fri, 05 Jul 2019 12:31:43: 41000000 INFO @ Fri, 05 Jul 2019 12:31:44: 41000000 INFO @ Fri, 05 Jul 2019 12:31:44: 36000000 INFO @ Fri, 05 Jul 2019 12:31:54: 42000000 INFO @ Fri, 05 Jul 2019 12:31:55: 42000000 INFO @ Fri, 05 Jul 2019 12:31:56: 37000000 INFO @ Fri, 05 Jul 2019 12:32:04: 43000000 INFO @ Fri, 05 Jul 2019 12:32:05: 43000000 INFO @ Fri, 05 Jul 2019 12:32:08: 38000000 INFO @ Fri, 05 Jul 2019 12:32:15: 44000000 INFO @ Fri, 05 Jul 2019 12:32:15: 44000000 INFO @ Fri, 05 Jul 2019 12:32:21: 39000000 INFO @ Fri, 05 Jul 2019 12:32:25: 45000000 INFO @ Fri, 05 Jul 2019 12:32:27: 45000000 INFO @ Fri, 05 Jul 2019 12:32:30: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:32:32: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:32:32: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:32:32: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:32:32: #1 total tags in treatment: 45454994 INFO @ Fri, 05 Jul 2019 12:32:32: #1 total tags in treatment: 45454994 INFO @ Fri, 05 Jul 2019 12:32:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:32:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:32:32: #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 12:32:32: #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 12:32:33: 40000000 INFO @ Fri, 05 Jul 2019 12:32:34: #1 tags after filtering in treatment: 45454830 INFO @ Fri, 05 Jul 2019 12:32:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:32:34: #1 finished! INFO @ Fri, 05 Jul 2019 12:32:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:32:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:32:34: #1 tags after filtering in treatment: 45454830 INFO @ Fri, 05 Jul 2019 12:32:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:32:34: #1 finished! INFO @ Fri, 05 Jul 2019 12:32:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:32:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:32:45: 41000000 INFO @ Fri, 05 Jul 2019 12:32:47: #2 number of paired peaks: 112054 INFO @ Fri, 05 Jul 2019 12:32:47: start model_add_line... INFO @ Fri, 05 Jul 2019 12:32:47: #2 number of paired peaks: 112054 INFO @ Fri, 05 Jul 2019 12:32:47: start model_add_line... INFO @ Fri, 05 Jul 2019 12:32:49: start X-correlation... INFO @ Fri, 05 Jul 2019 12:32:49: end of X-cor INFO @ Fri, 05 Jul 2019 12:32:49: #2 finished! INFO @ Fri, 05 Jul 2019 12:32:49: #2 predicted fragment length is 127 bps INFO @ Fri, 05 Jul 2019 12:32:49: #2 alternative fragment length(s) may be 3,127 bps INFO @ Fri, 05 Jul 2019 12:32:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.10_model.r INFO @ Fri, 05 Jul 2019 12:32:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:32:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:32:49: start X-correlation... INFO @ Fri, 05 Jul 2019 12:32:49: end of X-cor INFO @ Fri, 05 Jul 2019 12:32:49: #2 finished! INFO @ Fri, 05 Jul 2019 12:32:49: #2 predicted fragment length is 127 bps INFO @ Fri, 05 Jul 2019 12:32:49: #2 alternative fragment length(s) may be 3,127 bps INFO @ Fri, 05 Jul 2019 12:32:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.20_model.r INFO @ Fri, 05 Jul 2019 12:32:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:32:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:32:56: 42000000 INFO @ Fri, 05 Jul 2019 12:33:08: 43000000 INFO @ Fri, 05 Jul 2019 12:33:19: 44000000 INFO @ Fri, 05 Jul 2019 12:33:30: 45000000 INFO @ Fri, 05 Jul 2019 12:33:36: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:33:36: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:33:36: #1 total tags in treatment: 45454994 INFO @ Fri, 05 Jul 2019 12:33:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:33:36: #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 12:33:37: #1 tags after filtering in treatment: 45454830 INFO @ Fri, 05 Jul 2019 12:33:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:33:37: #1 finished! INFO @ Fri, 05 Jul 2019 12:33:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:33:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:33:49: #2 number of paired peaks: 112054 INFO @ Fri, 05 Jul 2019 12:33:49: start model_add_line... INFO @ Fri, 05 Jul 2019 12:33:51: start X-correlation... INFO @ Fri, 05 Jul 2019 12:33:51: end of X-cor INFO @ Fri, 05 Jul 2019 12:33:51: #2 finished! INFO @ Fri, 05 Jul 2019 12:33:51: #2 predicted fragment length is 127 bps INFO @ Fri, 05 Jul 2019 12:33:51: #2 alternative fragment length(s) may be 3,127 bps INFO @ Fri, 05 Jul 2019 12:33:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.05_model.r INFO @ Fri, 05 Jul 2019 12:33:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:33:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:35:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:35:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:36:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:36:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:36:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:36:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.20_summits.bed INFO @ Fri, 05 Jul 2019 12:36:32: Done! INFO @ Fri, 05 Jul 2019 12:36:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.10_peaks.xls pass1 - making usageList (134 chroms): 13 millis pass2 - checking and writing primary data (44134 records, 4 fields): 63 millis INFO @ Fri, 05 Jul 2019 12:36:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:36:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.10_summits.bed INFO @ Fri, 05 Jul 2019 12:36:34: Done! pass1 - making usageList (164 chroms): 17 millis pass2 - checking and writing primary data (68451 records, 4 fields): 99 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:37:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:37:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:37:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102017/ERX102017.05_summits.bed INFO @ Fri, 05 Jul 2019 12:37:39: Done! pass1 - making usageList (185 chroms): 18 millis pass2 - checking and writing primary data (92519 records, 4 fields): 127 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。