Job ID = 2640528 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:28:16 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 ) 2019-08-24T08:33:26 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 ) 2019-08-24T08:33:26 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 : 23,450,119 reads read : 46,900,238 reads written : 23,450,119 reads 0-length : 23,450,119 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:15:32 23450119 reads; of these: 23450119 (100.00%) were unpaired; of these: 740019 (3.16%) aligned 0 times 19368330 (82.59%) aligned exactly 1 time 3341770 (14.25%) aligned >1 times 96.84% overall alignment rate Time searching: 00:15:35 Overall time: 00:15:35 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 12 files... [bam_rmdupse_core] 4183580 / 22710100 = 0.1842 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:58:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.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 @ Sat, 24 Aug 2019 17:58:14: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:58:14: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:58:20: 1000000 INFO @ Sat, 24 Aug 2019 17:58:27: 2000000 INFO @ Sat, 24 Aug 2019 17:58:33: 3000000 INFO @ Sat, 24 Aug 2019 17:58:40: 4000000 INFO @ Sat, 24 Aug 2019 17:58:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.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 @ Sat, 24 Aug 2019 17:58:43: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:58:43: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:58:47: 5000000 INFO @ Sat, 24 Aug 2019 17:58:52: 1000000 INFO @ Sat, 24 Aug 2019 17:58:54: 6000000 INFO @ Sat, 24 Aug 2019 17:59:01: 7000000 INFO @ Sat, 24 Aug 2019 17:59:01: 2000000 INFO @ Sat, 24 Aug 2019 17:59:08: 8000000 INFO @ Sat, 24 Aug 2019 17:59:09: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:59:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.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 @ Sat, 24 Aug 2019 17:59:13: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:59:13: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:59:15: 9000000 INFO @ Sat, 24 Aug 2019 17:59:18: 4000000 INFO @ Sat, 24 Aug 2019 17:59:21: 1000000 INFO @ Sat, 24 Aug 2019 17:59:22: 10000000 INFO @ Sat, 24 Aug 2019 17:59:27: 5000000 INFO @ Sat, 24 Aug 2019 17:59:28: 2000000 INFO @ Sat, 24 Aug 2019 17:59:29: 11000000 INFO @ Sat, 24 Aug 2019 17:59:36: 3000000 INFO @ Sat, 24 Aug 2019 17:59:36: 6000000 INFO @ Sat, 24 Aug 2019 17:59:36: 12000000 INFO @ Sat, 24 Aug 2019 17:59:43: 13000000 INFO @ Sat, 24 Aug 2019 17:59:43: 4000000 INFO @ Sat, 24 Aug 2019 17:59:45: 7000000 INFO @ Sat, 24 Aug 2019 17:59:50: 14000000 INFO @ Sat, 24 Aug 2019 17:59:51: 5000000 INFO @ Sat, 24 Aug 2019 17:59:54: 8000000 INFO @ Sat, 24 Aug 2019 17:59:57: 15000000 INFO @ Sat, 24 Aug 2019 17:59:59: 6000000 INFO @ Sat, 24 Aug 2019 18:00:03: 9000000 INFO @ Sat, 24 Aug 2019 18:00:05: 16000000 INFO @ Sat, 24 Aug 2019 18:00:06: 7000000 INFO @ Sat, 24 Aug 2019 18:00:12: 17000000 INFO @ Sat, 24 Aug 2019 18:00:13: 10000000 INFO @ Sat, 24 Aug 2019 18:00:14: 8000000 INFO @ Sat, 24 Aug 2019 18:00:19: 18000000 INFO @ Sat, 24 Aug 2019 18:00:22: 9000000 INFO @ Sat, 24 Aug 2019 18:00:22: 11000000 INFO @ Sat, 24 Aug 2019 18:00:23: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:00:23: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:00:23: #1 total tags in treatment: 18526520 INFO @ Sat, 24 Aug 2019 18:00:23: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:00:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:00:23: #1 tags after filtering in treatment: 18526283 INFO @ Sat, 24 Aug 2019 18:00:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:00:23: #1 finished! INFO @ Sat, 24 Aug 2019 18:00:23: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:00:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:00:28: #2 number of paired peaks: 73760 INFO @ Sat, 24 Aug 2019 18:00:28: start model_add_line... INFO @ Sat, 24 Aug 2019 18:00:29: start X-correlation... INFO @ Sat, 24 Aug 2019 18:00:29: end of X-cor INFO @ Sat, 24 Aug 2019 18:00:29: #2 finished! INFO @ Sat, 24 Aug 2019 18:00:29: #2 predicted fragment length is 158 bps INFO @ Sat, 24 Aug 2019 18:00:29: #2 alternative fragment length(s) may be 158 bps INFO @ Sat, 24 Aug 2019 18:00:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.05_model.r INFO @ Sat, 24 Aug 2019 18:00:29: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:00:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:00:30: 10000000 INFO @ Sat, 24 Aug 2019 18:00:32: 12000000 INFO @ Sat, 24 Aug 2019 18:00:38: 11000000 INFO @ Sat, 24 Aug 2019 18:00:42: 13000000 INFO @ Sat, 24 Aug 2019 18:00:47: 12000000 INFO @ Sat, 24 Aug 2019 18:00:51: 14000000 INFO @ Sat, 24 Aug 2019 18:00:55: 13000000 INFO @ Sat, 24 Aug 2019 18:01:01: 15000000 INFO @ Sat, 24 Aug 2019 18:01:03: 14000000 INFO @ Sat, 24 Aug 2019 18:01:10: 16000000 INFO @ Sat, 24 Aug 2019 18:01:11: 15000000 INFO @ Sat, 24 Aug 2019 18:01:19: 16000000 INFO @ Sat, 24 Aug 2019 18:01:20: 17000000 INFO @ Sat, 24 Aug 2019 18:01:27: 17000000 INFO @ Sat, 24 Aug 2019 18:01:28: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:01:29: 18000000 INFO @ Sat, 24 Aug 2019 18:01:35: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:01:35: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:01:35: #1 total tags in treatment: 18526520 INFO @ Sat, 24 Aug 2019 18:01:35: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:01:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:01:35: #1 tags after filtering in treatment: 18526283 INFO @ Sat, 24 Aug 2019 18:01:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:01:35: #1 finished! INFO @ Sat, 24 Aug 2019 18:01:35: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:01:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:01:35: 18000000 INFO @ Sat, 24 Aug 2019 18:01:39: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:01:39: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:01:39: #1 total tags in treatment: 18526520 INFO @ Sat, 24 Aug 2019 18:01:39: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:01:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:01:40: #1 tags after filtering in treatment: 18526283 INFO @ Sat, 24 Aug 2019 18:01:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:01:40: #1 finished! INFO @ Sat, 24 Aug 2019 18:01:40: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:01:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:01:40: #2 number of paired peaks: 73760 INFO @ Sat, 24 Aug 2019 18:01:40: start model_add_line... INFO @ Sat, 24 Aug 2019 18:01:41: start X-correlation... INFO @ Sat, 24 Aug 2019 18:01:41: end of X-cor INFO @ Sat, 24 Aug 2019 18:01:41: #2 finished! INFO @ Sat, 24 Aug 2019 18:01:41: #2 predicted fragment length is 158 bps INFO @ Sat, 24 Aug 2019 18:01:41: #2 alternative fragment length(s) may be 158 bps INFO @ Sat, 24 Aug 2019 18:01:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.10_model.r INFO @ Sat, 24 Aug 2019 18:01:41: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:01:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:01:45: #2 number of paired peaks: 73760 INFO @ Sat, 24 Aug 2019 18:01:45: start model_add_line... INFO @ Sat, 24 Aug 2019 18:01:45: start X-correlation... INFO @ Sat, 24 Aug 2019 18:01:45: end of X-cor INFO @ Sat, 24 Aug 2019 18:01:45: #2 finished! INFO @ Sat, 24 Aug 2019 18:01:45: #2 predicted fragment length is 158 bps INFO @ Sat, 24 Aug 2019 18:01:45: #2 alternative fragment length(s) may be 158 bps INFO @ Sat, 24 Aug 2019 18:01:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.20_model.r INFO @ Sat, 24 Aug 2019 18:01:45: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:01:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:02:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:02:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:02:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.05_summits.bed INFO @ Sat, 24 Aug 2019 18:02:01: Done! pass1 - making usageList (133 chroms): 11 millis pass2 - checking and writing primary data (47239 records, 4 fields): 64 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:02:40: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:02:45: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:03:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:03:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:03:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.10_summits.bed INFO @ Sat, 24 Aug 2019 18:03:13: Done! pass1 - making usageList (114 chroms): 7 millis pass2 - checking and writing primary data (34834 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:03:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:03:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:03:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375004/SRX5375004.20_summits.bed INFO @ Sat, 24 Aug 2019 18:03:17: Done! pass1 - making usageList (87 chroms): 7 millis pass2 - checking and writing primary data (21426 records, 4 fields): 30 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。