Job ID = 2590324 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T11:53:46 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 ) 2019-08-12T12:54:28 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 : 142,082,745 reads read : 142,082,745 reads written : 142,082,745 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: 00:00:00 Multiseed full-index search: 00:41:42 142082745 reads; of these: 142082745 (100.00%) were unpaired; of these: 37389907 (26.32%) aligned 0 times 96699075 (68.06%) aligned exactly 1 time 7993763 (5.63%) aligned >1 times 73.68% overall alignment rate Time searching: 00:41:42 Overall time: 00:41:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 44 files... [bam_rmdupse_core] 62530471 / 104692838 = 0.5973 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 @ Tue, 13 Aug 2019 00:13:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 13 Aug 2019 00:13:15: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:13:15: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:13:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 13 Aug 2019 00:13:16: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:13:16: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:13:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 13 Aug 2019 00:13:17: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:13:17: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:13:25: 1000000 INFO @ Tue, 13 Aug 2019 00:13:30: 1000000 INFO @ Tue, 13 Aug 2019 00:13:30: 1000000 INFO @ Tue, 13 Aug 2019 00:13:36: 2000000 INFO @ Tue, 13 Aug 2019 00:13:43: 2000000 INFO @ Tue, 13 Aug 2019 00:13:43: 2000000 INFO @ Tue, 13 Aug 2019 00:13:46: 3000000 INFO @ Tue, 13 Aug 2019 00:13:55: 3000000 INFO @ Tue, 13 Aug 2019 00:13:55: 4000000 INFO @ Tue, 13 Aug 2019 00:13:55: 3000000 INFO @ Tue, 13 Aug 2019 00:14:05: 5000000 INFO @ Tue, 13 Aug 2019 00:14:07: 4000000 INFO @ Tue, 13 Aug 2019 00:14:08: 4000000 INFO @ Tue, 13 Aug 2019 00:14:16: 6000000 INFO @ Tue, 13 Aug 2019 00:14:19: 5000000 INFO @ Tue, 13 Aug 2019 00:14:20: 5000000 INFO @ Tue, 13 Aug 2019 00:14:26: 7000000 INFO @ Tue, 13 Aug 2019 00:14:31: 6000000 INFO @ Tue, 13 Aug 2019 00:14:32: 6000000 INFO @ Tue, 13 Aug 2019 00:14:35: 8000000 INFO @ Tue, 13 Aug 2019 00:14:43: 7000000 INFO @ Tue, 13 Aug 2019 00:14:44: 7000000 INFO @ Tue, 13 Aug 2019 00:14:45: 9000000 INFO @ Tue, 13 Aug 2019 00:14:55: 8000000 INFO @ Tue, 13 Aug 2019 00:14:55: 10000000 INFO @ Tue, 13 Aug 2019 00:14:57: 8000000 INFO @ Tue, 13 Aug 2019 00:15:05: 11000000 INFO @ Tue, 13 Aug 2019 00:15:06: 9000000 INFO @ Tue, 13 Aug 2019 00:15:09: 9000000 INFO @ Tue, 13 Aug 2019 00:15:14: 12000000 INFO @ Tue, 13 Aug 2019 00:15:18: 10000000 INFO @ Tue, 13 Aug 2019 00:15:21: 10000000 INFO @ Tue, 13 Aug 2019 00:15:24: 13000000 INFO @ Tue, 13 Aug 2019 00:15:30: 11000000 INFO @ Tue, 13 Aug 2019 00:15:33: 11000000 INFO @ Tue, 13 Aug 2019 00:15:34: 14000000 INFO @ Tue, 13 Aug 2019 00:15:42: 12000000 INFO @ Tue, 13 Aug 2019 00:15:43: 15000000 INFO @ Tue, 13 Aug 2019 00:15:46: 12000000 INFO @ Tue, 13 Aug 2019 00:15:53: 16000000 INFO @ Tue, 13 Aug 2019 00:15:53: 13000000 INFO @ Tue, 13 Aug 2019 00:15:58: 13000000 INFO @ Tue, 13 Aug 2019 00:16:03: 17000000 INFO @ Tue, 13 Aug 2019 00:16:05: 14000000 INFO @ Tue, 13 Aug 2019 00:16:10: 14000000 INFO @ Tue, 13 Aug 2019 00:16:13: 18000000 INFO @ Tue, 13 Aug 2019 00:16:17: 15000000 INFO @ Tue, 13 Aug 2019 00:16:22: 19000000 INFO @ Tue, 13 Aug 2019 00:16:23: 15000000 INFO @ Tue, 13 Aug 2019 00:16:29: 16000000 INFO @ Tue, 13 Aug 2019 00:16:32: 20000000 INFO @ Tue, 13 Aug 2019 00:16:35: 16000000 INFO @ Tue, 13 Aug 2019 00:16:41: 17000000 INFO @ Tue, 13 Aug 2019 00:16:43: 21000000 INFO @ Tue, 13 Aug 2019 00:16:47: 17000000 INFO @ Tue, 13 Aug 2019 00:16:52: 18000000 INFO @ Tue, 13 Aug 2019 00:16:53: 22000000 INFO @ Tue, 13 Aug 2019 00:16:59: 18000000 INFO @ Tue, 13 Aug 2019 00:17:03: 23000000 INFO @ Tue, 13 Aug 2019 00:17:04: 19000000 INFO @ Tue, 13 Aug 2019 00:17:12: 19000000 INFO @ Tue, 13 Aug 2019 00:17:13: 24000000 INFO @ Tue, 13 Aug 2019 00:17:16: 20000000 INFO @ Tue, 13 Aug 2019 00:17:22: 25000000 INFO @ Tue, 13 Aug 2019 00:17:25: 20000000 INFO @ Tue, 13 Aug 2019 00:17:27: 21000000 INFO @ Tue, 13 Aug 2019 00:17:32: 26000000 INFO @ Tue, 13 Aug 2019 00:17:37: 21000000 INFO @ Tue, 13 Aug 2019 00:17:39: 22000000 INFO @ Tue, 13 Aug 2019 00:17:42: 27000000 INFO @ Tue, 13 Aug 2019 00:17:49: 22000000 INFO @ Tue, 13 Aug 2019 00:17:51: 23000000 INFO @ Tue, 13 Aug 2019 00:17:51: 28000000 INFO @ Tue, 13 Aug 2019 00:18:01: 29000000 INFO @ Tue, 13 Aug 2019 00:18:01: 23000000 INFO @ Tue, 13 Aug 2019 00:18:02: 24000000 INFO @ Tue, 13 Aug 2019 00:18:11: 30000000 INFO @ Tue, 13 Aug 2019 00:18:14: 24000000 INFO @ Tue, 13 Aug 2019 00:18:14: 25000000 INFO @ Tue, 13 Aug 2019 00:18:20: 31000000 INFO @ Tue, 13 Aug 2019 00:18:26: 26000000 INFO @ Tue, 13 Aug 2019 00:18:26: 25000000 INFO @ Tue, 13 Aug 2019 00:18:30: 32000000 INFO @ Tue, 13 Aug 2019 00:18:38: 27000000 INFO @ Tue, 13 Aug 2019 00:18:38: 26000000 INFO @ Tue, 13 Aug 2019 00:18:40: 33000000 INFO @ Tue, 13 Aug 2019 00:18:49: 28000000 INFO @ Tue, 13 Aug 2019 00:18:50: 34000000 INFO @ Tue, 13 Aug 2019 00:18:51: 27000000 INFO @ Tue, 13 Aug 2019 00:18:59: 35000000 INFO @ Tue, 13 Aug 2019 00:19:01: 29000000 INFO @ Tue, 13 Aug 2019 00:19:03: 28000000 INFO @ Tue, 13 Aug 2019 00:19:09: 36000000 INFO @ Tue, 13 Aug 2019 00:19:13: 30000000 INFO @ Tue, 13 Aug 2019 00:19:16: 29000000 INFO @ Tue, 13 Aug 2019 00:19:19: 37000000 INFO @ Tue, 13 Aug 2019 00:19:25: 31000000 INFO @ Tue, 13 Aug 2019 00:19:28: 30000000 INFO @ Tue, 13 Aug 2019 00:19:28: 38000000 INFO @ Tue, 13 Aug 2019 00:19:36: 32000000 INFO @ Tue, 13 Aug 2019 00:19:38: 39000000 INFO @ Tue, 13 Aug 2019 00:19:41: 31000000 INFO @ Tue, 13 Aug 2019 00:19:48: 40000000 INFO @ Tue, 13 Aug 2019 00:19:48: 33000000 INFO @ Tue, 13 Aug 2019 00:19:53: 32000000 INFO @ Tue, 13 Aug 2019 00:19:57: 41000000 INFO @ Tue, 13 Aug 2019 00:20:00: 34000000 INFO @ Tue, 13 Aug 2019 00:20:06: 33000000 INFO @ Tue, 13 Aug 2019 00:20:07: 42000000 INFO @ Tue, 13 Aug 2019 00:20:09: #1 tag size is determined as 76 bps INFO @ Tue, 13 Aug 2019 00:20:09: #1 tag size = 76 INFO @ Tue, 13 Aug 2019 00:20:09: #1 total tags in treatment: 42162367 INFO @ Tue, 13 Aug 2019 00:20:09: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:20:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:20:10: #1 tags after filtering in treatment: 42162367 INFO @ Tue, 13 Aug 2019 00:20:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:20:10: #1 finished! INFO @ Tue, 13 Aug 2019 00:20:10: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:20:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:20:12: 35000000 INFO @ Tue, 13 Aug 2019 00:20:13: #2 number of paired peaks: 50 WARNING @ Tue, 13 Aug 2019 00:20:13: Too few paired peaks (50) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Tue, 13 Aug 2019 00:20:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:20:18: 34000000 INFO @ Tue, 13 Aug 2019 00:20:23: 36000000 INFO @ Tue, 13 Aug 2019 00:20:30: 35000000 INFO @ Tue, 13 Aug 2019 00:20:35: 37000000 INFO @ Tue, 13 Aug 2019 00:20:43: 36000000 INFO @ Tue, 13 Aug 2019 00:20:46: 38000000 INFO @ Tue, 13 Aug 2019 00:20:55: 37000000 INFO @ Tue, 13 Aug 2019 00:20:58: 39000000 INFO @ Tue, 13 Aug 2019 00:21:08: 38000000 INFO @ Tue, 13 Aug 2019 00:21:09: 40000000 INFO @ Tue, 13 Aug 2019 00:21:20: 39000000 INFO @ Tue, 13 Aug 2019 00:21:21: 41000000 INFO @ Tue, 13 Aug 2019 00:21:32: 42000000 INFO @ Tue, 13 Aug 2019 00:21:32: 40000000 INFO @ Tue, 13 Aug 2019 00:21:34: #1 tag size is determined as 76 bps INFO @ Tue, 13 Aug 2019 00:21:34: #1 tag size = 76 INFO @ Tue, 13 Aug 2019 00:21:34: #1 total tags in treatment: 42162367 INFO @ Tue, 13 Aug 2019 00:21:34: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:21:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:21:35: #1 tags after filtering in treatment: 42162367 INFO @ Tue, 13 Aug 2019 00:21:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:21:35: #1 finished! INFO @ Tue, 13 Aug 2019 00:21:35: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:21:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:21:38: #2 number of paired peaks: 50 WARNING @ Tue, 13 Aug 2019 00:21:38: Too few paired peaks (50) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Tue, 13 Aug 2019 00:21:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:21:44: 41000000 INFO @ Tue, 13 Aug 2019 00:21:56: 42000000 INFO @ Tue, 13 Aug 2019 00:21:58: #1 tag size is determined as 76 bps INFO @ Tue, 13 Aug 2019 00:21:58: #1 tag size = 76 INFO @ Tue, 13 Aug 2019 00:21:58: #1 total tags in treatment: 42162367 INFO @ Tue, 13 Aug 2019 00:21:58: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:21:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:21:59: #1 tags after filtering in treatment: 42162367 INFO @ Tue, 13 Aug 2019 00:21:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:21:59: #1 finished! INFO @ Tue, 13 Aug 2019 00:21:59: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:21:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:22:02: #2 number of paired peaks: 50 WARNING @ Tue, 13 Aug 2019 00:22:02: Too few paired peaks (50) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Tue, 13 Aug 2019 00:22:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX370360/SRX370360.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。