Job ID = 1298423 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:29:54 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 : 28,454,075 reads read : 28,454,075 reads written : 28,454,075 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:06:50 28454075 reads; of these: 28454075 (100.00%) were unpaired; of these: 1771274 (6.23%) aligned 0 times 24318213 (85.46%) aligned exactly 1 time 2364588 (8.31%) aligned >1 times 93.77% overall alignment rate Time searching: 00:06:50 Overall time: 00:06:50 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 12 files... [bam_rmdupse_core] 7210340 / 26682801 = 0.2702 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 @ Mon, 03 Jun 2019 17:50:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.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 @ Mon, 03 Jun 2019 17:50:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:50:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:50:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.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 @ Mon, 03 Jun 2019 17:50:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:50:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:50:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.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 @ Mon, 03 Jun 2019 17:50:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:50:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:50:07: 1000000 INFO @ Mon, 03 Jun 2019 17:50:08: 1000000 INFO @ Mon, 03 Jun 2019 17:50:08: 1000000 INFO @ Mon, 03 Jun 2019 17:50:14: 2000000 INFO @ Mon, 03 Jun 2019 17:50:16: 2000000 INFO @ Mon, 03 Jun 2019 17:50:16: 2000000 INFO @ Mon, 03 Jun 2019 17:50:21: 3000000 INFO @ Mon, 03 Jun 2019 17:50:24: 3000000 INFO @ Mon, 03 Jun 2019 17:50:25: 3000000 INFO @ Mon, 03 Jun 2019 17:50:29: 4000000 INFO @ Mon, 03 Jun 2019 17:50:32: 4000000 INFO @ Mon, 03 Jun 2019 17:50:33: 4000000 INFO @ Mon, 03 Jun 2019 17:50:36: 5000000 INFO @ Mon, 03 Jun 2019 17:50:39: 5000000 INFO @ Mon, 03 Jun 2019 17:50:40: 5000000 INFO @ Mon, 03 Jun 2019 17:50:44: 6000000 INFO @ Mon, 03 Jun 2019 17:50:47: 6000000 INFO @ Mon, 03 Jun 2019 17:50:48: 6000000 INFO @ Mon, 03 Jun 2019 17:50:51: 7000000 INFO @ Mon, 03 Jun 2019 17:50:54: 7000000 INFO @ Mon, 03 Jun 2019 17:50:55: 7000000 INFO @ Mon, 03 Jun 2019 17:50:58: 8000000 INFO @ Mon, 03 Jun 2019 17:51:01: 8000000 INFO @ Mon, 03 Jun 2019 17:51:02: 8000000 INFO @ Mon, 03 Jun 2019 17:51:05: 9000000 INFO @ Mon, 03 Jun 2019 17:51:08: 9000000 INFO @ Mon, 03 Jun 2019 17:51:10: 9000000 INFO @ Mon, 03 Jun 2019 17:51:11: 10000000 INFO @ Mon, 03 Jun 2019 17:51:14: 10000000 INFO @ Mon, 03 Jun 2019 17:51:17: 10000000 INFO @ Mon, 03 Jun 2019 17:51:18: 11000000 INFO @ Mon, 03 Jun 2019 17:51:22: 11000000 INFO @ Mon, 03 Jun 2019 17:51:25: 11000000 INFO @ Mon, 03 Jun 2019 17:51:25: 12000000 INFO @ Mon, 03 Jun 2019 17:51:28: 12000000 INFO @ Mon, 03 Jun 2019 17:51:32: 13000000 INFO @ Mon, 03 Jun 2019 17:51:32: 12000000 INFO @ Mon, 03 Jun 2019 17:51:35: 13000000 INFO @ Mon, 03 Jun 2019 17:51:38: 14000000 INFO @ Mon, 03 Jun 2019 17:51:39: 13000000 INFO @ Mon, 03 Jun 2019 17:51:42: 14000000 INFO @ Mon, 03 Jun 2019 17:51:45: 15000000 INFO @ Mon, 03 Jun 2019 17:51:46: 14000000 INFO @ Mon, 03 Jun 2019 17:51:49: 15000000 INFO @ Mon, 03 Jun 2019 17:51:52: 16000000 INFO @ Mon, 03 Jun 2019 17:51:54: 15000000 INFO @ Mon, 03 Jun 2019 17:51:56: 16000000 INFO @ Mon, 03 Jun 2019 17:51:59: 17000000 INFO @ Mon, 03 Jun 2019 17:52:01: 16000000 INFO @ Mon, 03 Jun 2019 17:52:03: 17000000 INFO @ Mon, 03 Jun 2019 17:52:06: 18000000 INFO @ Mon, 03 Jun 2019 17:52:08: 17000000 INFO @ Mon, 03 Jun 2019 17:52:09: 18000000 INFO @ Mon, 03 Jun 2019 17:52:12: 19000000 INFO @ Mon, 03 Jun 2019 17:52:15: 18000000 INFO @ Mon, 03 Jun 2019 17:52:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:52:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:52:16: #1 total tags in treatment: 19472461 INFO @ Mon, 03 Jun 2019 17:52:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:52:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 17:52:16: 19000000 INFO @ Mon, 03 Jun 2019 17:52:16: #1 tags after filtering in treatment: 19472461 INFO @ Mon, 03 Jun 2019 17:52:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:52:16: #1 finished! INFO @ Mon, 03 Jun 2019 17:52:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:52:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:52:18: #2 number of paired peaks: 30 WARNING @ Mon, 03 Jun 2019 17:52:18: Too few paired peaks (30) 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 @ Mon, 03 Jun 2019 17:52:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.20_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/SRX467031/SRX467031.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:52:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:52:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:52:19: #1 total tags in treatment: 19472461 INFO @ Mon, 03 Jun 2019 17:52:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:52:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 17:52:20: #1 tags after filtering in treatment: 19472461 INFO @ Mon, 03 Jun 2019 17:52:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:52:20: #1 finished! INFO @ Mon, 03 Jun 2019 17:52:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:52:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:52:21: #2 number of paired peaks: 30 WARNING @ Mon, 03 Jun 2019 17:52:21: Too few paired peaks (30) 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 @ Mon, 03 Jun 2019 17:52:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.05_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/SRX467031/SRX467031.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:52:22: 19000000 INFO @ Mon, 03 Jun 2019 17:52:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:52:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:52:26: #1 total tags in treatment: 19472461 INFO @ Mon, 03 Jun 2019 17:52:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:52:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 17:52:26: #1 tags after filtering in treatment: 19472461 INFO @ Mon, 03 Jun 2019 17:52:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:52:26: #1 finished! INFO @ Mon, 03 Jun 2019 17:52:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:52:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:52:28: #2 number of paired peaks: 30 WARNING @ Mon, 03 Jun 2019 17:52:28: Too few paired peaks (30) 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 @ Mon, 03 Jun 2019 17:52:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.10_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/SRX467031/SRX467031.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467031/SRX467031.10_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。