Job ID = 1303370 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T11:23:43 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 ) 2019-06-03T11:23:43 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 ) 2019-06-03T11:23:43 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 : 52,440,933 reads read : 52,440,933 reads written : 52,440,933 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: 00:25:41 52440933 reads; of these: 52440933 (100.00%) were unpaired; of these: 1587507 (3.03%) aligned 0 times 35435684 (67.57%) aligned exactly 1 time 15417742 (29.40%) aligned >1 times 96.97% overall alignment rate Time searching: 00:25:41 Overall time: 00:25:41 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 24 files... [bam_rmdupse_core] 9357946 / 50853426 = 0.1840 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 21:29:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.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 21:29:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:29:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:29:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.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 21:29:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:29:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:29:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.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 21:29:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:29:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:29:39: 1000000 INFO @ Mon, 03 Jun 2019 21:29:41: 1000000 INFO @ Mon, 03 Jun 2019 21:29:41: 1000000 INFO @ Mon, 03 Jun 2019 21:29:46: 2000000 INFO @ Mon, 03 Jun 2019 21:29:50: 2000000 INFO @ Mon, 03 Jun 2019 21:29:51: 2000000 INFO @ Mon, 03 Jun 2019 21:29:54: 3000000 INFO @ Mon, 03 Jun 2019 21:30:00: 3000000 INFO @ Mon, 03 Jun 2019 21:30:01: 3000000 INFO @ Mon, 03 Jun 2019 21:30:02: 4000000 INFO @ Mon, 03 Jun 2019 21:30:10: 4000000 INFO @ Mon, 03 Jun 2019 21:30:10: 5000000 INFO @ Mon, 03 Jun 2019 21:30:11: 4000000 INFO @ Mon, 03 Jun 2019 21:30:18: 6000000 INFO @ Mon, 03 Jun 2019 21:30:20: 5000000 INFO @ Mon, 03 Jun 2019 21:30:21: 5000000 INFO @ Mon, 03 Jun 2019 21:30:26: 7000000 INFO @ Mon, 03 Jun 2019 21:30:30: 6000000 INFO @ Mon, 03 Jun 2019 21:30:31: 6000000 INFO @ Mon, 03 Jun 2019 21:30:34: 8000000 INFO @ Mon, 03 Jun 2019 21:30:40: 7000000 INFO @ Mon, 03 Jun 2019 21:30:41: 9000000 INFO @ Mon, 03 Jun 2019 21:30:41: 7000000 INFO @ Mon, 03 Jun 2019 21:30:50: 10000000 INFO @ Mon, 03 Jun 2019 21:30:50: 8000000 INFO @ Mon, 03 Jun 2019 21:30:52: 8000000 INFO @ Mon, 03 Jun 2019 21:30:58: 11000000 INFO @ Mon, 03 Jun 2019 21:31:00: 9000000 INFO @ Mon, 03 Jun 2019 21:31:01: 9000000 INFO @ Mon, 03 Jun 2019 21:31:06: 12000000 INFO @ Mon, 03 Jun 2019 21:31:09: 10000000 INFO @ Mon, 03 Jun 2019 21:31:11: 10000000 INFO @ Mon, 03 Jun 2019 21:31:14: 13000000 INFO @ Mon, 03 Jun 2019 21:31:19: 11000000 INFO @ Mon, 03 Jun 2019 21:31:20: 11000000 INFO @ Mon, 03 Jun 2019 21:31:22: 14000000 INFO @ Mon, 03 Jun 2019 21:31:28: 12000000 INFO @ Mon, 03 Jun 2019 21:31:30: 12000000 INFO @ Mon, 03 Jun 2019 21:31:31: 15000000 INFO @ Mon, 03 Jun 2019 21:31:38: 13000000 INFO @ Mon, 03 Jun 2019 21:31:39: 16000000 INFO @ Mon, 03 Jun 2019 21:31:39: 13000000 INFO @ Mon, 03 Jun 2019 21:31:47: 14000000 INFO @ Mon, 03 Jun 2019 21:31:47: 17000000 INFO @ Mon, 03 Jun 2019 21:31:49: 14000000 INFO @ Mon, 03 Jun 2019 21:31:55: 18000000 INFO @ Mon, 03 Jun 2019 21:31:56: 15000000 INFO @ Mon, 03 Jun 2019 21:31:58: 15000000 INFO @ Mon, 03 Jun 2019 21:32:03: 19000000 INFO @ Mon, 03 Jun 2019 21:32:06: 16000000 INFO @ Mon, 03 Jun 2019 21:32:08: 16000000 INFO @ Mon, 03 Jun 2019 21:32:12: 20000000 INFO @ Mon, 03 Jun 2019 21:32:15: 17000000 INFO @ Mon, 03 Jun 2019 21:32:17: 17000000 INFO @ Mon, 03 Jun 2019 21:32:20: 21000000 INFO @ Mon, 03 Jun 2019 21:32:25: 18000000 INFO @ Mon, 03 Jun 2019 21:32:27: 18000000 INFO @ Mon, 03 Jun 2019 21:32:28: 22000000 INFO @ Mon, 03 Jun 2019 21:32:35: 19000000 INFO @ Mon, 03 Jun 2019 21:32:36: 23000000 INFO @ Mon, 03 Jun 2019 21:32:37: 19000000 INFO @ Mon, 03 Jun 2019 21:32:43: 24000000 INFO @ Mon, 03 Jun 2019 21:32:45: 20000000 INFO @ Mon, 03 Jun 2019 21:32:47: 20000000 INFO @ Mon, 03 Jun 2019 21:32:52: 25000000 INFO @ Mon, 03 Jun 2019 21:32:54: 21000000 INFO @ Mon, 03 Jun 2019 21:32:57: 21000000 INFO @ Mon, 03 Jun 2019 21:32:59: 26000000 INFO @ Mon, 03 Jun 2019 21:33:03: 22000000 INFO @ Mon, 03 Jun 2019 21:33:07: 22000000 INFO @ Mon, 03 Jun 2019 21:33:07: 27000000 INFO @ Mon, 03 Jun 2019 21:33:12: 23000000 INFO @ Mon, 03 Jun 2019 21:33:14: 28000000 INFO @ Mon, 03 Jun 2019 21:33:16: 23000000 INFO @ Mon, 03 Jun 2019 21:33:20: 24000000 INFO @ Mon, 03 Jun 2019 21:33:22: 29000000 INFO @ Mon, 03 Jun 2019 21:33:25: 24000000 INFO @ Mon, 03 Jun 2019 21:33:28: 25000000 INFO @ Mon, 03 Jun 2019 21:33:31: 30000000 INFO @ Mon, 03 Jun 2019 21:33:35: 25000000 INFO @ Mon, 03 Jun 2019 21:33:37: 26000000 INFO @ Mon, 03 Jun 2019 21:33:39: 31000000 INFO @ Mon, 03 Jun 2019 21:33:44: 26000000 INFO @ Mon, 03 Jun 2019 21:33:44: 27000000 INFO @ Mon, 03 Jun 2019 21:33:47: 32000000 INFO @ Mon, 03 Jun 2019 21:33:53: 28000000 INFO @ Mon, 03 Jun 2019 21:33:54: 27000000 INFO @ Mon, 03 Jun 2019 21:33:55: 33000000 INFO @ Mon, 03 Jun 2019 21:34:01: 29000000 INFO @ Mon, 03 Jun 2019 21:34:04: 34000000 INFO @ Mon, 03 Jun 2019 21:34:04: 28000000 INFO @ Mon, 03 Jun 2019 21:34:10: 30000000 INFO @ Mon, 03 Jun 2019 21:34:12: 35000000 INFO @ Mon, 03 Jun 2019 21:34:14: 29000000 INFO @ Mon, 03 Jun 2019 21:34:18: 31000000 INFO @ Mon, 03 Jun 2019 21:34:21: 36000000 INFO @ Mon, 03 Jun 2019 21:34:24: 30000000 INFO @ Mon, 03 Jun 2019 21:34:26: 32000000 INFO @ Mon, 03 Jun 2019 21:34:29: 37000000 INFO @ Mon, 03 Jun 2019 21:34:33: 31000000 INFO @ Mon, 03 Jun 2019 21:34:35: 33000000 INFO @ Mon, 03 Jun 2019 21:34:38: 38000000 INFO @ Mon, 03 Jun 2019 21:34:42: 34000000 INFO @ Mon, 03 Jun 2019 21:34:43: 32000000 INFO @ Mon, 03 Jun 2019 21:34:46: 39000000 INFO @ Mon, 03 Jun 2019 21:34:50: 35000000 INFO @ Mon, 03 Jun 2019 21:34:53: 33000000 INFO @ Mon, 03 Jun 2019 21:34:54: 40000000 INFO @ Mon, 03 Jun 2019 21:34:57: 36000000 INFO @ Mon, 03 Jun 2019 21:35:02: 34000000 INFO @ Mon, 03 Jun 2019 21:35:03: 41000000 INFO @ Mon, 03 Jun 2019 21:35:05: 37000000 INFO @ Mon, 03 Jun 2019 21:35:07: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 21:35:07: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 21:35:07: #1 total tags in treatment: 41495480 INFO @ Mon, 03 Jun 2019 21:35:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:35:07: #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 21:35:08: #1 tags after filtering in treatment: 41495480 INFO @ Mon, 03 Jun 2019 21:35:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:35:08: #1 finished! INFO @ Mon, 03 Jun 2019 21:35:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:35:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:35:11: #2 number of paired peaks: 3 WARNING @ Mon, 03 Jun 2019 21:35:11: Too few paired peaks (3) 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 21:35:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.05_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/SRX4933905/SRX4933905.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:35:12: 35000000 INFO @ Mon, 03 Jun 2019 21:35:12: 38000000 INFO @ Mon, 03 Jun 2019 21:35:19: 39000000 INFO @ Mon, 03 Jun 2019 21:35:21: 36000000 INFO @ Mon, 03 Jun 2019 21:35:26: 40000000 INFO @ Mon, 03 Jun 2019 21:35:30: 37000000 INFO @ Mon, 03 Jun 2019 21:35:34: 41000000 INFO @ Mon, 03 Jun 2019 21:35:38: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 21:35:38: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 21:35:38: #1 total tags in treatment: 41495480 INFO @ Mon, 03 Jun 2019 21:35:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:35:38: #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 21:35:39: #1 tags after filtering in treatment: 41495480 INFO @ Mon, 03 Jun 2019 21:35:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:35:39: #1 finished! INFO @ Mon, 03 Jun 2019 21:35:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:35:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:35:40: 38000000 INFO @ Mon, 03 Jun 2019 21:35:42: #2 number of paired peaks: 3 WARNING @ Mon, 03 Jun 2019 21:35:42: Too few paired peaks (3) 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 21:35:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.20_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/SRX4933905/SRX4933905.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:35:49: 39000000 INFO @ Mon, 03 Jun 2019 21:35:59: 40000000 INFO @ Mon, 03 Jun 2019 21:36:08: 41000000 INFO @ Mon, 03 Jun 2019 21:36:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 21:36:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 21:36:14: #1 total tags in treatment: 41495480 INFO @ Mon, 03 Jun 2019 21:36:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:36:14: #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 21:36:15: #1 tags after filtering in treatment: 41495480 INFO @ Mon, 03 Jun 2019 21:36:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:36:15: #1 finished! INFO @ Mon, 03 Jun 2019 21:36:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:36:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:36:18: #2 number of paired peaks: 3 WARNING @ Mon, 03 Jun 2019 21:36:18: Too few paired peaks (3) 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 21:36:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.10_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/SRX4933905/SRX4933905.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933905/SRX4933905.10_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。