Job ID = 1308611 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:53:41 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 ) 2019-06-03T14:04:02 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 : 53,659,970 reads read : 107,319,940 reads written : 53,659,970 reads 0-length : 53,659,970 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: 00:29:04 53659970 reads; of these: 53659970 (100.00%) were unpaired; of these: 1833479 (3.42%) aligned 0 times 35206430 (65.61%) aligned exactly 1 time 16620061 (30.97%) aligned >1 times 96.58% overall alignment rate Time searching: 00:29:04 Overall time: 00:29:04 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] 8570215 / 51826491 = 0.1654 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, 04 Jun 2019 00:11:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.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, 04 Jun 2019 00:11:16: #1 read tag files... INFO @ Tue, 04 Jun 2019 00:11:16: #1 read treatment tags... INFO @ Tue, 04 Jun 2019 00:11:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.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, 04 Jun 2019 00:11:16: #1 read tag files... INFO @ Tue, 04 Jun 2019 00:11:16: #1 read treatment tags... INFO @ Tue, 04 Jun 2019 00:11:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.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, 04 Jun 2019 00:11:16: #1 read tag files... INFO @ Tue, 04 Jun 2019 00:11:16: #1 read treatment tags... INFO @ Tue, 04 Jun 2019 00:11:25: 1000000 INFO @ Tue, 04 Jun 2019 00:11:26: 1000000 INFO @ Tue, 04 Jun 2019 00:11:26: 1000000 INFO @ Tue, 04 Jun 2019 00:11:34: 2000000 INFO @ Tue, 04 Jun 2019 00:11:35: 2000000 INFO @ Tue, 04 Jun 2019 00:11:36: 2000000 INFO @ Tue, 04 Jun 2019 00:11:42: 3000000 INFO @ Tue, 04 Jun 2019 00:11:44: 3000000 INFO @ Tue, 04 Jun 2019 00:11:47: 3000000 INFO @ Tue, 04 Jun 2019 00:11:53: 4000000 INFO @ Tue, 04 Jun 2019 00:11:54: 4000000 INFO @ Tue, 04 Jun 2019 00:11:57: 4000000 INFO @ Tue, 04 Jun 2019 00:12:02: 5000000 INFO @ Tue, 04 Jun 2019 00:12:03: 5000000 INFO @ Tue, 04 Jun 2019 00:12:07: 5000000 INFO @ Tue, 04 Jun 2019 00:12:12: 6000000 INFO @ Tue, 04 Jun 2019 00:12:13: 6000000 INFO @ Tue, 04 Jun 2019 00:12:17: 6000000 INFO @ Tue, 04 Jun 2019 00:12:21: 7000000 INFO @ Tue, 04 Jun 2019 00:12:23: 7000000 INFO @ Tue, 04 Jun 2019 00:12:27: 7000000 INFO @ Tue, 04 Jun 2019 00:12:30: 8000000 INFO @ Tue, 04 Jun 2019 00:12:32: 8000000 INFO @ Tue, 04 Jun 2019 00:12:38: 9000000 INFO @ Tue, 04 Jun 2019 00:12:38: 8000000 INFO @ Tue, 04 Jun 2019 00:12:41: 9000000 INFO @ Tue, 04 Jun 2019 00:12:48: 10000000 INFO @ Tue, 04 Jun 2019 00:12:48: 9000000 INFO @ Tue, 04 Jun 2019 00:12:52: 10000000 INFO @ Tue, 04 Jun 2019 00:12:58: 11000000 INFO @ Tue, 04 Jun 2019 00:12:59: 10000000 INFO @ Tue, 04 Jun 2019 00:13:01: 11000000 INFO @ Tue, 04 Jun 2019 00:13:07: 12000000 INFO @ Tue, 04 Jun 2019 00:13:08: 11000000 INFO @ Tue, 04 Jun 2019 00:13:10: 12000000 INFO @ Tue, 04 Jun 2019 00:13:16: 13000000 INFO @ Tue, 04 Jun 2019 00:13:18: 12000000 INFO @ Tue, 04 Jun 2019 00:13:20: 13000000 INFO @ Tue, 04 Jun 2019 00:13:25: 14000000 INFO @ Tue, 04 Jun 2019 00:13:28: 13000000 INFO @ Tue, 04 Jun 2019 00:13:29: 14000000 INFO @ Tue, 04 Jun 2019 00:13:33: 15000000 INFO @ Tue, 04 Jun 2019 00:13:38: 15000000 INFO @ Tue, 04 Jun 2019 00:13:38: 14000000 INFO @ Tue, 04 Jun 2019 00:13:41: 16000000 INFO @ Tue, 04 Jun 2019 00:13:47: 16000000 INFO @ Tue, 04 Jun 2019 00:13:48: 15000000 INFO @ Tue, 04 Jun 2019 00:13:52: 17000000 INFO @ Tue, 04 Jun 2019 00:13:57: 17000000 INFO @ Tue, 04 Jun 2019 00:13:58: 16000000 INFO @ Tue, 04 Jun 2019 00:14:02: 18000000 INFO @ Tue, 04 Jun 2019 00:14:06: 18000000 INFO @ Tue, 04 Jun 2019 00:14:08: 17000000 INFO @ Tue, 04 Jun 2019 00:14:11: 19000000 INFO @ Tue, 04 Jun 2019 00:14:16: 19000000 INFO @ Tue, 04 Jun 2019 00:14:18: 18000000 INFO @ Tue, 04 Jun 2019 00:14:20: 20000000 INFO @ Tue, 04 Jun 2019 00:14:25: 20000000 INFO @ Tue, 04 Jun 2019 00:14:27: 19000000 INFO @ Tue, 04 Jun 2019 00:14:29: 21000000 INFO @ Tue, 04 Jun 2019 00:14:33: 21000000 INFO @ Tue, 04 Jun 2019 00:14:37: 22000000 INFO @ Tue, 04 Jun 2019 00:14:38: 20000000 INFO @ Tue, 04 Jun 2019 00:14:42: 22000000 INFO @ Tue, 04 Jun 2019 00:14:45: 23000000 INFO @ Tue, 04 Jun 2019 00:14:47: 21000000 INFO @ Tue, 04 Jun 2019 00:14:52: 23000000 INFO @ Tue, 04 Jun 2019 00:14:56: 24000000 INFO @ Tue, 04 Jun 2019 00:14:57: 22000000 INFO @ Tue, 04 Jun 2019 00:15:01: 24000000 INFO @ Tue, 04 Jun 2019 00:15:05: 25000000 INFO @ Tue, 04 Jun 2019 00:15:07: 23000000 INFO @ Tue, 04 Jun 2019 00:15:10: 25000000 INFO @ Tue, 04 Jun 2019 00:15:14: 26000000 INFO @ Tue, 04 Jun 2019 00:15:16: 24000000 INFO @ Tue, 04 Jun 2019 00:15:19: 26000000 INFO @ Tue, 04 Jun 2019 00:15:23: 27000000 INFO @ Tue, 04 Jun 2019 00:15:26: 25000000 INFO @ Tue, 04 Jun 2019 00:15:28: 27000000 INFO @ Tue, 04 Jun 2019 00:15:31: 28000000 INFO @ Tue, 04 Jun 2019 00:15:36: 26000000 INFO @ Tue, 04 Jun 2019 00:15:37: 28000000 INFO @ Tue, 04 Jun 2019 00:15:39: 29000000 INFO @ Tue, 04 Jun 2019 00:15:46: 27000000 INFO @ Tue, 04 Jun 2019 00:15:46: 29000000 INFO @ Tue, 04 Jun 2019 00:15:48: 30000000 INFO @ Tue, 04 Jun 2019 00:15:56: 28000000 INFO @ Tue, 04 Jun 2019 00:15:56: 30000000 INFO @ Tue, 04 Jun 2019 00:15:59: 31000000 INFO @ Tue, 04 Jun 2019 00:16:05: 31000000 INFO @ Tue, 04 Jun 2019 00:16:06: 29000000 INFO @ Tue, 04 Jun 2019 00:16:07: 32000000 INFO @ Tue, 04 Jun 2019 00:16:14: 32000000 INFO @ Tue, 04 Jun 2019 00:16:15: 30000000 INFO @ Tue, 04 Jun 2019 00:16:17: 33000000 INFO @ Tue, 04 Jun 2019 00:16:24: 33000000 INFO @ Tue, 04 Jun 2019 00:16:24: 31000000 INFO @ Tue, 04 Jun 2019 00:16:25: 34000000 INFO @ Tue, 04 Jun 2019 00:16:33: 34000000 INFO @ Tue, 04 Jun 2019 00:16:34: 35000000 INFO @ Tue, 04 Jun 2019 00:16:35: 32000000 INFO @ Tue, 04 Jun 2019 00:16:42: 35000000 INFO @ Tue, 04 Jun 2019 00:16:42: 36000000 INFO @ Tue, 04 Jun 2019 00:16:44: 33000000 INFO @ Tue, 04 Jun 2019 00:16:51: 37000000 INFO @ Tue, 04 Jun 2019 00:16:51: 36000000 INFO @ Tue, 04 Jun 2019 00:16:54: 34000000 INFO @ Tue, 04 Jun 2019 00:17:01: 37000000 INFO @ Tue, 04 Jun 2019 00:17:02: 38000000 INFO @ Tue, 04 Jun 2019 00:17:05: 35000000 INFO @ Tue, 04 Jun 2019 00:17:10: 38000000 INFO @ Tue, 04 Jun 2019 00:17:10: 39000000 INFO @ Tue, 04 Jun 2019 00:17:14: 36000000 INFO @ Tue, 04 Jun 2019 00:17:20: 40000000 INFO @ Tue, 04 Jun 2019 00:17:20: 39000000 INFO @ Tue, 04 Jun 2019 00:17:23: 37000000 INFO @ Tue, 04 Jun 2019 00:17:29: 41000000 INFO @ Tue, 04 Jun 2019 00:17:30: 40000000 INFO @ Tue, 04 Jun 2019 00:17:34: 38000000 INFO @ Tue, 04 Jun 2019 00:17:37: 42000000 INFO @ Tue, 04 Jun 2019 00:17:41: 41000000 INFO @ Tue, 04 Jun 2019 00:17:45: 39000000 INFO @ Tue, 04 Jun 2019 00:17:45: 43000000 INFO @ Tue, 04 Jun 2019 00:17:48: #1 tag size is determined as 65 bps INFO @ Tue, 04 Jun 2019 00:17:48: #1 tag size = 65 INFO @ Tue, 04 Jun 2019 00:17:48: #1 total tags in treatment: 43256276 INFO @ Tue, 04 Jun 2019 00:17:48: #1 user defined the maximum tags... INFO @ Tue, 04 Jun 2019 00:17:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Jun 2019 00:17:49: #1 tags after filtering in treatment: 43256276 INFO @ Tue, 04 Jun 2019 00:17:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 04 Jun 2019 00:17:49: #1 finished! INFO @ Tue, 04 Jun 2019 00:17:49: #2 Build Peak Model... INFO @ Tue, 04 Jun 2019 00:17:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Jun 2019 00:17:51: 42000000 INFO @ Tue, 04 Jun 2019 00:17:52: #2 number of paired peaks: 7 WARNING @ Tue, 04 Jun 2019 00:17:52: Too few paired peaks (7) 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, 04 Jun 2019 00:17:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.05_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/SRX5343154/SRX5343154.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 04 Jun 2019 00:17:55: 40000000 INFO @ Tue, 04 Jun 2019 00:18:01: 43000000 INFO @ Tue, 04 Jun 2019 00:18:04: #1 tag size is determined as 65 bps INFO @ Tue, 04 Jun 2019 00:18:04: #1 tag size = 65 INFO @ Tue, 04 Jun 2019 00:18:04: #1 total tags in treatment: 43256276 INFO @ Tue, 04 Jun 2019 00:18:04: #1 user defined the maximum tags... INFO @ Tue, 04 Jun 2019 00:18:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Jun 2019 00:18:05: 41000000 INFO @ Tue, 04 Jun 2019 00:18:05: #1 tags after filtering in treatment: 43256276 INFO @ Tue, 04 Jun 2019 00:18:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 04 Jun 2019 00:18:05: #1 finished! INFO @ Tue, 04 Jun 2019 00:18:05: #2 Build Peak Model... INFO @ Tue, 04 Jun 2019 00:18:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Jun 2019 00:18:08: #2 number of paired peaks: 7 WARNING @ Tue, 04 Jun 2019 00:18:08: Too few paired peaks (7) 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, 04 Jun 2019 00:18:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.20_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/SRX5343154/SRX5343154.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 04 Jun 2019 00:18:14: 42000000 INFO @ Tue, 04 Jun 2019 00:18:23: 43000000 INFO @ Tue, 04 Jun 2019 00:18:26: #1 tag size is determined as 65 bps INFO @ Tue, 04 Jun 2019 00:18:26: #1 tag size = 65 INFO @ Tue, 04 Jun 2019 00:18:26: #1 total tags in treatment: 43256276 INFO @ Tue, 04 Jun 2019 00:18:26: #1 user defined the maximum tags... INFO @ Tue, 04 Jun 2019 00:18:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Jun 2019 00:18:27: #1 tags after filtering in treatment: 43256276 INFO @ Tue, 04 Jun 2019 00:18:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 04 Jun 2019 00:18:27: #1 finished! INFO @ Tue, 04 Jun 2019 00:18:27: #2 Build Peak Model... INFO @ Tue, 04 Jun 2019 00:18:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Jun 2019 00:18:30: #2 number of paired peaks: 7 WARNING @ Tue, 04 Jun 2019 00:18:30: Too few paired peaks (7) 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, 04 Jun 2019 00:18:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.10_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/SRX5343154/SRX5343154.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343154/SRX5343154.10_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。