Job ID = 1301969 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T11:13:24 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 ) 2019-06-03T11:13:24 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 ) 2019-06-03T11:30:51 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 ) 2019-06-03T11:31:29 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 ) 2019-06-03T11:32:20 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 ) 2019-06-03T11:34:00 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 ) 2019-06-03T11:37:28 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 : 80,130,616 reads read : 80,130,616 reads written : 80,130,616 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: 00:36:27 80130616 reads; of these: 80130616 (100.00%) were unpaired; of these: 1989182 (2.48%) aligned 0 times 54204122 (67.64%) aligned exactly 1 time 23937312 (29.87%) aligned >1 times 97.52% overall alignment rate Time searching: 00:36:27 Overall time: 00:36:27 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 32 files... [bam_rmdupse_core] 21682202 / 78141434 = 0.2775 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 21:42:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.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 21:42:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:42:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:42:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.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 21:42:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:42:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:42:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.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 21:42:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:42:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:42:23: 1000000 INFO @ Mon, 03 Jun 2019 21:42:25: 1000000 INFO @ Mon, 03 Jun 2019 21:42:25: 1000000 INFO @ Mon, 03 Jun 2019 21:42:33: 2000000 INFO @ Mon, 03 Jun 2019 21:42:36: 2000000 INFO @ Mon, 03 Jun 2019 21:42:37: 2000000 INFO @ Mon, 03 Jun 2019 21:42:42: 3000000 INFO @ Mon, 03 Jun 2019 21:42:48: 3000000 INFO @ Mon, 03 Jun 2019 21:42:48: 3000000 INFO @ Mon, 03 Jun 2019 21:42:52: 4000000 INFO @ Mon, 03 Jun 2019 21:42:59: 4000000 INFO @ Mon, 03 Jun 2019 21:42:59: 4000000 INFO @ Mon, 03 Jun 2019 21:43:01: 5000000 INFO @ Mon, 03 Jun 2019 21:43:10: 5000000 INFO @ Mon, 03 Jun 2019 21:43:11: 5000000 INFO @ Mon, 03 Jun 2019 21:43:11: 6000000 INFO @ Mon, 03 Jun 2019 21:43:20: 7000000 INFO @ Mon, 03 Jun 2019 21:43:22: 6000000 INFO @ Mon, 03 Jun 2019 21:43:22: 6000000 INFO @ Mon, 03 Jun 2019 21:43:30: 8000000 INFO @ Mon, 03 Jun 2019 21:43:33: 7000000 INFO @ Mon, 03 Jun 2019 21:43:33: 7000000 INFO @ Mon, 03 Jun 2019 21:43:39: 9000000 INFO @ Mon, 03 Jun 2019 21:43:43: 8000000 INFO @ Mon, 03 Jun 2019 21:43:45: 8000000 INFO @ Mon, 03 Jun 2019 21:43:49: 10000000 INFO @ Mon, 03 Jun 2019 21:43:55: 9000000 INFO @ Mon, 03 Jun 2019 21:43:57: 9000000 INFO @ Mon, 03 Jun 2019 21:43:58: 11000000 INFO @ Mon, 03 Jun 2019 21:44:06: 10000000 INFO @ Mon, 03 Jun 2019 21:44:08: 12000000 INFO @ Mon, 03 Jun 2019 21:44:08: 10000000 INFO @ Mon, 03 Jun 2019 21:44:15: 11000000 INFO @ Mon, 03 Jun 2019 21:44:18: 13000000 INFO @ Mon, 03 Jun 2019 21:44:19: 11000000 INFO @ Mon, 03 Jun 2019 21:44:24: 12000000 INFO @ Mon, 03 Jun 2019 21:44:27: 14000000 INFO @ Mon, 03 Jun 2019 21:44:30: 12000000 INFO @ Mon, 03 Jun 2019 21:44:34: 13000000 INFO @ Mon, 03 Jun 2019 21:44:37: 15000000 INFO @ Mon, 03 Jun 2019 21:44:41: 13000000 INFO @ Mon, 03 Jun 2019 21:44:43: 14000000 INFO @ Mon, 03 Jun 2019 21:44:47: 16000000 INFO @ Mon, 03 Jun 2019 21:44:51: 14000000 INFO @ Mon, 03 Jun 2019 21:44:52: 15000000 INFO @ Mon, 03 Jun 2019 21:44:57: 17000000 INFO @ Mon, 03 Jun 2019 21:45:01: 16000000 INFO @ Mon, 03 Jun 2019 21:45:02: 15000000 INFO @ Mon, 03 Jun 2019 21:45:06: 18000000 INFO @ Mon, 03 Jun 2019 21:45:10: 17000000 INFO @ Mon, 03 Jun 2019 21:45:13: 16000000 INFO @ Mon, 03 Jun 2019 21:45:16: 19000000 INFO @ Mon, 03 Jun 2019 21:45:19: 18000000 INFO @ Mon, 03 Jun 2019 21:45:24: 17000000 INFO @ Mon, 03 Jun 2019 21:45:26: 20000000 INFO @ Mon, 03 Jun 2019 21:45:28: 19000000 INFO @ Mon, 03 Jun 2019 21:45:34: 18000000 INFO @ Mon, 03 Jun 2019 21:45:35: 21000000 INFO @ Mon, 03 Jun 2019 21:45:39: 20000000 INFO @ Mon, 03 Jun 2019 21:45:44: 19000000 INFO @ Mon, 03 Jun 2019 21:45:45: 22000000 INFO @ Mon, 03 Jun 2019 21:45:48: 21000000 INFO @ Mon, 03 Jun 2019 21:45:54: 23000000 INFO @ Mon, 03 Jun 2019 21:45:55: 20000000 INFO @ Mon, 03 Jun 2019 21:45:58: 22000000 INFO @ Mon, 03 Jun 2019 21:46:04: 24000000 INFO @ Mon, 03 Jun 2019 21:46:06: 21000000 INFO @ Mon, 03 Jun 2019 21:46:08: 23000000 INFO @ Mon, 03 Jun 2019 21:46:13: 25000000 INFO @ Mon, 03 Jun 2019 21:46:16: 22000000 INFO @ Mon, 03 Jun 2019 21:46:17: 24000000 INFO @ Mon, 03 Jun 2019 21:46:23: 26000000 INFO @ Mon, 03 Jun 2019 21:46:26: 25000000 INFO @ Mon, 03 Jun 2019 21:46:27: 23000000 INFO @ Mon, 03 Jun 2019 21:46:32: 27000000 INFO @ Mon, 03 Jun 2019 21:46:35: 26000000 INFO @ Mon, 03 Jun 2019 21:46:37: 24000000 INFO @ Mon, 03 Jun 2019 21:46:41: 28000000 INFO @ Mon, 03 Jun 2019 21:46:44: 27000000 INFO @ Mon, 03 Jun 2019 21:46:47: 25000000 INFO @ Mon, 03 Jun 2019 21:46:50: 29000000 INFO @ Mon, 03 Jun 2019 21:46:55: 28000000 INFO @ Mon, 03 Jun 2019 21:46:59: 26000000 INFO @ Mon, 03 Jun 2019 21:46:59: 30000000 INFO @ Mon, 03 Jun 2019 21:47:04: 29000000 INFO @ Mon, 03 Jun 2019 21:47:08: 31000000 INFO @ Mon, 03 Jun 2019 21:47:09: 27000000 INFO @ Mon, 03 Jun 2019 21:47:12: 30000000 INFO @ Mon, 03 Jun 2019 21:47:17: 32000000 INFO @ Mon, 03 Jun 2019 21:47:20: 28000000 INFO @ Mon, 03 Jun 2019 21:47:20: 31000000 INFO @ Mon, 03 Jun 2019 21:47:26: 33000000 INFO @ Mon, 03 Jun 2019 21:47:28: 32000000 INFO @ Mon, 03 Jun 2019 21:47:30: 29000000 INFO @ Mon, 03 Jun 2019 21:47:35: 34000000 INFO @ Mon, 03 Jun 2019 21:47:37: 33000000 INFO @ Mon, 03 Jun 2019 21:47:41: 30000000 INFO @ Mon, 03 Jun 2019 21:47:44: 35000000 INFO @ Mon, 03 Jun 2019 21:47:45: 34000000 INFO @ Mon, 03 Jun 2019 21:47:52: 31000000 INFO @ Mon, 03 Jun 2019 21:47:52: 35000000 INFO @ Mon, 03 Jun 2019 21:47:53: 36000000 INFO @ Mon, 03 Jun 2019 21:48:01: 36000000 INFO @ Mon, 03 Jun 2019 21:48:02: 37000000 INFO @ Mon, 03 Jun 2019 21:48:02: 32000000 INFO @ Mon, 03 Jun 2019 21:48:09: 37000000 INFO @ Mon, 03 Jun 2019 21:48:11: 38000000 INFO @ Mon, 03 Jun 2019 21:48:13: 33000000 INFO @ Mon, 03 Jun 2019 21:48:17: 38000000 INFO @ Mon, 03 Jun 2019 21:48:20: 39000000 INFO @ Mon, 03 Jun 2019 21:48:23: 34000000 INFO @ Mon, 03 Jun 2019 21:48:24: 39000000 INFO @ Mon, 03 Jun 2019 21:48:29: 40000000 INFO @ Mon, 03 Jun 2019 21:48:33: 40000000 INFO @ Mon, 03 Jun 2019 21:48:34: 35000000 INFO @ Mon, 03 Jun 2019 21:48:38: 41000000 INFO @ Mon, 03 Jun 2019 21:48:42: 41000000 INFO @ Mon, 03 Jun 2019 21:48:45: 36000000 INFO @ Mon, 03 Jun 2019 21:48:47: 42000000 INFO @ Mon, 03 Jun 2019 21:48:51: 42000000 INFO @ Mon, 03 Jun 2019 21:48:56: 43000000 INFO @ Mon, 03 Jun 2019 21:48:56: 37000000 INFO @ Mon, 03 Jun 2019 21:48:59: 43000000 INFO @ Mon, 03 Jun 2019 21:49:05: 44000000 INFO @ Mon, 03 Jun 2019 21:49:08: 38000000 INFO @ Mon, 03 Jun 2019 21:49:08: 44000000 INFO @ Mon, 03 Jun 2019 21:49:14: 45000000 INFO @ Mon, 03 Jun 2019 21:49:16: 45000000 INFO @ Mon, 03 Jun 2019 21:49:18: 39000000 INFO @ Mon, 03 Jun 2019 21:49:23: 46000000 INFO @ Mon, 03 Jun 2019 21:49:25: 46000000 INFO @ Mon, 03 Jun 2019 21:49:30: 40000000 INFO @ Mon, 03 Jun 2019 21:49:32: 47000000 INFO @ Mon, 03 Jun 2019 21:49:33: 47000000 INFO @ Mon, 03 Jun 2019 21:49:41: 48000000 INFO @ Mon, 03 Jun 2019 21:49:41: 41000000 INFO @ Mon, 03 Jun 2019 21:49:42: 48000000 INFO @ Mon, 03 Jun 2019 21:49:49: 49000000 INFO @ Mon, 03 Jun 2019 21:49:51: 49000000 INFO @ Mon, 03 Jun 2019 21:49:52: 42000000 INFO @ Mon, 03 Jun 2019 21:49:58: 50000000 INFO @ Mon, 03 Jun 2019 21:49:59: 50000000 INFO @ Mon, 03 Jun 2019 21:50:03: 43000000 INFO @ Mon, 03 Jun 2019 21:50:07: 51000000 INFO @ Mon, 03 Jun 2019 21:50:08: 51000000 INFO @ Mon, 03 Jun 2019 21:50:14: 44000000 INFO @ Mon, 03 Jun 2019 21:50:17: 52000000 INFO @ Mon, 03 Jun 2019 21:50:17: 52000000 INFO @ Mon, 03 Jun 2019 21:50:25: 45000000 INFO @ Mon, 03 Jun 2019 21:50:26: 53000000 INFO @ Mon, 03 Jun 2019 21:50:26: 53000000 INFO @ Mon, 03 Jun 2019 21:50:35: 54000000 INFO @ Mon, 03 Jun 2019 21:50:35: 54000000 INFO @ Mon, 03 Jun 2019 21:50:36: 46000000 INFO @ Mon, 03 Jun 2019 21:50:44: 55000000 INFO @ Mon, 03 Jun 2019 21:50:44: 55000000 INFO @ Mon, 03 Jun 2019 21:50:47: 47000000 INFO @ Mon, 03 Jun 2019 21:50:52: 56000000 INFO @ Mon, 03 Jun 2019 21:50:53: 56000000 INFO @ Mon, 03 Jun 2019 21:50:57: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 21:50:57: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 21:50:57: #1 total tags in treatment: 56459232 INFO @ Mon, 03 Jun 2019 21:50:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:50:57: #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 21:50:57: 48000000 INFO @ Mon, 03 Jun 2019 21:50:58: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 21:50:58: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 21:50:58: #1 total tags in treatment: 56459232 INFO @ Mon, 03 Jun 2019 21:50:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:50:58: #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 21:50:58: #1 tags after filtering in treatment: 56459232 INFO @ Mon, 03 Jun 2019 21:50:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:50:58: #1 finished! INFO @ Mon, 03 Jun 2019 21:50:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:50:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:50:59: #1 tags after filtering in treatment: 56459232 INFO @ Mon, 03 Jun 2019 21:50:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:50:59: #1 finished! INFO @ Mon, 03 Jun 2019 21:50:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:50:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:51:03: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 21:51:03: Too few paired peaks (0) 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 21:51:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.10_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/SRX4933874/SRX4933874.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:51:04: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 21:51:04: Too few paired peaks (0) 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 21:51:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.05_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/SRX4933874/SRX4933874.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:51:08: 49000000 INFO @ Mon, 03 Jun 2019 21:51:19: 50000000 INFO @ Mon, 03 Jun 2019 21:51:29: 51000000 INFO @ Mon, 03 Jun 2019 21:51:40: 52000000 INFO @ Mon, 03 Jun 2019 21:51:50: 53000000 INFO @ Mon, 03 Jun 2019 21:52:01: 54000000 INFO @ Mon, 03 Jun 2019 21:52:11: 55000000 INFO @ Mon, 03 Jun 2019 21:52:21: 56000000 INFO @ Mon, 03 Jun 2019 21:52:26: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 21:52:26: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 21:52:26: #1 total tags in treatment: 56459232 INFO @ Mon, 03 Jun 2019 21:52:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:52:26: #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 21:52:27: #1 tags after filtering in treatment: 56459232 INFO @ Mon, 03 Jun 2019 21:52:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:52:27: #1 finished! INFO @ Mon, 03 Jun 2019 21:52:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:52:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:52:32: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 21:52:32: Too few paired peaks (0) 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 21:52:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.20_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/SRX4933874/SRX4933874.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933874/SRX4933874.20_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。