Job ID = 1302697 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T11:08:32 fasterq-dump.2.9.6 fatal: SIGNAL - Segmentation fault 2019-06-03T11:22:38 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 ) 2019-06-03T11:22:38 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 : 76,602,117 reads read : 76,602,117 reads written : 76,602,117 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: 00:37:00 76602117 reads; of these: 76602117 (100.00%) were unpaired; of these: 2143245 (2.80%) aligned 0 times 51307177 (66.98%) aligned exactly 1 time 23151695 (30.22%) aligned >1 times 97.20% overall alignment rate Time searching: 00:37:00 Overall time: 00:37:00 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] 18413875 / 74458872 = 0.2473 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 21:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.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 21:50:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:50:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.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 21:50:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:50:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.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 21:50:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:50:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:50:20: 1000000 INFO @ Mon, 03 Jun 2019 21:50:22: 1000000 INFO @ Mon, 03 Jun 2019 21:50:22: 1000000 INFO @ Mon, 03 Jun 2019 21:50:29: 2000000 INFO @ Mon, 03 Jun 2019 21:50:33: 2000000 INFO @ Mon, 03 Jun 2019 21:50:33: 2000000 INFO @ Mon, 03 Jun 2019 21:50:38: 3000000 INFO @ Mon, 03 Jun 2019 21:50:44: 3000000 INFO @ Mon, 03 Jun 2019 21:50:45: 3000000 INFO @ Mon, 03 Jun 2019 21:50:47: 4000000 INFO @ Mon, 03 Jun 2019 21:50:55: 4000000 INFO @ Mon, 03 Jun 2019 21:50:56: 5000000 INFO @ Mon, 03 Jun 2019 21:50:56: 4000000 INFO @ Mon, 03 Jun 2019 21:51:05: 6000000 INFO @ Mon, 03 Jun 2019 21:51:07: 5000000 INFO @ Mon, 03 Jun 2019 21:51:07: 5000000 INFO @ Mon, 03 Jun 2019 21:51:15: 7000000 INFO @ Mon, 03 Jun 2019 21:51:18: 6000000 INFO @ Mon, 03 Jun 2019 21:51:19: 6000000 INFO @ Mon, 03 Jun 2019 21:51:26: 8000000 INFO @ Mon, 03 Jun 2019 21:51:30: 7000000 INFO @ Mon, 03 Jun 2019 21:51:31: 7000000 INFO @ Mon, 03 Jun 2019 21:51:37: 9000000 INFO @ Mon, 03 Jun 2019 21:51:42: 8000000 INFO @ Mon, 03 Jun 2019 21:51:43: 8000000 INFO @ Mon, 03 Jun 2019 21:51:47: 10000000 INFO @ Mon, 03 Jun 2019 21:51:52: 9000000 INFO @ Mon, 03 Jun 2019 21:51:52: 9000000 INFO @ Mon, 03 Jun 2019 21:51:57: 11000000 INFO @ Mon, 03 Jun 2019 21:52:03: 10000000 INFO @ Mon, 03 Jun 2019 21:52:03: 10000000 INFO @ Mon, 03 Jun 2019 21:52:06: 12000000 INFO @ Mon, 03 Jun 2019 21:52:14: 11000000 INFO @ Mon, 03 Jun 2019 21:52:14: 11000000 INFO @ Mon, 03 Jun 2019 21:52:16: 13000000 INFO @ Mon, 03 Jun 2019 21:52:25: 14000000 INFO @ Mon, 03 Jun 2019 21:52:26: 12000000 INFO @ Mon, 03 Jun 2019 21:52:26: 12000000 INFO @ Mon, 03 Jun 2019 21:52:34: 15000000 INFO @ Mon, 03 Jun 2019 21:52:37: 13000000 INFO @ Mon, 03 Jun 2019 21:52:38: 13000000 INFO @ Mon, 03 Jun 2019 21:52:43: 16000000 INFO @ Mon, 03 Jun 2019 21:52:49: 14000000 INFO @ Mon, 03 Jun 2019 21:52:50: 14000000 INFO @ Mon, 03 Jun 2019 21:52:53: 17000000 INFO @ Mon, 03 Jun 2019 21:53:00: 15000000 INFO @ Mon, 03 Jun 2019 21:53:02: 18000000 INFO @ Mon, 03 Jun 2019 21:53:02: 15000000 INFO @ Mon, 03 Jun 2019 21:53:11: 19000000 INFO @ Mon, 03 Jun 2019 21:53:11: 16000000 INFO @ Mon, 03 Jun 2019 21:53:14: 16000000 INFO @ Mon, 03 Jun 2019 21:53:21: 20000000 INFO @ Mon, 03 Jun 2019 21:53:23: 17000000 INFO @ Mon, 03 Jun 2019 21:53:27: 17000000 INFO @ Mon, 03 Jun 2019 21:53:30: 21000000 INFO @ Mon, 03 Jun 2019 21:53:35: 18000000 INFO @ Mon, 03 Jun 2019 21:53:39: 22000000 INFO @ Mon, 03 Jun 2019 21:53:39: 18000000 INFO @ Mon, 03 Jun 2019 21:53:46: 19000000 INFO @ Mon, 03 Jun 2019 21:53:49: 23000000 INFO @ Mon, 03 Jun 2019 21:53:51: 19000000 INFO @ Mon, 03 Jun 2019 21:53:57: 20000000 INFO @ Mon, 03 Jun 2019 21:53:59: 24000000 INFO @ Mon, 03 Jun 2019 21:54:03: 20000000 INFO @ Mon, 03 Jun 2019 21:54:08: 25000000 INFO @ Mon, 03 Jun 2019 21:54:08: 21000000 INFO @ Mon, 03 Jun 2019 21:54:15: 21000000 INFO @ Mon, 03 Jun 2019 21:54:17: 26000000 INFO @ Mon, 03 Jun 2019 21:54:19: 22000000 INFO @ Mon, 03 Jun 2019 21:54:26: 22000000 INFO @ Mon, 03 Jun 2019 21:54:27: 27000000 INFO @ Mon, 03 Jun 2019 21:54:30: 23000000 INFO @ Mon, 03 Jun 2019 21:54:36: 28000000 INFO @ Mon, 03 Jun 2019 21:54:36: 23000000 INFO @ Mon, 03 Jun 2019 21:54:40: 24000000 INFO @ Mon, 03 Jun 2019 21:54:46: 29000000 INFO @ Mon, 03 Jun 2019 21:54:46: 24000000 INFO @ Mon, 03 Jun 2019 21:54:52: 25000000 INFO @ Mon, 03 Jun 2019 21:54:55: 30000000 INFO @ Mon, 03 Jun 2019 21:54:58: 25000000 INFO @ Mon, 03 Jun 2019 21:55:03: 26000000 INFO @ Mon, 03 Jun 2019 21:55:05: 31000000 INFO @ Mon, 03 Jun 2019 21:55:11: 26000000 INFO @ Mon, 03 Jun 2019 21:55:14: 32000000 INFO @ Mon, 03 Jun 2019 21:55:14: 27000000 INFO @ Mon, 03 Jun 2019 21:55:23: 33000000 INFO @ Mon, 03 Jun 2019 21:55:23: 27000000 INFO @ Mon, 03 Jun 2019 21:55:25: 28000000 INFO @ Mon, 03 Jun 2019 21:55:32: 34000000 INFO @ Mon, 03 Jun 2019 21:55:35: 28000000 INFO @ Mon, 03 Jun 2019 21:55:36: 29000000 INFO @ Mon, 03 Jun 2019 21:55:43: 35000000 INFO @ Mon, 03 Jun 2019 21:55:47: 30000000 INFO @ Mon, 03 Jun 2019 21:55:47: 29000000 INFO @ Mon, 03 Jun 2019 21:55:52: 36000000 INFO @ Mon, 03 Jun 2019 21:55:58: 31000000 INFO @ Mon, 03 Jun 2019 21:55:59: 30000000 INFO @ Mon, 03 Jun 2019 21:56:01: 37000000 INFO @ Mon, 03 Jun 2019 21:56:09: 32000000 INFO @ Mon, 03 Jun 2019 21:56:10: 38000000 INFO @ Mon, 03 Jun 2019 21:56:11: 31000000 INFO @ Mon, 03 Jun 2019 21:56:19: 39000000 INFO @ Mon, 03 Jun 2019 21:56:20: 33000000 INFO @ Mon, 03 Jun 2019 21:56:23: 32000000 INFO @ Mon, 03 Jun 2019 21:56:28: 40000000 INFO @ Mon, 03 Jun 2019 21:56:32: 34000000 INFO @ Mon, 03 Jun 2019 21:56:36: 33000000 INFO @ Mon, 03 Jun 2019 21:56:37: 41000000 INFO @ Mon, 03 Jun 2019 21:56:42: 35000000 INFO @ Mon, 03 Jun 2019 21:56:45: 42000000 INFO @ Mon, 03 Jun 2019 21:56:48: 34000000 INFO @ Mon, 03 Jun 2019 21:56:53: 36000000 INFO @ Mon, 03 Jun 2019 21:56:54: 43000000 INFO @ Mon, 03 Jun 2019 21:57:00: 35000000 INFO @ Mon, 03 Jun 2019 21:57:03: 44000000 INFO @ Mon, 03 Jun 2019 21:57:04: 37000000 INFO @ Mon, 03 Jun 2019 21:57:12: 45000000 INFO @ Mon, 03 Jun 2019 21:57:12: 36000000 INFO @ Mon, 03 Jun 2019 21:57:14: 38000000 INFO @ Mon, 03 Jun 2019 21:57:20: 46000000 INFO @ Mon, 03 Jun 2019 21:57:23: 37000000 INFO @ Mon, 03 Jun 2019 21:57:25: 39000000 INFO @ Mon, 03 Jun 2019 21:57:29: 47000000 INFO @ Mon, 03 Jun 2019 21:57:35: 38000000 INFO @ Mon, 03 Jun 2019 21:57:35: 40000000 INFO @ Mon, 03 Jun 2019 21:57:38: 48000000 INFO @ Mon, 03 Jun 2019 21:57:46: 41000000 INFO @ Mon, 03 Jun 2019 21:57:46: 39000000 INFO @ Mon, 03 Jun 2019 21:57:47: 49000000 INFO @ Mon, 03 Jun 2019 21:57:56: 50000000 INFO @ Mon, 03 Jun 2019 21:57:57: 42000000 INFO @ Mon, 03 Jun 2019 21:57:57: 40000000 INFO @ Mon, 03 Jun 2019 21:58:05: 51000000 INFO @ Mon, 03 Jun 2019 21:58:07: 43000000 INFO @ Mon, 03 Jun 2019 21:58:09: 41000000 INFO @ Mon, 03 Jun 2019 21:58:13: 52000000 INFO @ Mon, 03 Jun 2019 21:58:18: 44000000 INFO @ Mon, 03 Jun 2019 21:58:21: 42000000 INFO @ Mon, 03 Jun 2019 21:58:22: 53000000 INFO @ Mon, 03 Jun 2019 21:58:29: 45000000 INFO @ Mon, 03 Jun 2019 21:58:31: 54000000 INFO @ Mon, 03 Jun 2019 21:58:32: 43000000 INFO @ Mon, 03 Jun 2019 21:58:39: 46000000 INFO @ Mon, 03 Jun 2019 21:58:39: 55000000 INFO @ Mon, 03 Jun 2019 21:58:44: 44000000 INFO @ Mon, 03 Jun 2019 21:58:48: 56000000 INFO @ Mon, 03 Jun 2019 21:58:49: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 21:58:49: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 21:58:49: #1 total tags in treatment: 56044997 INFO @ Mon, 03 Jun 2019 21:58:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:58:49: #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 21:58:50: 47000000 INFO @ Mon, 03 Jun 2019 21:58:50: #1 tags after filtering in treatment: 56044997 INFO @ Mon, 03 Jun 2019 21:58:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:58:50: #1 finished! INFO @ Mon, 03 Jun 2019 21:58:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:58:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:58:55: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 21:58:55: 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 21:58:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.10_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/SRX4933890/SRX4933890.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:58:55: 45000000 INFO @ Mon, 03 Jun 2019 21:59:00: 48000000 INFO @ Mon, 03 Jun 2019 21:59:07: 46000000 INFO @ Mon, 03 Jun 2019 21:59:10: 49000000 INFO @ Mon, 03 Jun 2019 21:59:18: 47000000 INFO @ Mon, 03 Jun 2019 21:59:21: 50000000 INFO @ Mon, 03 Jun 2019 21:59:29: 48000000 INFO @ Mon, 03 Jun 2019 21:59:32: 51000000 INFO @ Mon, 03 Jun 2019 21:59:41: 49000000 INFO @ Mon, 03 Jun 2019 21:59:42: 52000000 INFO @ Mon, 03 Jun 2019 21:59:53: 50000000 INFO @ Mon, 03 Jun 2019 21:59:53: 53000000 INFO @ Mon, 03 Jun 2019 22:00:03: 54000000 INFO @ Mon, 03 Jun 2019 22:00:04: 51000000 INFO @ Mon, 03 Jun 2019 22:00:13: 55000000 INFO @ Mon, 03 Jun 2019 22:00:15: 52000000 INFO @ Mon, 03 Jun 2019 22:00:24: 56000000 INFO @ Mon, 03 Jun 2019 22:00:25: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 22:00:25: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 22:00:25: #1 total tags in treatment: 56044997 INFO @ Mon, 03 Jun 2019 22:00:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:00:25: #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 22:00:26: #1 tags after filtering in treatment: 56044997 INFO @ Mon, 03 Jun 2019 22:00:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:00:26: #1 finished! INFO @ Mon, 03 Jun 2019 22:00:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:00:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:00:27: 53000000 INFO @ Mon, 03 Jun 2019 22:00:30: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 22:00:30: 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 22:00:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.05_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/SRX4933890/SRX4933890.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:00:38: 54000000 INFO @ Mon, 03 Jun 2019 22:00:49: 55000000 INFO @ Mon, 03 Jun 2019 22:01:00: 56000000 INFO @ Mon, 03 Jun 2019 22:01:01: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 22:01:01: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 22:01:01: #1 total tags in treatment: 56044997 INFO @ Mon, 03 Jun 2019 22:01:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:01:01: #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 22:01:02: #1 tags after filtering in treatment: 56044997 INFO @ Mon, 03 Jun 2019 22:01:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:01:02: #1 finished! INFO @ Mon, 03 Jun 2019 22:01:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:01:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:01:07: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 22:01:07: 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 22:01:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.20_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/SRX4933890/SRX4933890.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933890/SRX4933890.20_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。