Job ID = 1295153 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T03:23:48 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 ) 2019-06-03T03:23:48 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 : 39,352,844 reads read : 78,705,688 reads written : 39,352,844 reads 0-length : 39,352,844 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: 00:10:04 39352844 reads; of these: 39352844 (100.00%) were unpaired; of these: 1114211 (2.83%) aligned 0 times 34297959 (87.15%) aligned exactly 1 time 3940674 (10.01%) aligned >1 times 97.17% overall alignment rate Time searching: 00:10:04 Overall time: 00:10:04 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 16 files... [bam_rmdupse_core] 4916756 / 38238633 = 0.1286 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 12:50:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.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 12:50:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:50:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:50:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.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 12:50:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:50:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:50:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.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 12:50:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:50:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:51:02: 1000000 INFO @ Mon, 03 Jun 2019 12:51:03: 1000000 INFO @ Mon, 03 Jun 2019 12:51:03: 1000000 INFO @ Mon, 03 Jun 2019 12:51:10: 2000000 INFO @ Mon, 03 Jun 2019 12:51:14: 2000000 INFO @ Mon, 03 Jun 2019 12:51:14: 2000000 INFO @ Mon, 03 Jun 2019 12:51:19: 3000000 INFO @ Mon, 03 Jun 2019 12:51:24: 3000000 INFO @ Mon, 03 Jun 2019 12:51:24: 3000000 INFO @ Mon, 03 Jun 2019 12:51:27: 4000000 INFO @ Mon, 03 Jun 2019 12:51:35: 4000000 INFO @ Mon, 03 Jun 2019 12:51:35: 4000000 INFO @ Mon, 03 Jun 2019 12:51:37: 5000000 INFO @ Mon, 03 Jun 2019 12:51:46: 6000000 INFO @ Mon, 03 Jun 2019 12:51:46: 5000000 INFO @ Mon, 03 Jun 2019 12:51:46: 5000000 INFO @ Mon, 03 Jun 2019 12:51:54: 7000000 INFO @ Mon, 03 Jun 2019 12:51:56: 6000000 INFO @ Mon, 03 Jun 2019 12:51:56: 6000000 INFO @ Mon, 03 Jun 2019 12:52:02: 8000000 INFO @ Mon, 03 Jun 2019 12:52:06: 7000000 INFO @ Mon, 03 Jun 2019 12:52:06: 7000000 INFO @ Mon, 03 Jun 2019 12:52:11: 9000000 INFO @ Mon, 03 Jun 2019 12:52:16: 8000000 INFO @ Mon, 03 Jun 2019 12:52:17: 8000000 INFO @ Mon, 03 Jun 2019 12:52:20: 10000000 INFO @ Mon, 03 Jun 2019 12:52:26: 9000000 INFO @ Mon, 03 Jun 2019 12:52:27: 9000000 INFO @ Mon, 03 Jun 2019 12:52:28: 11000000 INFO @ Mon, 03 Jun 2019 12:52:36: 12000000 INFO @ Mon, 03 Jun 2019 12:52:36: 10000000 INFO @ Mon, 03 Jun 2019 12:52:37: 10000000 INFO @ Mon, 03 Jun 2019 12:52:44: 13000000 INFO @ Mon, 03 Jun 2019 12:52:46: 11000000 INFO @ Mon, 03 Jun 2019 12:52:47: 11000000 INFO @ Mon, 03 Jun 2019 12:52:53: 14000000 INFO @ Mon, 03 Jun 2019 12:52:56: 12000000 INFO @ Mon, 03 Jun 2019 12:52:58: 12000000 INFO @ Mon, 03 Jun 2019 12:53:02: 15000000 INFO @ Mon, 03 Jun 2019 12:53:06: 13000000 INFO @ Mon, 03 Jun 2019 12:53:08: 13000000 INFO @ Mon, 03 Jun 2019 12:53:10: 16000000 INFO @ Mon, 03 Jun 2019 12:53:16: 14000000 INFO @ Mon, 03 Jun 2019 12:53:18: 14000000 INFO @ Mon, 03 Jun 2019 12:53:18: 17000000 INFO @ Mon, 03 Jun 2019 12:53:26: 15000000 INFO @ Mon, 03 Jun 2019 12:53:27: 18000000 INFO @ Mon, 03 Jun 2019 12:53:28: 15000000 INFO @ Mon, 03 Jun 2019 12:53:36: 19000000 INFO @ Mon, 03 Jun 2019 12:53:36: 16000000 INFO @ Mon, 03 Jun 2019 12:53:38: 16000000 INFO @ Mon, 03 Jun 2019 12:53:45: 20000000 INFO @ Mon, 03 Jun 2019 12:53:46: 17000000 INFO @ Mon, 03 Jun 2019 12:53:48: 17000000 INFO @ Mon, 03 Jun 2019 12:53:53: 21000000 INFO @ Mon, 03 Jun 2019 12:53:56: 18000000 INFO @ Mon, 03 Jun 2019 12:53:58: 18000000 INFO @ Mon, 03 Jun 2019 12:54:02: 22000000 INFO @ Mon, 03 Jun 2019 12:54:06: 19000000 INFO @ Mon, 03 Jun 2019 12:54:09: 19000000 INFO @ Mon, 03 Jun 2019 12:54:11: 23000000 INFO @ Mon, 03 Jun 2019 12:54:16: 20000000 INFO @ Mon, 03 Jun 2019 12:54:20: 20000000 INFO @ Mon, 03 Jun 2019 12:54:20: 24000000 INFO @ Mon, 03 Jun 2019 12:54:27: 21000000 INFO @ Mon, 03 Jun 2019 12:54:28: 25000000 INFO @ Mon, 03 Jun 2019 12:54:31: 21000000 INFO @ Mon, 03 Jun 2019 12:54:37: 26000000 INFO @ Mon, 03 Jun 2019 12:54:37: 22000000 INFO @ Mon, 03 Jun 2019 12:54:41: 22000000 INFO @ Mon, 03 Jun 2019 12:54:45: 27000000 INFO @ Mon, 03 Jun 2019 12:54:47: 23000000 INFO @ Mon, 03 Jun 2019 12:54:53: 23000000 INFO @ Mon, 03 Jun 2019 12:54:54: 28000000 INFO @ Mon, 03 Jun 2019 12:54:58: 24000000 INFO @ Mon, 03 Jun 2019 12:55:03: 29000000 INFO @ Mon, 03 Jun 2019 12:55:04: 24000000 INFO @ Mon, 03 Jun 2019 12:55:09: 25000000 INFO @ Mon, 03 Jun 2019 12:55:11: 30000000 INFO @ Mon, 03 Jun 2019 12:55:14: 25000000 INFO @ Mon, 03 Jun 2019 12:55:19: 31000000 INFO @ Mon, 03 Jun 2019 12:55:19: 26000000 INFO @ Mon, 03 Jun 2019 12:55:25: 26000000 INFO @ Mon, 03 Jun 2019 12:55:28: 32000000 INFO @ Mon, 03 Jun 2019 12:55:29: 27000000 INFO @ Mon, 03 Jun 2019 12:55:35: 27000000 INFO @ Mon, 03 Jun 2019 12:55:36: 33000000 INFO @ Mon, 03 Jun 2019 12:55:39: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 12:55:39: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 12:55:39: #1 total tags in treatment: 33321877 INFO @ Mon, 03 Jun 2019 12:55:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:55:39: #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 12:55:39: 28000000 INFO @ Mon, 03 Jun 2019 12:55:40: #1 tags after filtering in treatment: 33321877 INFO @ Mon, 03 Jun 2019 12:55:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:55:40: #1 finished! INFO @ Mon, 03 Jun 2019 12:55:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:55:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:55:42: #2 number of paired peaks: 25 WARNING @ Mon, 03 Jun 2019 12:55:42: Too few paired peaks (25) 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 12:55:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.20_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/SRX3279765/SRX3279765.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:55:45: 28000000 INFO @ Mon, 03 Jun 2019 12:55:49: 29000000 INFO @ Mon, 03 Jun 2019 12:55:55: 29000000 INFO @ Mon, 03 Jun 2019 12:55:58: 30000000 INFO @ Mon, 03 Jun 2019 12:56:05: 30000000 INFO @ Mon, 03 Jun 2019 12:56:08: 31000000 INFO @ Mon, 03 Jun 2019 12:56:15: 31000000 INFO @ Mon, 03 Jun 2019 12:56:17: 32000000 INFO @ Mon, 03 Jun 2019 12:56:25: 32000000 INFO @ Mon, 03 Jun 2019 12:56:27: 33000000 INFO @ Mon, 03 Jun 2019 12:56:30: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 12:56:30: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 12:56:30: #1 total tags in treatment: 33321877 INFO @ Mon, 03 Jun 2019 12:56:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:56:30: #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 12:56:31: #1 tags after filtering in treatment: 33321877 INFO @ Mon, 03 Jun 2019 12:56:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:56:31: #1 finished! INFO @ Mon, 03 Jun 2019 12:56:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:56:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:56:34: #2 number of paired peaks: 25 WARNING @ Mon, 03 Jun 2019 12:56:34: Too few paired peaks (25) 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 12:56:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.10_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/SRX3279765/SRX3279765.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:56:35: 33000000 INFO @ Mon, 03 Jun 2019 12:56:38: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 12:56:38: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 12:56:38: #1 total tags in treatment: 33321877 INFO @ Mon, 03 Jun 2019 12:56:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:56:38: #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 12:56:39: #1 tags after filtering in treatment: 33321877 INFO @ Mon, 03 Jun 2019 12:56:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:56:39: #1 finished! INFO @ Mon, 03 Jun 2019 12:56:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:56:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:56:41: #2 number of paired peaks: 25 WARNING @ Mon, 03 Jun 2019 12:56:41: Too few paired peaks (25) 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 12:56:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.05_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/SRX3279765/SRX3279765.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3279765/SRX3279765.05_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。