Job ID = 1309250 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 1900-01-00T00:00:00 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 ) 2019-06-03T14:13:52 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 ) 2019-06-03T14:13:52 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 ) 2019-06-03T14:13:52 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 ) 2019-06-03T14:13:52 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 ) 2019-06-03T14:13:52 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 : 48,706,360 reads read : 48,706,360 reads written : 48,706,360 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:04 48706360 reads; of these: 48706360 (100.00%) were unpaired; of these: 8648689 (17.76%) aligned 0 times 36220914 (74.37%) aligned exactly 1 time 3836757 (7.88%) aligned >1 times 82.24% overall alignment rate Time searching: 00:09:05 Overall time: 00:09:05 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 12 files... [bam_rmdupse_core] 4627113 / 40057671 = 0.1155 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 23:44:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.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 23:44:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:44:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:44:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.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 23:44:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:44:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:44:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.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 23:44:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:44:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:45:01: 1000000 INFO @ Mon, 03 Jun 2019 23:45:01: 1000000 INFO @ Mon, 03 Jun 2019 23:45:01: 1000000 INFO @ Mon, 03 Jun 2019 23:45:08: 2000000 INFO @ Mon, 03 Jun 2019 23:45:09: 2000000 INFO @ Mon, 03 Jun 2019 23:45:09: 2000000 INFO @ Mon, 03 Jun 2019 23:45:14: 3000000 INFO @ Mon, 03 Jun 2019 23:45:16: 3000000 INFO @ Mon, 03 Jun 2019 23:45:17: 3000000 INFO @ Mon, 03 Jun 2019 23:45:21: 4000000 INFO @ Mon, 03 Jun 2019 23:45:24: 4000000 INFO @ Mon, 03 Jun 2019 23:45:25: 4000000 INFO @ Mon, 03 Jun 2019 23:45:28: 5000000 INFO @ Mon, 03 Jun 2019 23:45:32: 5000000 INFO @ Mon, 03 Jun 2019 23:45:32: 5000000 INFO @ Mon, 03 Jun 2019 23:45:35: 6000000 INFO @ Mon, 03 Jun 2019 23:45:39: 6000000 INFO @ Mon, 03 Jun 2019 23:45:40: 6000000 INFO @ Mon, 03 Jun 2019 23:45:42: 7000000 INFO @ Mon, 03 Jun 2019 23:45:46: 7000000 INFO @ Mon, 03 Jun 2019 23:45:48: 7000000 INFO @ Mon, 03 Jun 2019 23:45:49: 8000000 INFO @ Mon, 03 Jun 2019 23:45:54: 8000000 INFO @ Mon, 03 Jun 2019 23:45:56: 8000000 INFO @ Mon, 03 Jun 2019 23:45:56: 9000000 INFO @ Mon, 03 Jun 2019 23:46:01: 9000000 INFO @ Mon, 03 Jun 2019 23:46:03: 10000000 INFO @ Mon, 03 Jun 2019 23:46:03: 9000000 INFO @ Mon, 03 Jun 2019 23:46:09: 10000000 INFO @ Mon, 03 Jun 2019 23:46:10: 11000000 INFO @ Mon, 03 Jun 2019 23:46:10: 10000000 INFO @ Mon, 03 Jun 2019 23:46:17: 11000000 INFO @ Mon, 03 Jun 2019 23:46:17: 12000000 INFO @ Mon, 03 Jun 2019 23:46:19: 11000000 INFO @ Mon, 03 Jun 2019 23:46:24: 12000000 INFO @ Mon, 03 Jun 2019 23:46:24: 13000000 INFO @ Mon, 03 Jun 2019 23:46:26: 12000000 INFO @ Mon, 03 Jun 2019 23:46:32: 14000000 INFO @ Mon, 03 Jun 2019 23:46:32: 13000000 INFO @ Mon, 03 Jun 2019 23:46:34: 13000000 INFO @ Mon, 03 Jun 2019 23:46:39: 15000000 INFO @ Mon, 03 Jun 2019 23:46:40: 14000000 INFO @ Mon, 03 Jun 2019 23:46:42: 14000000 INFO @ Mon, 03 Jun 2019 23:46:46: 16000000 INFO @ Mon, 03 Jun 2019 23:46:48: 15000000 INFO @ Mon, 03 Jun 2019 23:46:50: 15000000 INFO @ Mon, 03 Jun 2019 23:46:53: 17000000 INFO @ Mon, 03 Jun 2019 23:46:55: 16000000 INFO @ Mon, 03 Jun 2019 23:46:59: 16000000 INFO @ Mon, 03 Jun 2019 23:47:00: 18000000 INFO @ Mon, 03 Jun 2019 23:47:03: 17000000 INFO @ Mon, 03 Jun 2019 23:47:07: 17000000 INFO @ Mon, 03 Jun 2019 23:47:07: 19000000 INFO @ Mon, 03 Jun 2019 23:47:11: 18000000 INFO @ Mon, 03 Jun 2019 23:47:14: 20000000 INFO @ Mon, 03 Jun 2019 23:47:15: 18000000 INFO @ Mon, 03 Jun 2019 23:47:18: 19000000 INFO @ Mon, 03 Jun 2019 23:47:21: 21000000 INFO @ Mon, 03 Jun 2019 23:47:23: 19000000 INFO @ Mon, 03 Jun 2019 23:47:26: 20000000 INFO @ Mon, 03 Jun 2019 23:47:28: 22000000 INFO @ Mon, 03 Jun 2019 23:47:31: 20000000 INFO @ Mon, 03 Jun 2019 23:47:33: 21000000 INFO @ Mon, 03 Jun 2019 23:47:35: 23000000 INFO @ Mon, 03 Jun 2019 23:47:39: 21000000 INFO @ Mon, 03 Jun 2019 23:47:41: 22000000 INFO @ Mon, 03 Jun 2019 23:47:42: 24000000 INFO @ Mon, 03 Jun 2019 23:47:46: 22000000 INFO @ Mon, 03 Jun 2019 23:47:49: 23000000 INFO @ Mon, 03 Jun 2019 23:47:49: 25000000 INFO @ Mon, 03 Jun 2019 23:47:55: 23000000 INFO @ Mon, 03 Jun 2019 23:47:58: 26000000 INFO @ Mon, 03 Jun 2019 23:47:58: 24000000 INFO @ Mon, 03 Jun 2019 23:48:04: 24000000 INFO @ Mon, 03 Jun 2019 23:48:06: 27000000 INFO @ Mon, 03 Jun 2019 23:48:06: 25000000 INFO @ Mon, 03 Jun 2019 23:48:12: 25000000 INFO @ Mon, 03 Jun 2019 23:48:13: 28000000 INFO @ Mon, 03 Jun 2019 23:48:14: 26000000 INFO @ Mon, 03 Jun 2019 23:48:19: 26000000 INFO @ Mon, 03 Jun 2019 23:48:20: 29000000 INFO @ Mon, 03 Jun 2019 23:48:21: 27000000 INFO @ Mon, 03 Jun 2019 23:48:27: 30000000 INFO @ Mon, 03 Jun 2019 23:48:27: 27000000 INFO @ Mon, 03 Jun 2019 23:48:29: 28000000 INFO @ Mon, 03 Jun 2019 23:48:34: 31000000 INFO @ Mon, 03 Jun 2019 23:48:35: 28000000 INFO @ Mon, 03 Jun 2019 23:48:36: 29000000 INFO @ Mon, 03 Jun 2019 23:48:41: 32000000 INFO @ Mon, 03 Jun 2019 23:48:43: 29000000 INFO @ Mon, 03 Jun 2019 23:48:44: 30000000 INFO @ Mon, 03 Jun 2019 23:48:49: 33000000 INFO @ Mon, 03 Jun 2019 23:48:50: 30000000 INFO @ Mon, 03 Jun 2019 23:48:51: 31000000 INFO @ Mon, 03 Jun 2019 23:48:55: 34000000 INFO @ Mon, 03 Jun 2019 23:48:58: 31000000 INFO @ Mon, 03 Jun 2019 23:48:58: 32000000 INFO @ Mon, 03 Jun 2019 23:49:02: 35000000 INFO @ Mon, 03 Jun 2019 23:49:05: 32000000 INFO @ Mon, 03 Jun 2019 23:49:05: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 23:49:05: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 23:49:05: #1 total tags in treatment: 35430558 INFO @ Mon, 03 Jun 2019 23:49:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:49:05: #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 23:49:06: 33000000 INFO @ Mon, 03 Jun 2019 23:49:06: #1 tags after filtering in treatment: 35430558 INFO @ Mon, 03 Jun 2019 23:49:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:49:06: #1 finished! INFO @ Mon, 03 Jun 2019 23:49:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:49:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:49:09: #2 number of paired peaks: 17 WARNING @ Mon, 03 Jun 2019 23:49:09: Too few paired peaks (17) 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 23:49:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.05_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/SRX826336/SRX826336.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:49:13: 34000000 INFO @ Mon, 03 Jun 2019 23:49:13: 33000000 INFO @ Mon, 03 Jun 2019 23:49:20: 35000000 INFO @ Mon, 03 Jun 2019 23:49:20: 34000000 INFO @ Mon, 03 Jun 2019 23:49:23: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 23:49:23: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 23:49:23: #1 total tags in treatment: 35430558 INFO @ Mon, 03 Jun 2019 23:49:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:49:23: #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 23:49:24: #1 tags after filtering in treatment: 35430558 INFO @ Mon, 03 Jun 2019 23:49:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:49:24: #1 finished! INFO @ Mon, 03 Jun 2019 23:49:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:49:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:49:27: #2 number of paired peaks: 17 WARNING @ Mon, 03 Jun 2019 23:49:27: Too few paired peaks (17) 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 23:49:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.20_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/SRX826336/SRX826336.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:49:28: 35000000 INFO @ Mon, 03 Jun 2019 23:49:31: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 23:49:31: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 23:49:31: #1 total tags in treatment: 35430558 INFO @ Mon, 03 Jun 2019 23:49:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:49:31: #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 23:49:32: #1 tags after filtering in treatment: 35430558 INFO @ Mon, 03 Jun 2019 23:49:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:49:32: #1 finished! INFO @ Mon, 03 Jun 2019 23:49:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:49:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:49:35: #2 number of paired peaks: 17 WARNING @ Mon, 03 Jun 2019 23:49:35: Too few paired peaks (17) 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 23:49:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.10_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/SRX826336/SRX826336.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX826336/SRX826336.10_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。