Job ID = 1306022 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T12:40:57 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 ) 2019-06-03T12:40:57 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 ) 2019-06-03T12:40:57 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 ) 2019-06-03T12:45:49 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 ) 2019-06-03T12:45:49 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 : 55,261,147 reads read : 55,261,147 reads written : 55,261,147 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: 00:17:56 55261147 reads; of these: 55261147 (100.00%) were unpaired; of these: 1066886 (1.93%) aligned 0 times 45427327 (82.20%) aligned exactly 1 time 8766934 (15.86%) aligned >1 times 98.07% overall alignment rate Time searching: 00:17:56 Overall time: 00:17:56 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] 16999580 / 54194261 = 0.3137 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 22:28:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.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 22:28:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:28:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:28:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.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 22:28:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:28:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:28:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.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 22:28:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:28:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:28:56: 1000000 INFO @ Mon, 03 Jun 2019 22:28:56: 1000000 INFO @ Mon, 03 Jun 2019 22:28:58: 1000000 INFO @ Mon, 03 Jun 2019 22:29:03: 2000000 INFO @ Mon, 03 Jun 2019 22:29:04: 2000000 INFO @ Mon, 03 Jun 2019 22:29:07: 2000000 INFO @ Mon, 03 Jun 2019 22:29:11: 3000000 INFO @ Mon, 03 Jun 2019 22:29:11: 3000000 INFO @ Mon, 03 Jun 2019 22:29:17: 3000000 INFO @ Mon, 03 Jun 2019 22:29:18: 4000000 INFO @ Mon, 03 Jun 2019 22:29:18: 4000000 INFO @ Mon, 03 Jun 2019 22:29:25: 5000000 INFO @ Mon, 03 Jun 2019 22:29:26: 5000000 INFO @ Mon, 03 Jun 2019 22:29:26: 4000000 INFO @ Mon, 03 Jun 2019 22:29:33: 6000000 INFO @ Mon, 03 Jun 2019 22:29:33: 6000000 INFO @ Mon, 03 Jun 2019 22:29:35: 5000000 INFO @ Mon, 03 Jun 2019 22:29:40: 7000000 INFO @ Mon, 03 Jun 2019 22:29:40: 7000000 INFO @ Mon, 03 Jun 2019 22:29:44: 6000000 INFO @ Mon, 03 Jun 2019 22:29:47: 8000000 INFO @ Mon, 03 Jun 2019 22:29:48: 8000000 INFO @ Mon, 03 Jun 2019 22:29:53: 7000000 INFO @ Mon, 03 Jun 2019 22:29:55: 9000000 INFO @ Mon, 03 Jun 2019 22:29:55: 9000000 INFO @ Mon, 03 Jun 2019 22:30:02: 10000000 INFO @ Mon, 03 Jun 2019 22:30:02: 10000000 INFO @ Mon, 03 Jun 2019 22:30:02: 8000000 INFO @ Mon, 03 Jun 2019 22:30:09: 11000000 INFO @ Mon, 03 Jun 2019 22:30:10: 11000000 INFO @ Mon, 03 Jun 2019 22:30:12: 9000000 INFO @ Mon, 03 Jun 2019 22:30:16: 12000000 INFO @ Mon, 03 Jun 2019 22:30:17: 12000000 INFO @ Mon, 03 Jun 2019 22:30:21: 10000000 INFO @ Mon, 03 Jun 2019 22:30:24: 13000000 INFO @ Mon, 03 Jun 2019 22:30:25: 13000000 INFO @ Mon, 03 Jun 2019 22:30:30: 11000000 INFO @ Mon, 03 Jun 2019 22:30:31: 14000000 INFO @ Mon, 03 Jun 2019 22:30:32: 14000000 INFO @ Mon, 03 Jun 2019 22:30:38: 15000000 INFO @ Mon, 03 Jun 2019 22:30:39: 12000000 INFO @ Mon, 03 Jun 2019 22:30:40: 15000000 INFO @ Mon, 03 Jun 2019 22:30:45: 16000000 INFO @ Mon, 03 Jun 2019 22:30:47: 16000000 INFO @ Mon, 03 Jun 2019 22:30:48: 13000000 INFO @ Mon, 03 Jun 2019 22:30:52: 17000000 INFO @ Mon, 03 Jun 2019 22:30:54: 17000000 INFO @ Mon, 03 Jun 2019 22:30:57: 14000000 INFO @ Mon, 03 Jun 2019 22:30:59: 18000000 INFO @ Mon, 03 Jun 2019 22:31:01: 18000000 INFO @ Mon, 03 Jun 2019 22:31:06: 15000000 INFO @ Mon, 03 Jun 2019 22:31:06: 19000000 INFO @ Mon, 03 Jun 2019 22:31:08: 19000000 INFO @ Mon, 03 Jun 2019 22:31:14: 20000000 INFO @ Mon, 03 Jun 2019 22:31:15: 16000000 INFO @ Mon, 03 Jun 2019 22:31:16: 20000000 INFO @ Mon, 03 Jun 2019 22:31:21: 21000000 INFO @ Mon, 03 Jun 2019 22:31:23: 21000000 INFO @ Mon, 03 Jun 2019 22:31:24: 17000000 INFO @ Mon, 03 Jun 2019 22:31:28: 22000000 INFO @ Mon, 03 Jun 2019 22:31:30: 22000000 INFO @ Mon, 03 Jun 2019 22:31:33: 18000000 INFO @ Mon, 03 Jun 2019 22:31:35: 23000000 INFO @ Mon, 03 Jun 2019 22:31:37: 23000000 INFO @ Mon, 03 Jun 2019 22:31:42: 24000000 INFO @ Mon, 03 Jun 2019 22:31:42: 19000000 INFO @ Mon, 03 Jun 2019 22:31:44: 24000000 INFO @ Mon, 03 Jun 2019 22:31:49: 25000000 INFO @ Mon, 03 Jun 2019 22:31:51: 20000000 INFO @ Mon, 03 Jun 2019 22:31:51: 25000000 INFO @ Mon, 03 Jun 2019 22:31:56: 26000000 INFO @ Mon, 03 Jun 2019 22:31:59: 26000000 INFO @ Mon, 03 Jun 2019 22:32:00: 21000000 INFO @ Mon, 03 Jun 2019 22:32:03: 27000000 INFO @ Mon, 03 Jun 2019 22:32:06: 27000000 INFO @ Mon, 03 Jun 2019 22:32:09: 22000000 INFO @ Mon, 03 Jun 2019 22:32:11: 28000000 INFO @ Mon, 03 Jun 2019 22:32:13: 28000000 INFO @ Mon, 03 Jun 2019 22:32:18: 29000000 INFO @ Mon, 03 Jun 2019 22:32:18: 23000000 INFO @ Mon, 03 Jun 2019 22:32:20: 29000000 INFO @ Mon, 03 Jun 2019 22:32:25: 30000000 INFO @ Mon, 03 Jun 2019 22:32:27: 24000000 INFO @ Mon, 03 Jun 2019 22:32:28: 30000000 INFO @ Mon, 03 Jun 2019 22:32:32: 31000000 INFO @ Mon, 03 Jun 2019 22:32:35: 31000000 INFO @ Mon, 03 Jun 2019 22:32:36: 25000000 INFO @ Mon, 03 Jun 2019 22:32:39: 32000000 INFO @ Mon, 03 Jun 2019 22:32:42: 32000000 INFO @ Mon, 03 Jun 2019 22:32:45: 26000000 INFO @ Mon, 03 Jun 2019 22:32:47: 33000000 INFO @ Mon, 03 Jun 2019 22:32:49: 33000000 INFO @ Mon, 03 Jun 2019 22:32:54: 27000000 INFO @ Mon, 03 Jun 2019 22:32:54: 34000000 INFO @ Mon, 03 Jun 2019 22:32:57: 34000000 INFO @ Mon, 03 Jun 2019 22:33:01: 35000000 INFO @ Mon, 03 Jun 2019 22:33:03: 28000000 INFO @ Mon, 03 Jun 2019 22:33:04: 35000000 INFO @ Mon, 03 Jun 2019 22:33:08: 36000000 INFO @ Mon, 03 Jun 2019 22:33:11: 36000000 INFO @ Mon, 03 Jun 2019 22:33:12: 29000000 INFO @ Mon, 03 Jun 2019 22:33:15: 37000000 INFO @ Mon, 03 Jun 2019 22:33:17: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:33:17: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:33:17: #1 total tags in treatment: 37194681 INFO @ Mon, 03 Jun 2019 22:33:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:33:17: #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 22:33:17: #1 tags after filtering in treatment: 37194681 INFO @ Mon, 03 Jun 2019 22:33:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:33:17: #1 finished! INFO @ Mon, 03 Jun 2019 22:33:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:33:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:33:19: 37000000 INFO @ Mon, 03 Jun 2019 22:33:20: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 22:33:20: 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 22:33:20: Process for pairing-model is terminated! INFO @ Mon, 03 Jun 2019 22:33:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:33:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:33:20: #1 total tags in treatment: 37194681 INFO @ Mon, 03 Jun 2019 22:33:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:33:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) cut: /home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.10_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/SRX495316/SRX495316.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:33:21: #1 tags after filtering in treatment: 37194681 INFO @ Mon, 03 Jun 2019 22:33:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:33:21: #1 finished! INFO @ Mon, 03 Jun 2019 22:33:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:33:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:33:21: 30000000 INFO @ Mon, 03 Jun 2019 22:33:24: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 22:33:24: 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 22:33:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.20_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/SRX495316/SRX495316.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:33:30: 31000000 INFO @ Mon, 03 Jun 2019 22:33:38: 32000000 INFO @ Mon, 03 Jun 2019 22:33:46: 33000000 INFO @ Mon, 03 Jun 2019 22:33:54: 34000000 INFO @ Mon, 03 Jun 2019 22:34:02: 35000000 INFO @ Mon, 03 Jun 2019 22:34:10: 36000000 INFO @ Mon, 03 Jun 2019 22:34:18: 37000000 INFO @ Mon, 03 Jun 2019 22:34:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:34:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:34:20: #1 total tags in treatment: 37194681 INFO @ Mon, 03 Jun 2019 22:34:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:34:20: #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 22:34:21: #1 tags after filtering in treatment: 37194681 INFO @ Mon, 03 Jun 2019 22:34:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:34:21: #1 finished! INFO @ Mon, 03 Jun 2019 22:34:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:34:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:34:24: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 22:34:24: 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 22:34:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.05_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/SRX495316/SRX495316.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495316/SRX495316.05_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。