Job ID = 1305978 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T12:27:11 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 ) 2019-06-03T12:50:29 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 ) 2019-06-03T12:50:29 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 ) 2019-06-03T12:50:29 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 ) 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: 00:16:22 55261147 reads; of these: 55261147 (100.00%) were unpaired; of these: 1066868 (1.93%) aligned 0 times 45427270 (82.20%) aligned exactly 1 time 8767009 (15.86%) aligned >1 times 98.07% overall alignment rate Time searching: 00:16:22 Overall time: 00:16:22 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] 16999387 / 54194279 = 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 22:25:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.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 22:25:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:25:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:25:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.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 22:25:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:25:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:25:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.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 22:25:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:25:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:25:40: 1000000 INFO @ Mon, 03 Jun 2019 22:25:40: 1000000 INFO @ Mon, 03 Jun 2019 22:25:40: 1000000 INFO @ Mon, 03 Jun 2019 22:25:49: 2000000 INFO @ Mon, 03 Jun 2019 22:25:49: 2000000 INFO @ Mon, 03 Jun 2019 22:25:49: 2000000 INFO @ Mon, 03 Jun 2019 22:25:57: 3000000 INFO @ Mon, 03 Jun 2019 22:25:58: 3000000 INFO @ Mon, 03 Jun 2019 22:25:58: 3000000 INFO @ Mon, 03 Jun 2019 22:26:05: 4000000 INFO @ Mon, 03 Jun 2019 22:26:06: 4000000 INFO @ Mon, 03 Jun 2019 22:26:07: 4000000 INFO @ Mon, 03 Jun 2019 22:26:13: 5000000 INFO @ Mon, 03 Jun 2019 22:26:14: 5000000 INFO @ Mon, 03 Jun 2019 22:26:16: 5000000 INFO @ Mon, 03 Jun 2019 22:26:20: 6000000 INFO @ Mon, 03 Jun 2019 22:26:23: 6000000 INFO @ Mon, 03 Jun 2019 22:26:24: 6000000 INFO @ Mon, 03 Jun 2019 22:26:28: 7000000 INFO @ Mon, 03 Jun 2019 22:26:31: 7000000 INFO @ Mon, 03 Jun 2019 22:26:33: 7000000 INFO @ Mon, 03 Jun 2019 22:26:36: 8000000 INFO @ Mon, 03 Jun 2019 22:26:39: 8000000 INFO @ Mon, 03 Jun 2019 22:26:42: 8000000 INFO @ Mon, 03 Jun 2019 22:26:44: 9000000 INFO @ Mon, 03 Jun 2019 22:26:48: 9000000 INFO @ Mon, 03 Jun 2019 22:26:50: 9000000 INFO @ Mon, 03 Jun 2019 22:26:51: 10000000 INFO @ Mon, 03 Jun 2019 22:26:56: 10000000 INFO @ Mon, 03 Jun 2019 22:26:59: 10000000 INFO @ Mon, 03 Jun 2019 22:26:59: 11000000 INFO @ Mon, 03 Jun 2019 22:27:04: 11000000 INFO @ Mon, 03 Jun 2019 22:27:07: 12000000 INFO @ Mon, 03 Jun 2019 22:27:07: 11000000 INFO @ Mon, 03 Jun 2019 22:27:13: 12000000 INFO @ Mon, 03 Jun 2019 22:27:15: 13000000 INFO @ Mon, 03 Jun 2019 22:27:16: 12000000 INFO @ Mon, 03 Jun 2019 22:27:21: 13000000 INFO @ Mon, 03 Jun 2019 22:27:22: 14000000 INFO @ Mon, 03 Jun 2019 22:27:25: 13000000 INFO @ Mon, 03 Jun 2019 22:27:29: 14000000 INFO @ Mon, 03 Jun 2019 22:27:30: 15000000 INFO @ Mon, 03 Jun 2019 22:27:33: 14000000 INFO @ Mon, 03 Jun 2019 22:27:37: 15000000 INFO @ Mon, 03 Jun 2019 22:27:38: 16000000 INFO @ Mon, 03 Jun 2019 22:27:42: 15000000 INFO @ Mon, 03 Jun 2019 22:27:45: 17000000 INFO @ Mon, 03 Jun 2019 22:27:46: 16000000 INFO @ Mon, 03 Jun 2019 22:27:50: 16000000 INFO @ Mon, 03 Jun 2019 22:27:53: 18000000 INFO @ Mon, 03 Jun 2019 22:27:54: 17000000 INFO @ Mon, 03 Jun 2019 22:27:59: 17000000 INFO @ Mon, 03 Jun 2019 22:28:01: 19000000 INFO @ Mon, 03 Jun 2019 22:28:02: 18000000 INFO @ Mon, 03 Jun 2019 22:28:07: 18000000 INFO @ Mon, 03 Jun 2019 22:28:09: 20000000 INFO @ Mon, 03 Jun 2019 22:28:10: 19000000 INFO @ Mon, 03 Jun 2019 22:28:16: 19000000 INFO @ Mon, 03 Jun 2019 22:28:16: 21000000 INFO @ Mon, 03 Jun 2019 22:28:19: 20000000 INFO @ Mon, 03 Jun 2019 22:28:24: 22000000 INFO @ Mon, 03 Jun 2019 22:28:24: 20000000 INFO @ Mon, 03 Jun 2019 22:28:28: 21000000 INFO @ Mon, 03 Jun 2019 22:28:32: 23000000 INFO @ Mon, 03 Jun 2019 22:28:33: 21000000 INFO @ Mon, 03 Jun 2019 22:28:36: 22000000 INFO @ Mon, 03 Jun 2019 22:28:40: 24000000 INFO @ Mon, 03 Jun 2019 22:28:41: 22000000 INFO @ Mon, 03 Jun 2019 22:28:45: 23000000 INFO @ Mon, 03 Jun 2019 22:28:47: 25000000 INFO @ Mon, 03 Jun 2019 22:28:50: 23000000 INFO @ Mon, 03 Jun 2019 22:28:53: 24000000 INFO @ Mon, 03 Jun 2019 22:28:55: 26000000 INFO @ Mon, 03 Jun 2019 22:28:58: 24000000 INFO @ Mon, 03 Jun 2019 22:29:02: 25000000 INFO @ Mon, 03 Jun 2019 22:29:03: 27000000 INFO @ Mon, 03 Jun 2019 22:29:07: 25000000 INFO @ Mon, 03 Jun 2019 22:29:10: 26000000 INFO @ Mon, 03 Jun 2019 22:29:11: 28000000 INFO @ Mon, 03 Jun 2019 22:29:15: 26000000 INFO @ Mon, 03 Jun 2019 22:29:19: 27000000 INFO @ Mon, 03 Jun 2019 22:29:19: 29000000 INFO @ Mon, 03 Jun 2019 22:29:24: 27000000 INFO @ Mon, 03 Jun 2019 22:29:27: 30000000 INFO @ Mon, 03 Jun 2019 22:29:27: 28000000 INFO @ Mon, 03 Jun 2019 22:29:32: 28000000 INFO @ Mon, 03 Jun 2019 22:29:35: 31000000 INFO @ Mon, 03 Jun 2019 22:29:36: 29000000 INFO @ Mon, 03 Jun 2019 22:29:41: 29000000 INFO @ Mon, 03 Jun 2019 22:29:43: 32000000 INFO @ Mon, 03 Jun 2019 22:29:44: 30000000 INFO @ Mon, 03 Jun 2019 22:29:50: 30000000 INFO @ Mon, 03 Jun 2019 22:29:51: 33000000 INFO @ Mon, 03 Jun 2019 22:29:53: 31000000 INFO @ Mon, 03 Jun 2019 22:29:58: 31000000 INFO @ Mon, 03 Jun 2019 22:29:59: 34000000 INFO @ Mon, 03 Jun 2019 22:30:01: 32000000 INFO @ Mon, 03 Jun 2019 22:30:06: 35000000 INFO @ Mon, 03 Jun 2019 22:30:07: 32000000 INFO @ Mon, 03 Jun 2019 22:30:09: 33000000 INFO @ Mon, 03 Jun 2019 22:30:14: 36000000 INFO @ Mon, 03 Jun 2019 22:30:15: 33000000 INFO @ Mon, 03 Jun 2019 22:30:18: 34000000 INFO @ Mon, 03 Jun 2019 22:30:22: 37000000 INFO @ Mon, 03 Jun 2019 22:30:24: 34000000 INFO @ Mon, 03 Jun 2019 22:30:24: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:30:24: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:30:24: #1 total tags in treatment: 37194892 INFO @ Mon, 03 Jun 2019 22:30:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:30:24: #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 22:30:25: #1 tags after filtering in treatment: 37194892 INFO @ Mon, 03 Jun 2019 22:30:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:30:25: #1 finished! INFO @ Mon, 03 Jun 2019 22:30:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:30:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:30:26: 35000000 INFO @ Mon, 03 Jun 2019 22:30:28: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 22:30:28: 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 22:30:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.05_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/SRX495314/SRX495314.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:30:32: 35000000 INFO @ Mon, 03 Jun 2019 22:30:34: 36000000 INFO @ Mon, 03 Jun 2019 22:30:40: 36000000 INFO @ Mon, 03 Jun 2019 22:30:42: 37000000 INFO @ Mon, 03 Jun 2019 22:30:44: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:30:44: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:30:44: #1 total tags in treatment: 37194892 INFO @ Mon, 03 Jun 2019 22:30:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:30:44: #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 22:30:45: #1 tags after filtering in treatment: 37194892 INFO @ Mon, 03 Jun 2019 22:30:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:30:45: #1 finished! INFO @ Mon, 03 Jun 2019 22:30:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:30:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:30:48: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 22:30:48: 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 22:30:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.10_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/SRX495314/SRX495314.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:30:48: 37000000 INFO @ Mon, 03 Jun 2019 22:30:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:30:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:30:50: #1 total tags in treatment: 37194892 INFO @ Mon, 03 Jun 2019 22:30:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:30:50: #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 22:30:51: #1 tags after filtering in treatment: 37194892 INFO @ Mon, 03 Jun 2019 22:30:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:30:51: #1 finished! INFO @ Mon, 03 Jun 2019 22:30:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:30:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:30:54: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 22:30:54: 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 22:30:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.20_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/SRX495314/SRX495314.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495314/SRX495314.20_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。