Job ID = 1295377 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T04:22:28 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 ) 2019-06-03T04:22:28 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 ) 2019-06-03T04:22:28 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 ) 2019-06-03T04:24:41 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 : 31,886,596 reads read : 31,886,596 reads written : 31,886,596 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: 00:10:02 31886596 reads; of these: 31886596 (100.00%) were unpaired; of these: 2849264 (8.94%) aligned 0 times 22878940 (71.75%) aligned exactly 1 time 6158392 (19.31%) aligned >1 times 91.06% overall alignment rate Time searching: 00:10:02 Overall time: 00:10:02 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] 7306942 / 29037332 = 0.2516 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 13:52:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.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 13:52:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:52:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:52:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.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 13:52:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:52:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:52:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.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 13:52:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:52:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:52:09: 1000000 INFO @ Mon, 03 Jun 2019 13:52:10: 1000000 INFO @ Mon, 03 Jun 2019 13:52:12: 1000000 INFO @ Mon, 03 Jun 2019 13:52:17: 2000000 INFO @ Mon, 03 Jun 2019 13:52:19: 2000000 INFO @ Mon, 03 Jun 2019 13:52:24: 2000000 INFO @ Mon, 03 Jun 2019 13:52:25: 3000000 INFO @ Mon, 03 Jun 2019 13:52:28: 3000000 INFO @ Mon, 03 Jun 2019 13:52:33: 4000000 INFO @ Mon, 03 Jun 2019 13:52:35: 3000000 INFO @ Mon, 03 Jun 2019 13:52:37: 4000000 INFO @ Mon, 03 Jun 2019 13:52:41: 5000000 INFO @ Mon, 03 Jun 2019 13:52:46: 5000000 INFO @ Mon, 03 Jun 2019 13:52:47: 4000000 INFO @ Mon, 03 Jun 2019 13:52:50: 6000000 INFO @ Mon, 03 Jun 2019 13:52:55: 6000000 INFO @ Mon, 03 Jun 2019 13:52:58: 7000000 INFO @ Mon, 03 Jun 2019 13:53:00: 5000000 INFO @ Mon, 03 Jun 2019 13:53:04: 7000000 INFO @ Mon, 03 Jun 2019 13:53:08: 8000000 INFO @ Mon, 03 Jun 2019 13:53:12: 6000000 INFO @ Mon, 03 Jun 2019 13:53:13: 8000000 INFO @ Mon, 03 Jun 2019 13:53:17: 9000000 INFO @ Mon, 03 Jun 2019 13:53:22: 9000000 INFO @ Mon, 03 Jun 2019 13:53:24: 7000000 INFO @ Mon, 03 Jun 2019 13:53:27: 10000000 INFO @ Mon, 03 Jun 2019 13:53:31: 10000000 INFO @ Mon, 03 Jun 2019 13:53:36: 8000000 INFO @ Mon, 03 Jun 2019 13:53:38: 11000000 INFO @ Mon, 03 Jun 2019 13:53:41: 11000000 INFO @ Mon, 03 Jun 2019 13:53:47: 12000000 INFO @ Mon, 03 Jun 2019 13:53:48: 9000000 INFO @ Mon, 03 Jun 2019 13:53:50: 12000000 INFO @ Mon, 03 Jun 2019 13:53:55: 13000000 INFO @ Mon, 03 Jun 2019 13:53:59: 13000000 INFO @ Mon, 03 Jun 2019 13:54:00: 10000000 INFO @ Mon, 03 Jun 2019 13:54:06: 14000000 INFO @ Mon, 03 Jun 2019 13:54:09: 14000000 INFO @ Mon, 03 Jun 2019 13:54:13: 11000000 INFO @ Mon, 03 Jun 2019 13:54:15: 15000000 INFO @ Mon, 03 Jun 2019 13:54:18: 15000000 INFO @ Mon, 03 Jun 2019 13:54:24: 12000000 INFO @ Mon, 03 Jun 2019 13:54:24: 16000000 INFO @ Mon, 03 Jun 2019 13:54:28: 16000000 INFO @ Mon, 03 Jun 2019 13:54:33: 17000000 INFO @ Mon, 03 Jun 2019 13:54:34: 13000000 INFO @ Mon, 03 Jun 2019 13:54:37: 17000000 INFO @ Mon, 03 Jun 2019 13:54:41: 18000000 INFO @ Mon, 03 Jun 2019 13:54:45: 14000000 INFO @ Mon, 03 Jun 2019 13:54:46: 18000000 INFO @ Mon, 03 Jun 2019 13:54:50: 19000000 INFO @ Mon, 03 Jun 2019 13:54:55: 19000000 INFO @ Mon, 03 Jun 2019 13:54:56: 15000000 INFO @ Mon, 03 Jun 2019 13:55:01: 20000000 INFO @ Mon, 03 Jun 2019 13:55:05: 20000000 INFO @ Mon, 03 Jun 2019 13:55:07: 16000000 INFO @ Mon, 03 Jun 2019 13:55:09: 21000000 INFO @ Mon, 03 Jun 2019 13:55:14: 21000000 INFO @ Mon, 03 Jun 2019 13:55:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:55:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:55:16: #1 total tags in treatment: 21730390 INFO @ Mon, 03 Jun 2019 13:55:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:55:16: #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 13:55:16: #1 tags after filtering in treatment: 21730390 INFO @ Mon, 03 Jun 2019 13:55:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:55:16: #1 finished! INFO @ Mon, 03 Jun 2019 13:55:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:55:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:55:18: #2 number of paired peaks: 7 WARNING @ Mon, 03 Jun 2019 13:55:18: Too few paired peaks (7) 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 13:55:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.10_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/SRX335511/SRX335511.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:55:19: 17000000 INFO @ Mon, 03 Jun 2019 13:55:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:55:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:55:21: #1 total tags in treatment: 21730390 INFO @ Mon, 03 Jun 2019 13:55:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:55:21: #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 13:55:22: #1 tags after filtering in treatment: 21730390 INFO @ Mon, 03 Jun 2019 13:55:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:55:22: #1 finished! INFO @ Mon, 03 Jun 2019 13:55:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:55:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:55:23: #2 number of paired peaks: 7 WARNING @ Mon, 03 Jun 2019 13:55:23: Too few paired peaks (7) 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 13:55:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.20_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/SRX335511/SRX335511.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:55:30: 18000000 INFO @ Mon, 03 Jun 2019 13:55:40: 19000000 INFO @ Mon, 03 Jun 2019 13:55:49: 20000000 INFO @ Mon, 03 Jun 2019 13:55:59: 21000000 INFO @ Mon, 03 Jun 2019 13:56:07: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:56:07: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:56:07: #1 total tags in treatment: 21730390 INFO @ Mon, 03 Jun 2019 13:56:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:56:07: #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 13:56:07: #1 tags after filtering in treatment: 21730390 INFO @ Mon, 03 Jun 2019 13:56:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:56:07: #1 finished! INFO @ Mon, 03 Jun 2019 13:56:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:56:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:56:09: #2 number of paired peaks: 7 WARNING @ Mon, 03 Jun 2019 13:56:09: Too few paired peaks (7) 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 13:56:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.05_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/SRX335511/SRX335511.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335511/SRX335511.05_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。