Job ID = 1298529 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:25:45 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 ) 2019-06-03T08:25:45 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 ) 2019-06-03T08:37:17 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 : 38,980,643 reads read : 38,980,643 reads written : 38,980,643 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: 00:13:30 38980643 reads; of these: 38980643 (100.00%) were unpaired; of these: 1882134 (4.83%) aligned 0 times 31347382 (80.42%) aligned exactly 1 time 5751127 (14.75%) aligned >1 times 95.17% overall alignment rate Time searching: 00:13:30 Overall time: 00:13:30 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] 13405590 / 37098509 = 0.3614 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 18:07:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.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 18:07:19: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:07:19: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:07:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.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 18:07:19: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:07:19: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:07:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.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 18:07:19: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:07:19: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:07:27: 1000000 INFO @ Mon, 03 Jun 2019 18:07:28: 1000000 INFO @ Mon, 03 Jun 2019 18:07:29: 1000000 INFO @ Mon, 03 Jun 2019 18:07:36: 2000000 INFO @ Mon, 03 Jun 2019 18:07:36: 2000000 INFO @ Mon, 03 Jun 2019 18:07:38: 2000000 INFO @ Mon, 03 Jun 2019 18:07:45: 3000000 INFO @ Mon, 03 Jun 2019 18:07:45: 3000000 INFO @ Mon, 03 Jun 2019 18:07:48: 3000000 INFO @ Mon, 03 Jun 2019 18:07:54: 4000000 INFO @ Mon, 03 Jun 2019 18:07:54: 4000000 INFO @ Mon, 03 Jun 2019 18:08:01: 4000000 INFO @ Mon, 03 Jun 2019 18:08:03: 5000000 INFO @ Mon, 03 Jun 2019 18:08:04: 5000000 INFO @ Mon, 03 Jun 2019 18:08:11: 6000000 INFO @ Mon, 03 Jun 2019 18:08:12: 5000000 INFO @ Mon, 03 Jun 2019 18:08:12: 6000000 INFO @ Mon, 03 Jun 2019 18:08:19: 7000000 INFO @ Mon, 03 Jun 2019 18:08:21: 7000000 INFO @ Mon, 03 Jun 2019 18:08:22: 6000000 INFO @ Mon, 03 Jun 2019 18:08:27: 8000000 INFO @ Mon, 03 Jun 2019 18:08:30: 8000000 INFO @ Mon, 03 Jun 2019 18:08:33: 7000000 INFO @ Mon, 03 Jun 2019 18:08:35: 9000000 INFO @ Mon, 03 Jun 2019 18:08:39: 9000000 INFO @ Mon, 03 Jun 2019 18:08:42: 8000000 INFO @ Mon, 03 Jun 2019 18:08:43: 10000000 INFO @ Mon, 03 Jun 2019 18:08:47: 10000000 INFO @ Mon, 03 Jun 2019 18:08:51: 11000000 INFO @ Mon, 03 Jun 2019 18:08:51: 9000000 INFO @ Mon, 03 Jun 2019 18:08:57: 11000000 INFO @ Mon, 03 Jun 2019 18:09:00: 12000000 INFO @ Mon, 03 Jun 2019 18:09:03: 10000000 INFO @ Mon, 03 Jun 2019 18:09:05: 12000000 INFO @ Mon, 03 Jun 2019 18:09:08: 13000000 INFO @ Mon, 03 Jun 2019 18:09:14: 11000000 INFO @ Mon, 03 Jun 2019 18:09:14: 13000000 INFO @ Mon, 03 Jun 2019 18:09:16: 14000000 INFO @ Mon, 03 Jun 2019 18:09:23: 14000000 INFO @ Mon, 03 Jun 2019 18:09:24: 15000000 INFO @ Mon, 03 Jun 2019 18:09:24: 12000000 INFO @ Mon, 03 Jun 2019 18:09:31: 15000000 INFO @ Mon, 03 Jun 2019 18:09:33: 16000000 INFO @ Mon, 03 Jun 2019 18:09:35: 13000000 INFO @ Mon, 03 Jun 2019 18:09:40: 16000000 INFO @ Mon, 03 Jun 2019 18:09:41: 17000000 INFO @ Mon, 03 Jun 2019 18:09:45: 14000000 INFO @ Mon, 03 Jun 2019 18:09:48: 17000000 INFO @ Mon, 03 Jun 2019 18:09:50: 18000000 INFO @ Mon, 03 Jun 2019 18:09:55: 15000000 INFO @ Mon, 03 Jun 2019 18:09:57: 18000000 INFO @ Mon, 03 Jun 2019 18:10:00: 19000000 INFO @ Mon, 03 Jun 2019 18:10:06: 16000000 INFO @ Mon, 03 Jun 2019 18:10:07: 19000000 INFO @ Mon, 03 Jun 2019 18:10:10: 20000000 INFO @ Mon, 03 Jun 2019 18:10:16: 20000000 INFO @ Mon, 03 Jun 2019 18:10:16: 17000000 INFO @ Mon, 03 Jun 2019 18:10:19: 21000000 INFO @ Mon, 03 Jun 2019 18:10:24: 21000000 INFO @ Mon, 03 Jun 2019 18:10:27: 18000000 INFO @ Mon, 03 Jun 2019 18:10:28: 22000000 INFO @ Mon, 03 Jun 2019 18:10:33: 22000000 INFO @ Mon, 03 Jun 2019 18:10:36: 23000000 INFO @ Mon, 03 Jun 2019 18:10:38: 19000000 INFO @ Mon, 03 Jun 2019 18:10:41: 23000000 INFO @ Mon, 03 Jun 2019 18:10:42: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:10:42: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:10:42: #1 total tags in treatment: 23692919 INFO @ Mon, 03 Jun 2019 18:10:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:10:42: #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 18:10:43: #1 tags after filtering in treatment: 23692919 INFO @ Mon, 03 Jun 2019 18:10:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:10:43: #1 finished! INFO @ Mon, 03 Jun 2019 18:10:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:10:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:10:45: #2 number of paired peaks: 10 WARNING @ Mon, 03 Jun 2019 18:10:45: Too few paired peaks (10) 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 18:10:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.10_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/SRX467038/SRX467038.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:10:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:10:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:10:47: #1 total tags in treatment: 23692919 INFO @ Mon, 03 Jun 2019 18:10:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:10:47: #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 18:10:47: #1 tags after filtering in treatment: 23692919 INFO @ Mon, 03 Jun 2019 18:10:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:10:47: #1 finished! INFO @ Mon, 03 Jun 2019 18:10:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:10:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:10:49: 20000000 INFO @ Mon, 03 Jun 2019 18:10:49: #2 number of paired peaks: 10 WARNING @ Mon, 03 Jun 2019 18:10:49: Too few paired peaks (10) 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 18:10:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.20_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/SRX467038/SRX467038.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:10:59: 21000000 INFO @ Mon, 03 Jun 2019 18:11:09: 22000000 INFO @ Mon, 03 Jun 2019 18:11:18: 23000000 INFO @ Mon, 03 Jun 2019 18:11:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:11:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:11:25: #1 total tags in treatment: 23692919 INFO @ Mon, 03 Jun 2019 18:11:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:11:25: #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 18:11:25: #1 tags after filtering in treatment: 23692919 INFO @ Mon, 03 Jun 2019 18:11:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:11:25: #1 finished! INFO @ Mon, 03 Jun 2019 18:11:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:11:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:11:27: #2 number of paired peaks: 10 WARNING @ Mon, 03 Jun 2019 18:11:27: Too few paired peaks (10) 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 18:11:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.05_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/SRX467038/SRX467038.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467038/SRX467038.05_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。