Job ID = 1298818 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:35:06 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 ) 2019-06-03T08:39:56 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 ) 2019-06-03T08:40:33 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 ) 2019-06-03T08:41:52 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 : 37,021,579 reads read : 37,021,579 reads written : 37,021,579 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: 00:13:36 37021579 reads; of these: 37021579 (100.00%) were unpaired; of these: 1598045 (4.32%) aligned 0 times 26317125 (71.09%) aligned exactly 1 time 9106409 (24.60%) aligned >1 times 95.68% overall alignment rate Time searching: 00:13:36 Overall time: 00:13:36 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] 9396961 / 35423534 = 0.2653 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 18:18:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.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 18:18:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:18:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:18:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.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 18:18:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:18:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:18:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.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 18:18:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:18:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:18:18: 1000000 INFO @ Mon, 03 Jun 2019 18:18:18: 1000000 INFO @ Mon, 03 Jun 2019 18:18:19: 1000000 INFO @ Mon, 03 Jun 2019 18:18:27: 2000000 INFO @ Mon, 03 Jun 2019 18:18:27: 2000000 INFO @ Mon, 03 Jun 2019 18:18:28: 2000000 INFO @ Mon, 03 Jun 2019 18:18:35: 3000000 INFO @ Mon, 03 Jun 2019 18:18:35: 3000000 INFO @ Mon, 03 Jun 2019 18:18:37: 3000000 INFO @ Mon, 03 Jun 2019 18:18:44: 4000000 INFO @ Mon, 03 Jun 2019 18:18:44: 4000000 INFO @ Mon, 03 Jun 2019 18:18:46: 4000000 INFO @ Mon, 03 Jun 2019 18:18:52: 5000000 INFO @ Mon, 03 Jun 2019 18:18:52: 5000000 INFO @ Mon, 03 Jun 2019 18:18:55: 5000000 INFO @ Mon, 03 Jun 2019 18:19:00: 6000000 INFO @ Mon, 03 Jun 2019 18:19:00: 6000000 INFO @ Mon, 03 Jun 2019 18:19:04: 6000000 INFO @ Mon, 03 Jun 2019 18:19:09: 7000000 INFO @ Mon, 03 Jun 2019 18:19:09: 7000000 INFO @ Mon, 03 Jun 2019 18:19:13: 7000000 INFO @ Mon, 03 Jun 2019 18:19:17: 8000000 INFO @ Mon, 03 Jun 2019 18:19:17: 8000000 INFO @ Mon, 03 Jun 2019 18:19:22: 8000000 INFO @ Mon, 03 Jun 2019 18:19:25: 9000000 INFO @ Mon, 03 Jun 2019 18:19:26: 9000000 INFO @ Mon, 03 Jun 2019 18:19:30: 9000000 INFO @ Mon, 03 Jun 2019 18:19:34: 10000000 INFO @ Mon, 03 Jun 2019 18:19:34: 10000000 INFO @ Mon, 03 Jun 2019 18:19:39: 10000000 INFO @ Mon, 03 Jun 2019 18:19:42: 11000000 INFO @ Mon, 03 Jun 2019 18:19:42: 11000000 INFO @ Mon, 03 Jun 2019 18:19:48: 11000000 INFO @ Mon, 03 Jun 2019 18:19:50: 12000000 INFO @ Mon, 03 Jun 2019 18:19:50: 12000000 INFO @ Mon, 03 Jun 2019 18:19:56: 12000000 INFO @ Mon, 03 Jun 2019 18:19:58: 13000000 INFO @ Mon, 03 Jun 2019 18:19:58: 13000000 INFO @ Mon, 03 Jun 2019 18:20:05: 13000000 INFO @ Mon, 03 Jun 2019 18:20:07: 14000000 INFO @ Mon, 03 Jun 2019 18:20:07: 14000000 INFO @ Mon, 03 Jun 2019 18:20:14: 14000000 INFO @ Mon, 03 Jun 2019 18:20:15: 15000000 INFO @ Mon, 03 Jun 2019 18:20:15: 15000000 INFO @ Mon, 03 Jun 2019 18:20:23: 15000000 INFO @ Mon, 03 Jun 2019 18:20:23: 16000000 INFO @ Mon, 03 Jun 2019 18:20:23: 16000000 INFO @ Mon, 03 Jun 2019 18:20:31: 17000000 INFO @ Mon, 03 Jun 2019 18:20:31: 17000000 INFO @ Mon, 03 Jun 2019 18:20:31: 16000000 INFO @ Mon, 03 Jun 2019 18:20:39: 18000000 INFO @ Mon, 03 Jun 2019 18:20:39: 18000000 INFO @ Mon, 03 Jun 2019 18:20:40: 17000000 INFO @ Mon, 03 Jun 2019 18:20:47: 19000000 INFO @ Mon, 03 Jun 2019 18:20:47: 19000000 INFO @ Mon, 03 Jun 2019 18:20:49: 18000000 INFO @ Mon, 03 Jun 2019 18:20:55: 20000000 INFO @ Mon, 03 Jun 2019 18:20:56: 20000000 INFO @ Mon, 03 Jun 2019 18:20:58: 19000000 INFO @ Mon, 03 Jun 2019 18:21:03: 21000000 INFO @ Mon, 03 Jun 2019 18:21:03: 21000000 INFO @ Mon, 03 Jun 2019 18:21:06: 20000000 INFO @ Mon, 03 Jun 2019 18:21:11: 22000000 INFO @ Mon, 03 Jun 2019 18:21:11: 22000000 INFO @ Mon, 03 Jun 2019 18:21:15: 21000000 INFO @ Mon, 03 Jun 2019 18:21:19: 23000000 INFO @ Mon, 03 Jun 2019 18:21:20: 23000000 INFO @ Mon, 03 Jun 2019 18:21:23: 22000000 INFO @ Mon, 03 Jun 2019 18:21:27: 24000000 INFO @ Mon, 03 Jun 2019 18:21:27: 24000000 INFO @ Mon, 03 Jun 2019 18:21:32: 23000000 INFO @ Mon, 03 Jun 2019 18:21:35: 25000000 INFO @ Mon, 03 Jun 2019 18:21:36: 25000000 INFO @ Mon, 03 Jun 2019 18:21:40: 24000000 INFO @ Mon, 03 Jun 2019 18:21:44: 26000000 INFO @ Mon, 03 Jun 2019 18:21:44: 26000000 INFO @ Mon, 03 Jun 2019 18:21:44: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:21:44: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:21:44: #1 total tags in treatment: 26026573 INFO @ Mon, 03 Jun 2019 18:21:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:21:44: #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 18:21:45: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:21:45: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:21:45: #1 total tags in treatment: 26026573 INFO @ Mon, 03 Jun 2019 18:21:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:21:45: #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 18:21:45: #1 tags after filtering in treatment: 26026573 INFO @ Mon, 03 Jun 2019 18:21:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:21:45: #1 finished! INFO @ Mon, 03 Jun 2019 18:21:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:21:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:21:45: #1 tags after filtering in treatment: 26026573 INFO @ Mon, 03 Jun 2019 18:21:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:21:45: #1 finished! INFO @ Mon, 03 Jun 2019 18:21:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:21:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:21:47: #2 number of paired peaks: 18 WARNING @ Mon, 03 Jun 2019 18:21:47: Too few paired peaks (18) 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 18:21:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.10_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/SRX467053/SRX467053.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:21:47: #2 number of paired peaks: 18 WARNING @ Mon, 03 Jun 2019 18:21:47: Too few paired peaks (18) 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 18:21:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.05_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/SRX467053/SRX467053.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:21:49: 25000000 INFO @ Mon, 03 Jun 2019 18:21:58: 26000000 INFO @ Mon, 03 Jun 2019 18:21:58: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:21:58: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:21:58: #1 total tags in treatment: 26026573 INFO @ Mon, 03 Jun 2019 18:21:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:21:58: #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 18:21:59: #1 tags after filtering in treatment: 26026573 INFO @ Mon, 03 Jun 2019 18:21:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:21:59: #1 finished! INFO @ Mon, 03 Jun 2019 18:21:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:21:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:22:01: #2 number of paired peaks: 18 WARNING @ Mon, 03 Jun 2019 18:22:01: Too few paired peaks (18) 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 18:22:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.20_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/SRX467053/SRX467053.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467053/SRX467053.20_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。