Job ID = 1298998 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:44:36 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-03T08:44:36 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-03T08:44:36 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading inform004C) ) 2019-06-03T08:44:36 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading inform004C) ) 2019-06-03T08:44:36 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-03T08:50:24 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 : 37,757,409 reads read : 37,757,409 reads written : 37,757,409 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: 00:10:58 37757409 reads; of these: 37757409 (100.00%) were unpaired; of these: 2549291 (6.75%) aligned 0 times 30042286 (79.57%) aligned exactly 1 time 5165832 (13.68%) aligned >1 times 93.25% overall alignment rate Time searching: 00:10:58 Overall time: 00:10:58 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] 9202057 / 35208118 = 0.2614 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 18:19:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.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 18:19:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:19:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:19:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.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 18:19:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:19:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:19:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.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 18:19:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:19:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:19:43: 1000000 INFO @ Mon, 03 Jun 2019 18:19:46: 1000000 INFO @ Mon, 03 Jun 2019 18:19:46: 1000000 INFO @ Mon, 03 Jun 2019 18:19:52: 2000000 INFO @ Mon, 03 Jun 2019 18:19:58: 2000000 INFO @ Mon, 03 Jun 2019 18:19:58: 2000000 INFO @ Mon, 03 Jun 2019 18:20:01: 3000000 INFO @ Mon, 03 Jun 2019 18:20:10: 3000000 INFO @ Mon, 03 Jun 2019 18:20:10: 3000000 INFO @ Mon, 03 Jun 2019 18:20:10: 4000000 INFO @ Mon, 03 Jun 2019 18:20:19: 5000000 INFO @ Mon, 03 Jun 2019 18:20:21: 4000000 INFO @ Mon, 03 Jun 2019 18:20:22: 4000000 INFO @ Mon, 03 Jun 2019 18:20:28: 6000000 INFO @ Mon, 03 Jun 2019 18:20:33: 5000000 INFO @ Mon, 03 Jun 2019 18:20:33: 5000000 INFO @ Mon, 03 Jun 2019 18:20:36: 7000000 INFO @ Mon, 03 Jun 2019 18:20:45: 6000000 INFO @ Mon, 03 Jun 2019 18:20:45: 6000000 INFO @ Mon, 03 Jun 2019 18:20:45: 8000000 INFO @ Mon, 03 Jun 2019 18:20:54: 9000000 INFO @ Mon, 03 Jun 2019 18:20:57: 7000000 INFO @ Mon, 03 Jun 2019 18:20:57: 7000000 INFO @ Mon, 03 Jun 2019 18:21:03: 10000000 INFO @ Mon, 03 Jun 2019 18:21:08: 8000000 INFO @ Mon, 03 Jun 2019 18:21:08: 8000000 INFO @ Mon, 03 Jun 2019 18:21:12: 11000000 INFO @ Mon, 03 Jun 2019 18:21:20: 9000000 INFO @ Mon, 03 Jun 2019 18:21:20: 9000000 INFO @ Mon, 03 Jun 2019 18:21:21: 12000000 INFO @ Mon, 03 Jun 2019 18:21:29: 13000000 INFO @ Mon, 03 Jun 2019 18:21:31: 10000000 INFO @ Mon, 03 Jun 2019 18:21:32: 10000000 INFO @ Mon, 03 Jun 2019 18:21:38: 14000000 INFO @ Mon, 03 Jun 2019 18:21:43: 11000000 INFO @ Mon, 03 Jun 2019 18:21:43: 11000000 INFO @ Mon, 03 Jun 2019 18:21:47: 15000000 INFO @ Mon, 03 Jun 2019 18:21:55: 12000000 INFO @ Mon, 03 Jun 2019 18:21:55: 12000000 INFO @ Mon, 03 Jun 2019 18:21:56: 16000000 INFO @ Mon, 03 Jun 2019 18:22:05: 17000000 INFO @ Mon, 03 Jun 2019 18:22:07: 13000000 INFO @ Mon, 03 Jun 2019 18:22:07: 13000000 INFO @ Mon, 03 Jun 2019 18:22:13: 18000000 INFO @ Mon, 03 Jun 2019 18:22:18: 14000000 INFO @ Mon, 03 Jun 2019 18:22:18: 14000000 INFO @ Mon, 03 Jun 2019 18:22:22: 19000000 INFO @ Mon, 03 Jun 2019 18:22:30: 15000000 INFO @ Mon, 03 Jun 2019 18:22:30: 15000000 INFO @ Mon, 03 Jun 2019 18:22:30: 20000000 INFO @ Mon, 03 Jun 2019 18:22:39: 21000000 INFO @ Mon, 03 Jun 2019 18:22:42: 16000000 INFO @ Mon, 03 Jun 2019 18:22:42: 16000000 INFO @ Mon, 03 Jun 2019 18:22:48: 22000000 INFO @ Mon, 03 Jun 2019 18:22:54: 17000000 INFO @ Mon, 03 Jun 2019 18:22:54: 17000000 INFO @ Mon, 03 Jun 2019 18:22:57: 23000000 INFO @ Mon, 03 Jun 2019 18:23:05: 18000000 INFO @ Mon, 03 Jun 2019 18:23:05: 18000000 INFO @ Mon, 03 Jun 2019 18:23:05: 24000000 INFO @ Mon, 03 Jun 2019 18:23:14: 25000000 INFO @ Mon, 03 Jun 2019 18:23:17: 19000000 INFO @ Mon, 03 Jun 2019 18:23:17: 19000000 INFO @ Mon, 03 Jun 2019 18:23:23: 26000000 INFO @ Mon, 03 Jun 2019 18:23:23: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:23:23: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:23:23: #1 total tags in treatment: 26006061 INFO @ Mon, 03 Jun 2019 18:23:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:23:23: #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 18:23:23: #1 tags after filtering in treatment: 26006061 INFO @ Mon, 03 Jun 2019 18:23:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:23:23: #1 finished! INFO @ Mon, 03 Jun 2019 18:23:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:23:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:23:26: #2 number of paired peaks: 8 WARNING @ Mon, 03 Jun 2019 18:23:26: Too few paired peaks (8) 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 18:23:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.05_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/SRX467068/SRX467068.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:23:28: 20000000 INFO @ Mon, 03 Jun 2019 18:23:28: 20000000 INFO @ Mon, 03 Jun 2019 18:23:40: 21000000 INFO @ Mon, 03 Jun 2019 18:23:40: 21000000 INFO @ Mon, 03 Jun 2019 18:23:51: 22000000 INFO @ Mon, 03 Jun 2019 18:23:51: 22000000 INFO @ Mon, 03 Jun 2019 18:24:02: 23000000 INFO @ Mon, 03 Jun 2019 18:24:02: 23000000 INFO @ Mon, 03 Jun 2019 18:24:13: 24000000 INFO @ Mon, 03 Jun 2019 18:24:13: 24000000 INFO @ Mon, 03 Jun 2019 18:24:24: 25000000 INFO @ Mon, 03 Jun 2019 18:24:24: 25000000 INFO @ Mon, 03 Jun 2019 18:24:35: 26000000 INFO @ Mon, 03 Jun 2019 18:24:35: 26000000 INFO @ Mon, 03 Jun 2019 18:24:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:24:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:24:35: #1 total tags in treatment: 26006061 INFO @ Mon, 03 Jun 2019 18:24:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:24:35: #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 18:24:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:24:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:24:35: #1 total tags in treatment: 26006061 INFO @ Mon, 03 Jun 2019 18:24:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:24:35: #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 18:24:36: #1 tags after filtering in treatment: 26006061 INFO @ Mon, 03 Jun 2019 18:24:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:24:36: #1 finished! INFO @ Mon, 03 Jun 2019 18:24:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:24:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:24:36: #1 tags after filtering in treatment: 26006061 INFO @ Mon, 03 Jun 2019 18:24:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:24:36: #1 finished! INFO @ Mon, 03 Jun 2019 18:24:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:24:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:24:38: #2 number of paired peaks: 8 WARNING @ Mon, 03 Jun 2019 18:24:38: Too few paired peaks (8) 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 18:24:38: Process for pairing-model is terminated! INFO @ Mon, 03 Jun 2019 18:24:38: #2 number of paired peaks: 8 WARNING @ Mon, 03 Jun 2019 18:24:38: Too few paired peaks (8) 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 18:24:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) cut: /home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.20_peaks.narrowPeak: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467068/SRX467068.20_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。