Job ID = 1295363 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T04:24:11 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 ) 2019-06-03T04:24:33 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 ) 2019-06-03T04:24:33 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 ) spots read : 30,968,303 reads read : 30,968,303 reads written : 30,968,303 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: 00:08:54 30968303 reads; of these: 30968303 (100.00%) were unpaired; of these: 3705115 (11.96%) aligned 0 times 21866366 (70.61%) aligned exactly 1 time 5396822 (17.43%) aligned >1 times 88.04% overall alignment rate Time searching: 00:08:54 Overall time: 00:08:54 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] 6864484 / 27263188 = 0.2518 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 13:44:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.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 13:44:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:44:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:44:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.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 13:44:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:44:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:44:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.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 13:44:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:44:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:44:50: 1000000 INFO @ Mon, 03 Jun 2019 13:44:51: 1000000 INFO @ Mon, 03 Jun 2019 13:44:51: 1000000 INFO @ Mon, 03 Jun 2019 13:44:57: 2000000 INFO @ Mon, 03 Jun 2019 13:45:00: 2000000 INFO @ Mon, 03 Jun 2019 13:45:00: 2000000 INFO @ Mon, 03 Jun 2019 13:45:04: 3000000 INFO @ Mon, 03 Jun 2019 13:45:08: 3000000 INFO @ Mon, 03 Jun 2019 13:45:08: 3000000 INFO @ Mon, 03 Jun 2019 13:45:10: 4000000 INFO @ Mon, 03 Jun 2019 13:45:16: 4000000 INFO @ Mon, 03 Jun 2019 13:45:16: 4000000 INFO @ Mon, 03 Jun 2019 13:45:17: 5000000 INFO @ Mon, 03 Jun 2019 13:45:24: 5000000 INFO @ Mon, 03 Jun 2019 13:45:24: 5000000 INFO @ Mon, 03 Jun 2019 13:45:24: 6000000 INFO @ Mon, 03 Jun 2019 13:45:31: 7000000 INFO @ Mon, 03 Jun 2019 13:45:31: 6000000 INFO @ Mon, 03 Jun 2019 13:45:31: 6000000 INFO @ Mon, 03 Jun 2019 13:45:38: 8000000 INFO @ Mon, 03 Jun 2019 13:45:39: 7000000 INFO @ Mon, 03 Jun 2019 13:45:39: 7000000 INFO @ Mon, 03 Jun 2019 13:45:44: 9000000 INFO @ Mon, 03 Jun 2019 13:45:47: 8000000 INFO @ Mon, 03 Jun 2019 13:45:47: 8000000 INFO @ Mon, 03 Jun 2019 13:45:51: 10000000 INFO @ Mon, 03 Jun 2019 13:45:54: 9000000 INFO @ Mon, 03 Jun 2019 13:45:54: 9000000 INFO @ Mon, 03 Jun 2019 13:45:58: 11000000 INFO @ Mon, 03 Jun 2019 13:46:02: 10000000 INFO @ Mon, 03 Jun 2019 13:46:02: 10000000 INFO @ Mon, 03 Jun 2019 13:46:05: 12000000 INFO @ Mon, 03 Jun 2019 13:46:10: 11000000 INFO @ Mon, 03 Jun 2019 13:46:10: 11000000 INFO @ Mon, 03 Jun 2019 13:46:12: 13000000 INFO @ Mon, 03 Jun 2019 13:46:17: 12000000 INFO @ Mon, 03 Jun 2019 13:46:18: 12000000 INFO @ Mon, 03 Jun 2019 13:46:18: 14000000 INFO @ Mon, 03 Jun 2019 13:46:25: 13000000 INFO @ Mon, 03 Jun 2019 13:46:25: 15000000 INFO @ Mon, 03 Jun 2019 13:46:25: 13000000 INFO @ Mon, 03 Jun 2019 13:46:32: 16000000 INFO @ Mon, 03 Jun 2019 13:46:33: 14000000 INFO @ Mon, 03 Jun 2019 13:46:33: 14000000 INFO @ Mon, 03 Jun 2019 13:46:39: 17000000 INFO @ Mon, 03 Jun 2019 13:46:40: 15000000 INFO @ Mon, 03 Jun 2019 13:46:41: 15000000 INFO @ Mon, 03 Jun 2019 13:46:46: 18000000 INFO @ Mon, 03 Jun 2019 13:46:48: 16000000 INFO @ Mon, 03 Jun 2019 13:46:49: 16000000 INFO @ Mon, 03 Jun 2019 13:46:52: 19000000 INFO @ Mon, 03 Jun 2019 13:46:56: 17000000 INFO @ Mon, 03 Jun 2019 13:46:57: 17000000 INFO @ Mon, 03 Jun 2019 13:46:59: 20000000 INFO @ Mon, 03 Jun 2019 13:47:02: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:47:02: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:47:02: #1 total tags in treatment: 20398704 INFO @ Mon, 03 Jun 2019 13:47:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:47:02: #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 13:47:03: #1 tags after filtering in treatment: 20398704 INFO @ Mon, 03 Jun 2019 13:47:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:47:03: #1 finished! INFO @ Mon, 03 Jun 2019 13:47:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:47:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:47:04: 18000000 INFO @ Mon, 03 Jun 2019 13:47:04: 18000000 INFO @ Mon, 03 Jun 2019 13:47:04: #2 number of paired peaks: 41 WARNING @ Mon, 03 Jun 2019 13:47:04: Too few paired peaks (41) 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 13:47:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.05_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/SRX335502/SRX335502.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:47:11: 19000000 INFO @ Mon, 03 Jun 2019 13:47:12: 19000000 INFO @ Mon, 03 Jun 2019 13:47:19: 20000000 INFO @ Mon, 03 Jun 2019 13:47:19: 20000000 INFO @ Mon, 03 Jun 2019 13:47:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:47:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:47:22: #1 total tags in treatment: 20398704 INFO @ Mon, 03 Jun 2019 13:47:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:47:22: #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 13:47:23: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:47:23: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:47:23: #1 total tags in treatment: 20398704 INFO @ Mon, 03 Jun 2019 13:47:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:47:23: #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 13:47:23: #1 tags after filtering in treatment: 20398704 INFO @ Mon, 03 Jun 2019 13:47:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:47:23: #1 finished! INFO @ Mon, 03 Jun 2019 13:47:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:47:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:47:23: #1 tags after filtering in treatment: 20398704 INFO @ Mon, 03 Jun 2019 13:47:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:47:23: #1 finished! INFO @ Mon, 03 Jun 2019 13:47:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:47:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:47:24: #2 number of paired peaks: 41 WARNING @ Mon, 03 Jun 2019 13:47:24: Too few paired peaks (41) 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 13:47:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.10_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/SRX335502/SRX335502.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:47:25: #2 number of paired peaks: 41 WARNING @ Mon, 03 Jun 2019 13:47:25: Too few paired peaks (41) 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 13:47:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.20_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/SRX335502/SRX335502.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335502/SRX335502.20_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。