Job ID = 1295393 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T04:27:14 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 ) 2019-06-03T04:27:14 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 ) 2019-06-03T04:27:14 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 ) 2019-06-03T04:27:14 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 : 22,615,922 reads read : 22,615,922 reads written : 22,615,922 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: 00:06:22 22615922 reads; of these: 22615922 (100.00%) were unpaired; of these: 2060591 (9.11%) aligned 0 times 17410264 (76.98%) aligned exactly 1 time 3145067 (13.91%) aligned >1 times 90.89% overall alignment rate Time searching: 00:06:22 Overall time: 00:06:22 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] 4553048 / 20555331 = 0.2215 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 13:48:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.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 13:48:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:48:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:49:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.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 13:49:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:49:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:49:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.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 13:49:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:49:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:49:14: 1000000 INFO @ Mon, 03 Jun 2019 13:49:16: 1000000 INFO @ Mon, 03 Jun 2019 13:49:16: 1000000 INFO @ Mon, 03 Jun 2019 13:49:28: 2000000 INFO @ Mon, 03 Jun 2019 13:49:32: 2000000 INFO @ Mon, 03 Jun 2019 13:49:32: 2000000 INFO @ Mon, 03 Jun 2019 13:49:42: 3000000 INFO @ Mon, 03 Jun 2019 13:49:48: 3000000 INFO @ Mon, 03 Jun 2019 13:49:48: 3000000 INFO @ Mon, 03 Jun 2019 13:49:56: 4000000 INFO @ Mon, 03 Jun 2019 13:50:04: 4000000 INFO @ Mon, 03 Jun 2019 13:50:04: 4000000 INFO @ Mon, 03 Jun 2019 13:50:10: 5000000 INFO @ Mon, 03 Jun 2019 13:50:20: 5000000 INFO @ Mon, 03 Jun 2019 13:50:20: 5000000 INFO @ Mon, 03 Jun 2019 13:50:24: 6000000 INFO @ Mon, 03 Jun 2019 13:50:36: 6000000 INFO @ Mon, 03 Jun 2019 13:50:36: 6000000 INFO @ Mon, 03 Jun 2019 13:50:38: 7000000 INFO @ Mon, 03 Jun 2019 13:50:52: 8000000 INFO @ Mon, 03 Jun 2019 13:50:52: 7000000 INFO @ Mon, 03 Jun 2019 13:50:52: 7000000 INFO @ Mon, 03 Jun 2019 13:51:05: 9000000 INFO @ Mon, 03 Jun 2019 13:51:07: 8000000 INFO @ Mon, 03 Jun 2019 13:51:08: 8000000 INFO @ Mon, 03 Jun 2019 13:51:19: 10000000 INFO @ Mon, 03 Jun 2019 13:51:23: 9000000 INFO @ Mon, 03 Jun 2019 13:51:25: 9000000 INFO @ Mon, 03 Jun 2019 13:51:34: 11000000 INFO @ Mon, 03 Jun 2019 13:51:39: 10000000 INFO @ Mon, 03 Jun 2019 13:51:43: 10000000 INFO @ Mon, 03 Jun 2019 13:51:48: 12000000 INFO @ Mon, 03 Jun 2019 13:51:55: 11000000 INFO @ Mon, 03 Jun 2019 13:52:00: 11000000 INFO @ Mon, 03 Jun 2019 13:52:02: 13000000 INFO @ Mon, 03 Jun 2019 13:52:11: 12000000 INFO @ Mon, 03 Jun 2019 13:52:16: 14000000 INFO @ Mon, 03 Jun 2019 13:52:17: 12000000 INFO @ Mon, 03 Jun 2019 13:52:27: 13000000 INFO @ Mon, 03 Jun 2019 13:52:30: 15000000 INFO @ Mon, 03 Jun 2019 13:52:34: 13000000 INFO @ Mon, 03 Jun 2019 13:52:43: 14000000 INFO @ Mon, 03 Jun 2019 13:52:45: 16000000 INFO @ Mon, 03 Jun 2019 13:52:45: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:52:45: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:52:45: #1 total tags in treatment: 16002283 INFO @ Mon, 03 Jun 2019 13:52:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:52:45: #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 13:52:46: #1 tags after filtering in treatment: 16002283 INFO @ Mon, 03 Jun 2019 13:52:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:52:46: #1 finished! INFO @ Mon, 03 Jun 2019 13:52:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:52:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:52:49: #2 number of paired peaks: 49 WARNING @ Mon, 03 Jun 2019 13:52:49: Too few paired peaks (49) 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 13:52:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.20_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/SRX335518/SRX335518.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:52:51: 14000000 INFO @ Mon, 03 Jun 2019 13:52:59: 15000000 INFO @ Mon, 03 Jun 2019 13:53:08: 15000000 INFO @ Mon, 03 Jun 2019 13:53:14: 16000000 INFO @ Mon, 03 Jun 2019 13:53:15: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:53:15: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:53:15: #1 total tags in treatment: 16002283 INFO @ Mon, 03 Jun 2019 13:53:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:53:15: #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 13:53:15: #1 tags after filtering in treatment: 16002283 INFO @ Mon, 03 Jun 2019 13:53:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:53:15: #1 finished! INFO @ Mon, 03 Jun 2019 13:53:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:53:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:53:18: #2 number of paired peaks: 49 WARNING @ Mon, 03 Jun 2019 13:53:18: Too few paired peaks (49) 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 13:53:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.05_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/SRX335518/SRX335518.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:53:25: 16000000 INFO @ Mon, 03 Jun 2019 13:53:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:53:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:53:26: #1 total tags in treatment: 16002283 INFO @ Mon, 03 Jun 2019 13:53:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:53:26: #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 13:53:26: #1 tags after filtering in treatment: 16002283 INFO @ Mon, 03 Jun 2019 13:53:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:53:26: #1 finished! INFO @ Mon, 03 Jun 2019 13:53:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:53:29: #2 number of paired peaks: 49 WARNING @ Mon, 03 Jun 2019 13:53:29: Too few paired peaks (49) 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 13:53:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.10_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/SRX335518/SRX335518.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335518/SRX335518.10_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。