Job ID = 1295374 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T04:21:42 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 ) 2019-06-03T04:34:18 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 ) 2019-06-03T04:34:18 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 ) 2019-06-03T04:34:18 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 ) 2019-06-03T04:34:18 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 ) 2019-06-03T04:36:36 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 ) 2019-06-03T04:40:23 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 : 56,147,132 reads read : 56,147,132 reads written : 56,147,132 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: 00:14:08 56147132 reads; of these: 56147132 (100.00%) were unpaired; of these: 12208382 (21.74%) aligned 0 times 36778375 (65.50%) aligned exactly 1 time 7160375 (12.75%) aligned >1 times 78.26% overall alignment rate Time searching: 00:14:08 Overall time: 00:14:08 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 20 files... [bam_rmdupse_core] 16582037 / 43938750 = 0.3774 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 14:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.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 14:13:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:13:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.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 14:13:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:13:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.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 14:13:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:13:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:13:15: 1000000 INFO @ Mon, 03 Jun 2019 14:13:16: 1000000 INFO @ Mon, 03 Jun 2019 14:13:17: 1000000 INFO @ Mon, 03 Jun 2019 14:13:24: 2000000 INFO @ Mon, 03 Jun 2019 14:13:26: 2000000 INFO @ Mon, 03 Jun 2019 14:13:28: 2000000 INFO @ Mon, 03 Jun 2019 14:13:33: 3000000 INFO @ Mon, 03 Jun 2019 14:13:36: 3000000 INFO @ Mon, 03 Jun 2019 14:13:38: 3000000 INFO @ Mon, 03 Jun 2019 14:13:42: 4000000 INFO @ Mon, 03 Jun 2019 14:13:46: 4000000 INFO @ Mon, 03 Jun 2019 14:13:48: 4000000 INFO @ Mon, 03 Jun 2019 14:13:51: 5000000 INFO @ Mon, 03 Jun 2019 14:13:55: 5000000 INFO @ Mon, 03 Jun 2019 14:13:59: 5000000 INFO @ Mon, 03 Jun 2019 14:14:00: 6000000 INFO @ Mon, 03 Jun 2019 14:14:06: 6000000 INFO @ Mon, 03 Jun 2019 14:14:08: 7000000 INFO @ Mon, 03 Jun 2019 14:14:10: 6000000 INFO @ Mon, 03 Jun 2019 14:14:16: 7000000 INFO @ Mon, 03 Jun 2019 14:14:18: 8000000 INFO @ Mon, 03 Jun 2019 14:14:20: 7000000 INFO @ Mon, 03 Jun 2019 14:14:26: 8000000 INFO @ Mon, 03 Jun 2019 14:14:26: 9000000 INFO @ Mon, 03 Jun 2019 14:14:30: 8000000 INFO @ Mon, 03 Jun 2019 14:14:35: 10000000 INFO @ Mon, 03 Jun 2019 14:14:35: 9000000 INFO @ Mon, 03 Jun 2019 14:14:40: 9000000 INFO @ Mon, 03 Jun 2019 14:14:44: 11000000 INFO @ Mon, 03 Jun 2019 14:14:45: 10000000 INFO @ Mon, 03 Jun 2019 14:14:50: 10000000 INFO @ Mon, 03 Jun 2019 14:14:52: 12000000 INFO @ Mon, 03 Jun 2019 14:14:55: 11000000 INFO @ Mon, 03 Jun 2019 14:15:00: 11000000 INFO @ Mon, 03 Jun 2019 14:15:01: 13000000 INFO @ Mon, 03 Jun 2019 14:15:05: 12000000 INFO @ Mon, 03 Jun 2019 14:15:10: 14000000 INFO @ Mon, 03 Jun 2019 14:15:10: 12000000 INFO @ Mon, 03 Jun 2019 14:15:14: 13000000 INFO @ Mon, 03 Jun 2019 14:15:18: 15000000 INFO @ Mon, 03 Jun 2019 14:15:21: 13000000 INFO @ Mon, 03 Jun 2019 14:15:24: 14000000 INFO @ Mon, 03 Jun 2019 14:15:27: 16000000 INFO @ Mon, 03 Jun 2019 14:15:31: 14000000 INFO @ Mon, 03 Jun 2019 14:15:33: 15000000 INFO @ Mon, 03 Jun 2019 14:15:35: 17000000 INFO @ Mon, 03 Jun 2019 14:15:41: 15000000 INFO @ Mon, 03 Jun 2019 14:15:43: 16000000 INFO @ Mon, 03 Jun 2019 14:15:44: 18000000 INFO @ Mon, 03 Jun 2019 14:15:51: 16000000 INFO @ Mon, 03 Jun 2019 14:15:53: 17000000 INFO @ Mon, 03 Jun 2019 14:15:53: 19000000 INFO @ Mon, 03 Jun 2019 14:16:02: 17000000 INFO @ Mon, 03 Jun 2019 14:16:02: 20000000 INFO @ Mon, 03 Jun 2019 14:16:03: 18000000 INFO @ Mon, 03 Jun 2019 14:16:11: 21000000 INFO @ Mon, 03 Jun 2019 14:16:12: 18000000 INFO @ Mon, 03 Jun 2019 14:16:12: 19000000 INFO @ Mon, 03 Jun 2019 14:16:20: 22000000 INFO @ Mon, 03 Jun 2019 14:16:22: 20000000 INFO @ Mon, 03 Jun 2019 14:16:22: 19000000 INFO @ Mon, 03 Jun 2019 14:16:28: 23000000 INFO @ Mon, 03 Jun 2019 14:16:32: 21000000 INFO @ Mon, 03 Jun 2019 14:16:32: 20000000 INFO @ Mon, 03 Jun 2019 14:16:38: 24000000 INFO @ Mon, 03 Jun 2019 14:16:41: 22000000 INFO @ Mon, 03 Jun 2019 14:16:42: 21000000 INFO @ Mon, 03 Jun 2019 14:16:48: 25000000 INFO @ Mon, 03 Jun 2019 14:16:51: 23000000 INFO @ Mon, 03 Jun 2019 14:16:52: 22000000 INFO @ Mon, 03 Jun 2019 14:16:57: 26000000 INFO @ Mon, 03 Jun 2019 14:17:01: 24000000 INFO @ Mon, 03 Jun 2019 14:17:02: 23000000 INFO @ Mon, 03 Jun 2019 14:17:06: 27000000 INFO @ Mon, 03 Jun 2019 14:17:10: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 14:17:10: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 14:17:10: #1 total tags in treatment: 27356713 INFO @ Mon, 03 Jun 2019 14:17:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:17:10: #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 14:17:10: #1 tags after filtering in treatment: 27356713 INFO @ Mon, 03 Jun 2019 14:17:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:17:10: #1 finished! INFO @ Mon, 03 Jun 2019 14:17:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:17:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:17:10: 25000000 INFO @ Mon, 03 Jun 2019 14:17:11: 24000000 INFO @ Mon, 03 Jun 2019 14:17:12: #2 number of paired peaks: 3 WARNING @ Mon, 03 Jun 2019 14:17:12: Too few paired peaks (3) 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 14:17:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.10_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/SRX335509/SRX335509.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:17:20: 26000000 INFO @ Mon, 03 Jun 2019 14:17:21: 25000000 INFO @ Mon, 03 Jun 2019 14:17:30: 27000000 INFO @ Mon, 03 Jun 2019 14:17:30: 26000000 INFO @ Mon, 03 Jun 2019 14:17:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 14:17:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 14:17:33: #1 total tags in treatment: 27356713 INFO @ Mon, 03 Jun 2019 14:17:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:17:33: #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 14:17:34: #1 tags after filtering in treatment: 27356713 INFO @ Mon, 03 Jun 2019 14:17:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:17:34: #1 finished! INFO @ Mon, 03 Jun 2019 14:17:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:17:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:17:36: #2 number of paired peaks: 3 WARNING @ Mon, 03 Jun 2019 14:17:36: Too few paired peaks (3) 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 14:17:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.20_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/SRX335509/SRX335509.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:17:39: 27000000 INFO @ Mon, 03 Jun 2019 14:17:43: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 14:17:43: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 14:17:43: #1 total tags in treatment: 27356713 INFO @ Mon, 03 Jun 2019 14:17:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:17:43: #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 14:17:43: #1 tags after filtering in treatment: 27356713 INFO @ Mon, 03 Jun 2019 14:17:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:17:43: #1 finished! INFO @ Mon, 03 Jun 2019 14:17:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:17:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:17:46: #2 number of paired peaks: 3 WARNING @ Mon, 03 Jun 2019 14:17:46: Too few paired peaks (3) 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 14:17:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.05_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/SRX335509/SRX335509.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335509/SRX335509.05_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。