Job ID = 1298726 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:29:54 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 ) 2019-06-03T08:29:54 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 ) 2019-06-03T08:31:39 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 ) 2019-06-03T08:35:06 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 ) 2019-06-03T08:44:29 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 : 40,386,659 reads read : 40,386,659 reads written : 40,386,659 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: 00:18:08 40386659 reads; of these: 40386659 (100.00%) were unpaired; of these: 1079889 (2.67%) aligned 0 times 25818197 (63.93%) aligned exactly 1 time 13488573 (33.40%) aligned >1 times 97.33% overall alignment rate Time searching: 00:18:08 Overall time: 00:18:08 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] 11965880 / 39306770 = 0.3044 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 18:19:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.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 18:19:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:19:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:19:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.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 18:19:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:19:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:19:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.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 18:19:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:19:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:19:40: 1000000 INFO @ Mon, 03 Jun 2019 18:19:41: 1000000 INFO @ Mon, 03 Jun 2019 18:19:42: 1000000 INFO @ Mon, 03 Jun 2019 18:19:48: 2000000 INFO @ Mon, 03 Jun 2019 18:19:49: 2000000 INFO @ Mon, 03 Jun 2019 18:19:51: 2000000 INFO @ Mon, 03 Jun 2019 18:19:55: 3000000 INFO @ Mon, 03 Jun 2019 18:19:57: 3000000 INFO @ Mon, 03 Jun 2019 18:20:00: 3000000 INFO @ Mon, 03 Jun 2019 18:20:03: 4000000 INFO @ Mon, 03 Jun 2019 18:20:05: 4000000 INFO @ Mon, 03 Jun 2019 18:20:09: 4000000 INFO @ Mon, 03 Jun 2019 18:20:11: 5000000 INFO @ Mon, 03 Jun 2019 18:20:13: 5000000 INFO @ Mon, 03 Jun 2019 18:20:18: 5000000 INFO @ Mon, 03 Jun 2019 18:20:19: 6000000 INFO @ Mon, 03 Jun 2019 18:20:21: 6000000 INFO @ Mon, 03 Jun 2019 18:20:26: 7000000 INFO @ Mon, 03 Jun 2019 18:20:27: 6000000 INFO @ Mon, 03 Jun 2019 18:20:29: 7000000 INFO @ Mon, 03 Jun 2019 18:20:35: 8000000 INFO @ Mon, 03 Jun 2019 18:20:37: 7000000 INFO @ Mon, 03 Jun 2019 18:20:37: 8000000 INFO @ Mon, 03 Jun 2019 18:20:42: 9000000 INFO @ Mon, 03 Jun 2019 18:20:46: 8000000 INFO @ Mon, 03 Jun 2019 18:20:46: 9000000 INFO @ Mon, 03 Jun 2019 18:20:50: 10000000 INFO @ Mon, 03 Jun 2019 18:20:54: 10000000 INFO @ Mon, 03 Jun 2019 18:20:56: 9000000 INFO @ Mon, 03 Jun 2019 18:20:58: 11000000 INFO @ Mon, 03 Jun 2019 18:21:02: 11000000 INFO @ Mon, 03 Jun 2019 18:21:06: 12000000 INFO @ Mon, 03 Jun 2019 18:21:06: 10000000 INFO @ Mon, 03 Jun 2019 18:21:10: 12000000 INFO @ Mon, 03 Jun 2019 18:21:13: 13000000 INFO @ Mon, 03 Jun 2019 18:21:16: 11000000 INFO @ Mon, 03 Jun 2019 18:21:18: 13000000 INFO @ Mon, 03 Jun 2019 18:21:21: 14000000 INFO @ Mon, 03 Jun 2019 18:21:25: 12000000 INFO @ Mon, 03 Jun 2019 18:21:26: 14000000 INFO @ Mon, 03 Jun 2019 18:21:29: 15000000 INFO @ Mon, 03 Jun 2019 18:21:34: 15000000 INFO @ Mon, 03 Jun 2019 18:21:35: 13000000 INFO @ Mon, 03 Jun 2019 18:21:36: 16000000 INFO @ Mon, 03 Jun 2019 18:21:42: 16000000 INFO @ Mon, 03 Jun 2019 18:21:44: 17000000 INFO @ Mon, 03 Jun 2019 18:21:44: 14000000 INFO @ Mon, 03 Jun 2019 18:21:50: 17000000 INFO @ Mon, 03 Jun 2019 18:21:52: 18000000 INFO @ Mon, 03 Jun 2019 18:21:54: 15000000 INFO @ Mon, 03 Jun 2019 18:21:59: 18000000 INFO @ Mon, 03 Jun 2019 18:22:00: 19000000 INFO @ Mon, 03 Jun 2019 18:22:03: 16000000 INFO @ Mon, 03 Jun 2019 18:22:07: 19000000 INFO @ Mon, 03 Jun 2019 18:22:07: 20000000 INFO @ Mon, 03 Jun 2019 18:22:13: 17000000 INFO @ Mon, 03 Jun 2019 18:22:15: 20000000 INFO @ Mon, 03 Jun 2019 18:22:15: 21000000 INFO @ Mon, 03 Jun 2019 18:22:22: 18000000 INFO @ Mon, 03 Jun 2019 18:22:23: 21000000 INFO @ Mon, 03 Jun 2019 18:22:23: 22000000 INFO @ Mon, 03 Jun 2019 18:22:31: 23000000 INFO @ Mon, 03 Jun 2019 18:22:31: 22000000 INFO @ Mon, 03 Jun 2019 18:22:32: 19000000 INFO @ Mon, 03 Jun 2019 18:22:38: 24000000 INFO @ Mon, 03 Jun 2019 18:22:39: 23000000 INFO @ Mon, 03 Jun 2019 18:22:41: 20000000 INFO @ Mon, 03 Jun 2019 18:22:46: 25000000 INFO @ Mon, 03 Jun 2019 18:22:47: 24000000 INFO @ Mon, 03 Jun 2019 18:22:52: 21000000 INFO @ Mon, 03 Jun 2019 18:22:54: 26000000 INFO @ Mon, 03 Jun 2019 18:22:55: 25000000 INFO @ Mon, 03 Jun 2019 18:23:01: 22000000 INFO @ Mon, 03 Jun 2019 18:23:02: 27000000 INFO @ Mon, 03 Jun 2019 18:23:04: 26000000 INFO @ Mon, 03 Jun 2019 18:23:05: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:23:05: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:23:05: #1 total tags in treatment: 27340890 INFO @ Mon, 03 Jun 2019 18:23:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:23:05: #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 18:23:05: #1 tags after filtering in treatment: 27340890 INFO @ Mon, 03 Jun 2019 18:23:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:23:05: #1 finished! INFO @ Mon, 03 Jun 2019 18:23:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:23:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:23:08: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 18:23:08: Too few paired peaks (0) 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 18:23:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.20_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/SRX467046/SRX467046.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:23:10: 23000000 INFO @ Mon, 03 Jun 2019 18:23:12: 27000000 INFO @ Mon, 03 Jun 2019 18:23:15: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:23:15: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:23:15: #1 total tags in treatment: 27340890 INFO @ Mon, 03 Jun 2019 18:23:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:23:15: #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 18:23:16: #1 tags after filtering in treatment: 27340890 INFO @ Mon, 03 Jun 2019 18:23:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:23:16: #1 finished! INFO @ Mon, 03 Jun 2019 18:23:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:23:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:23:18: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 18:23:18: Too few paired peaks (0) 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 18:23:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.05_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/SRX467046/SRX467046.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:23:20: 24000000 INFO @ Mon, 03 Jun 2019 18:23:30: 25000000 INFO @ Mon, 03 Jun 2019 18:23:39: 26000000 INFO @ Mon, 03 Jun 2019 18:23:48: 27000000 INFO @ Mon, 03 Jun 2019 18:23:52: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:23:52: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:23:52: #1 total tags in treatment: 27340890 INFO @ Mon, 03 Jun 2019 18:23:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:23:52: #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 18:23:52: #1 tags after filtering in treatment: 27340890 INFO @ Mon, 03 Jun 2019 18:23:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:23:52: #1 finished! INFO @ Mon, 03 Jun 2019 18:23:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:23:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:23:55: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 18:23:55: Too few paired peaks (0) 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 18:23:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.10_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/SRX467046/SRX467046.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467046/SRX467046.10_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。