Job ID = 2590933 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T14:56:44 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 : 30,324,004 reads read : 30,324,004 reads written : 30,324,004 rm: cannot remove ‘[DSE]RR*’: 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: 00:13:15 30324004 reads; of these: 30324004 (100.00%) were unpaired; of these: 1799988 (5.94%) aligned 0 times 19478004 (64.23%) aligned exactly 1 time 9046012 (29.83%) aligned >1 times 94.06% overall alignment rate Time searching: 00:13:15 Overall time: 00:13:15 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] 3408706 / 28524016 = 0.1195 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 @ Tue, 13 Aug 2019 00:29:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.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 @ Tue, 13 Aug 2019 00:29:23: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:29:23: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:29:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.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 @ Tue, 13 Aug 2019 00:29:24: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:29:24: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:29:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.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 @ Tue, 13 Aug 2019 00:29:25: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:29:25: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:29:32: 1000000 INFO @ Tue, 13 Aug 2019 00:29:34: 1000000 INFO @ Tue, 13 Aug 2019 00:29:34: 1000000 INFO @ Tue, 13 Aug 2019 00:29:41: 2000000 INFO @ Tue, 13 Aug 2019 00:29:43: 2000000 INFO @ Tue, 13 Aug 2019 00:29:44: 2000000 INFO @ Tue, 13 Aug 2019 00:29:50: 3000000 INFO @ Tue, 13 Aug 2019 00:29:53: 3000000 INFO @ Tue, 13 Aug 2019 00:29:54: 3000000 INFO @ Tue, 13 Aug 2019 00:29:59: 4000000 INFO @ Tue, 13 Aug 2019 00:30:02: 4000000 INFO @ Tue, 13 Aug 2019 00:30:04: 4000000 INFO @ Tue, 13 Aug 2019 00:30:09: 5000000 INFO @ Tue, 13 Aug 2019 00:30:11: 5000000 INFO @ Tue, 13 Aug 2019 00:30:14: 5000000 INFO @ Tue, 13 Aug 2019 00:30:18: 6000000 INFO @ Tue, 13 Aug 2019 00:30:20: 6000000 INFO @ Tue, 13 Aug 2019 00:30:24: 6000000 INFO @ Tue, 13 Aug 2019 00:30:26: 7000000 INFO @ Tue, 13 Aug 2019 00:30:27: 7000000 INFO @ Tue, 13 Aug 2019 00:30:34: 8000000 INFO @ Tue, 13 Aug 2019 00:30:34: 7000000 INFO @ Tue, 13 Aug 2019 00:30:35: 8000000 INFO @ Tue, 13 Aug 2019 00:30:41: 9000000 INFO @ Tue, 13 Aug 2019 00:30:42: 9000000 INFO @ Tue, 13 Aug 2019 00:30:44: 8000000 INFO @ Tue, 13 Aug 2019 00:30:49: 10000000 INFO @ Tue, 13 Aug 2019 00:30:50: 10000000 INFO @ Tue, 13 Aug 2019 00:30:54: 9000000 INFO @ Tue, 13 Aug 2019 00:30:56: 11000000 INFO @ Tue, 13 Aug 2019 00:30:57: 11000000 INFO @ Tue, 13 Aug 2019 00:31:04: 12000000 INFO @ Tue, 13 Aug 2019 00:31:04: 10000000 INFO @ Tue, 13 Aug 2019 00:31:05: 12000000 INFO @ Tue, 13 Aug 2019 00:31:12: 13000000 INFO @ Tue, 13 Aug 2019 00:31:12: 13000000 INFO @ Tue, 13 Aug 2019 00:31:14: 11000000 INFO @ Tue, 13 Aug 2019 00:31:19: 14000000 INFO @ Tue, 13 Aug 2019 00:31:20: 14000000 INFO @ Tue, 13 Aug 2019 00:31:24: 12000000 INFO @ Tue, 13 Aug 2019 00:31:27: 15000000 INFO @ Tue, 13 Aug 2019 00:31:28: 15000000 INFO @ Tue, 13 Aug 2019 00:31:34: 13000000 INFO @ Tue, 13 Aug 2019 00:31:34: 16000000 INFO @ Tue, 13 Aug 2019 00:31:35: 16000000 INFO @ Tue, 13 Aug 2019 00:31:42: 17000000 INFO @ Tue, 13 Aug 2019 00:31:43: 17000000 INFO @ Tue, 13 Aug 2019 00:31:44: 14000000 INFO @ Tue, 13 Aug 2019 00:31:49: 18000000 INFO @ Tue, 13 Aug 2019 00:31:50: 18000000 INFO @ Tue, 13 Aug 2019 00:31:53: 15000000 INFO @ Tue, 13 Aug 2019 00:31:57: 19000000 INFO @ Tue, 13 Aug 2019 00:31:58: 19000000 INFO @ Tue, 13 Aug 2019 00:32:03: 16000000 INFO @ Tue, 13 Aug 2019 00:32:04: 20000000 INFO @ Tue, 13 Aug 2019 00:32:05: 20000000 INFO @ Tue, 13 Aug 2019 00:32:12: 21000000 INFO @ Tue, 13 Aug 2019 00:32:13: 21000000 INFO @ Tue, 13 Aug 2019 00:32:13: 17000000 INFO @ Tue, 13 Aug 2019 00:32:19: 22000000 INFO @ Tue, 13 Aug 2019 00:32:20: 22000000 INFO @ Tue, 13 Aug 2019 00:32:23: 18000000 INFO @ Tue, 13 Aug 2019 00:32:27: 23000000 INFO @ Tue, 13 Aug 2019 00:32:28: 23000000 INFO @ Tue, 13 Aug 2019 00:32:32: 19000000 INFO @ Tue, 13 Aug 2019 00:32:34: 24000000 INFO @ Tue, 13 Aug 2019 00:32:35: 24000000 INFO @ Tue, 13 Aug 2019 00:32:42: 25000000 INFO @ Tue, 13 Aug 2019 00:32:42: 20000000 INFO @ Tue, 13 Aug 2019 00:32:43: 25000000 INFO @ Tue, 13 Aug 2019 00:32:43: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:32:43: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:32:43: #1 total tags in treatment: 25115310 INFO @ Tue, 13 Aug 2019 00:32:43: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:32:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:32:43: #1 tags after filtering in treatment: 25115310 INFO @ Tue, 13 Aug 2019 00:32:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:32:43: #1 finished! INFO @ Tue, 13 Aug 2019 00:32:43: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:32:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:32:44: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:32:44: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:32:44: #1 total tags in treatment: 25115310 INFO @ Tue, 13 Aug 2019 00:32:44: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:32:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:32:44: #1 tags after filtering in treatment: 25115310 INFO @ Tue, 13 Aug 2019 00:32:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:32:44: #1 finished! INFO @ Tue, 13 Aug 2019 00:32:44: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:32:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:32:45: #2 number of paired peaks: 89 WARNING @ Tue, 13 Aug 2019 00:32:45: Too few paired peaks (89) 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 @ Tue, 13 Aug 2019 00:32:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.05_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/SRX5431045/SRX5431045.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:32:46: #2 number of paired peaks: 89 WARNING @ Tue, 13 Aug 2019 00:32:46: Too few paired peaks (89) 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 @ Tue, 13 Aug 2019 00:32:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.20_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/SRX5431045/SRX5431045.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:32:52: 21000000 INFO @ Tue, 13 Aug 2019 00:33:01: 22000000 INFO @ Tue, 13 Aug 2019 00:33:10: 23000000 INFO @ Tue, 13 Aug 2019 00:33:18: 24000000 INFO @ Tue, 13 Aug 2019 00:33:26: 25000000 INFO @ Tue, 13 Aug 2019 00:33:27: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:33:27: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:33:27: #1 total tags in treatment: 25115310 INFO @ Tue, 13 Aug 2019 00:33:27: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:33:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:33:28: #1 tags after filtering in treatment: 25115310 INFO @ Tue, 13 Aug 2019 00:33:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:33:28: #1 finished! INFO @ Tue, 13 Aug 2019 00:33:28: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:33:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:33:30: #2 number of paired peaks: 89 WARNING @ Tue, 13 Aug 2019 00:33:30: Too few paired peaks (89) 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 @ Tue, 13 Aug 2019 00:33:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.10_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/SRX5431045/SRX5431045.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5431045/SRX5431045.10_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。