Job ID = 4289223 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T04:59:27 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 : 78,301,658 reads read : 156,603,316 reads written : 78,301,658 reads 0-length : 78,301,658 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: 00:12:27 78301658 reads; of these: 78301658 (100.00%) were unpaired; of these: 6896074 (8.81%) aligned 0 times 48320221 (61.71%) aligned exactly 1 time 23085363 (29.48%) aligned >1 times 91.19% overall alignment rate Time searching: 00:12:27 Overall time: 00:12:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 32 files... [bam_rmdupse_core] 54652485 / 71405584 = 0.7654 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:39:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 10 Dec 2019 14:39:15: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:39:15: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:39:22: 1000000 INFO @ Tue, 10 Dec 2019 14:39:29: 2000000 INFO @ Tue, 10 Dec 2019 14:39:36: 3000000 INFO @ Tue, 10 Dec 2019 14:39:43: 4000000 INFO @ Tue, 10 Dec 2019 14:39:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 10 Dec 2019 14:39:45: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:39:45: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:39:50: 5000000 INFO @ Tue, 10 Dec 2019 14:39:53: 1000000 INFO @ Tue, 10 Dec 2019 14:39:56: 6000000 INFO @ Tue, 10 Dec 2019 14:39:59: 2000000 INFO @ Tue, 10 Dec 2019 14:40:03: 7000000 INFO @ Tue, 10 Dec 2019 14:40:06: 3000000 INFO @ Tue, 10 Dec 2019 14:40:10: 8000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:40:14: 4000000 INFO @ Tue, 10 Dec 2019 14:40:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 10 Dec 2019 14:40:15: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:40:15: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:40:18: 9000000 INFO @ Tue, 10 Dec 2019 14:40:21: 5000000 INFO @ Tue, 10 Dec 2019 14:40:24: 1000000 INFO @ Tue, 10 Dec 2019 14:40:25: 10000000 INFO @ Tue, 10 Dec 2019 14:40:28: 6000000 INFO @ Tue, 10 Dec 2019 14:40:32: 2000000 INFO @ Tue, 10 Dec 2019 14:40:33: 11000000 INFO @ Tue, 10 Dec 2019 14:40:35: 7000000 INFO @ Tue, 10 Dec 2019 14:40:39: 3000000 INFO @ Tue, 10 Dec 2019 14:40:41: 12000000 INFO @ Tue, 10 Dec 2019 14:40:42: 8000000 INFO @ Tue, 10 Dec 2019 14:40:47: 4000000 INFO @ Tue, 10 Dec 2019 14:40:48: 13000000 INFO @ Tue, 10 Dec 2019 14:40:49: 9000000 INFO @ Tue, 10 Dec 2019 14:40:55: 5000000 INFO @ Tue, 10 Dec 2019 14:40:56: 14000000 INFO @ Tue, 10 Dec 2019 14:40:57: 10000000 INFO @ Tue, 10 Dec 2019 14:41:03: 6000000 INFO @ Tue, 10 Dec 2019 14:41:03: 15000000 INFO @ Tue, 10 Dec 2019 14:41:04: 11000000 INFO @ Tue, 10 Dec 2019 14:41:11: 12000000 INFO @ Tue, 10 Dec 2019 14:41:11: 16000000 INFO @ Tue, 10 Dec 2019 14:41:11: 7000000 INFO @ Tue, 10 Dec 2019 14:41:16: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:41:16: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:41:16: #1 total tags in treatment: 16753099 INFO @ Tue, 10 Dec 2019 14:41:16: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:41:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:41:17: #1 tags after filtering in treatment: 16753099 INFO @ Tue, 10 Dec 2019 14:41:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:41:17: #1 finished! INFO @ Tue, 10 Dec 2019 14:41:17: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:41:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:41:18: 13000000 INFO @ Tue, 10 Dec 2019 14:41:18: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:41:18: 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 @ Tue, 10 Dec 2019 14:41:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.05_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/sacCer3/SRX6635425/SRX6635425.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:41:18: 8000000 INFO @ Tue, 10 Dec 2019 14:41:24: 14000000 INFO @ Tue, 10 Dec 2019 14:41:25: 9000000 INFO @ Tue, 10 Dec 2019 14:41:31: 15000000 INFO @ Tue, 10 Dec 2019 14:41:32: 10000000 INFO @ Tue, 10 Dec 2019 14:41:38: 16000000 INFO @ Tue, 10 Dec 2019 14:41:39: 11000000 INFO @ Tue, 10 Dec 2019 14:41:43: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:41:43: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:41:43: #1 total tags in treatment: 16753099 INFO @ Tue, 10 Dec 2019 14:41:43: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:41:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:41:43: #1 tags after filtering in treatment: 16753099 INFO @ Tue, 10 Dec 2019 14:41:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:41:43: #1 finished! INFO @ Tue, 10 Dec 2019 14:41:43: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:41:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:41:44: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:41:44: 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 @ Tue, 10 Dec 2019 14:41:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.10_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/sacCer3/SRX6635425/SRX6635425.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:41:46: 12000000 INFO @ Tue, 10 Dec 2019 14:41:52: 13000000 INFO @ Tue, 10 Dec 2019 14:41:59: 14000000 INFO @ Tue, 10 Dec 2019 14:42:06: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:42:12: 16000000 INFO @ Tue, 10 Dec 2019 14:42:17: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:42:17: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:42:17: #1 total tags in treatment: 16753099 INFO @ Tue, 10 Dec 2019 14:42:17: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:42:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:42:18: #1 tags after filtering in treatment: 16753099 INFO @ Tue, 10 Dec 2019 14:42:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:42:18: #1 finished! INFO @ Tue, 10 Dec 2019 14:42:18: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:42:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:42:19: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:42:19: 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 @ Tue, 10 Dec 2019 14:42:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.20_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/sacCer3/SRX6635425/SRX6635425.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635425/SRX6635425.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。