Job ID = 2641103 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T12:27:00 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 ) 2019-08-24T12:27:00 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 : 68,331,777 reads read : 68,331,777 reads written : 68,331,777 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: 00:12:12 68331777 reads; of these: 68331777 (100.00%) were unpaired; of these: 1438540 (2.11%) aligned 0 times 55439393 (81.13%) aligned exactly 1 time 11453844 (16.76%) aligned >1 times 97.89% overall alignment rate Time searching: 00:12:12 Overall time: 00:12:12 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 28 files... [bam_rmdupse_core] 46425289 / 66893237 = 0.6940 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:09:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.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 @ Sat, 24 Aug 2019 22:09:22: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:09:22: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:09:30: 1000000 INFO @ Sat, 24 Aug 2019 22:09:37: 2000000 INFO @ Sat, 24 Aug 2019 22:09:44: 3000000 INFO @ Sat, 24 Aug 2019 22:09:51: 4000000 INFO @ Sat, 24 Aug 2019 22:09:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.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 @ Sat, 24 Aug 2019 22:09:51: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:09:51: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:10:00: 5000000 INFO @ Sat, 24 Aug 2019 22:10:01: 1000000 INFO @ Sat, 24 Aug 2019 22:10:09: 6000000 INFO @ Sat, 24 Aug 2019 22:10:09: 2000000 INFO @ Sat, 24 Aug 2019 22:10:17: 7000000 INFO @ Sat, 24 Aug 2019 22:10:18: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:10:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.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 @ Sat, 24 Aug 2019 22:10:22: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:10:22: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:10:25: 8000000 INFO @ Sat, 24 Aug 2019 22:10:26: 4000000 INFO @ Sat, 24 Aug 2019 22:10:32: 9000000 INFO @ Sat, 24 Aug 2019 22:10:33: 1000000 INFO @ Sat, 24 Aug 2019 22:10:35: 5000000 INFO @ Sat, 24 Aug 2019 22:10:39: 10000000 INFO @ Sat, 24 Aug 2019 22:10:44: 6000000 INFO @ Sat, 24 Aug 2019 22:10:45: 2000000 INFO @ Sat, 24 Aug 2019 22:10:47: 11000000 INFO @ Sat, 24 Aug 2019 22:10:53: 7000000 INFO @ Sat, 24 Aug 2019 22:10:54: 12000000 INFO @ Sat, 24 Aug 2019 22:10:56: 3000000 INFO @ Sat, 24 Aug 2019 22:11:01: 13000000 INFO @ Sat, 24 Aug 2019 22:11:02: 8000000 INFO @ Sat, 24 Aug 2019 22:11:08: 4000000 INFO @ Sat, 24 Aug 2019 22:11:09: 14000000 INFO @ Sat, 24 Aug 2019 22:11:11: 9000000 INFO @ Sat, 24 Aug 2019 22:11:16: 15000000 INFO @ Sat, 24 Aug 2019 22:11:20: 10000000 INFO @ Sat, 24 Aug 2019 22:11:21: 5000000 INFO @ Sat, 24 Aug 2019 22:11:24: 16000000 INFO @ Sat, 24 Aug 2019 22:11:29: 11000000 INFO @ Sat, 24 Aug 2019 22:11:31: 17000000 INFO @ Sat, 24 Aug 2019 22:11:32: 6000000 INFO @ Sat, 24 Aug 2019 22:11:37: 12000000 INFO @ Sat, 24 Aug 2019 22:11:39: 18000000 INFO @ Sat, 24 Aug 2019 22:11:42: 7000000 INFO @ Sat, 24 Aug 2019 22:11:46: 13000000 INFO @ Sat, 24 Aug 2019 22:11:46: 19000000 INFO @ Sat, 24 Aug 2019 22:11:52: 8000000 INFO @ Sat, 24 Aug 2019 22:11:53: 20000000 INFO @ Sat, 24 Aug 2019 22:11:54: 14000000 INFO @ Sat, 24 Aug 2019 22:11:57: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:11:57: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:11:57: #1 total tags in treatment: 20467948 INFO @ Sat, 24 Aug 2019 22:11:57: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:11:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:11:57: #1 tags after filtering in treatment: 20467948 INFO @ Sat, 24 Aug 2019 22:11:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 22:11:57: #1 finished! INFO @ Sat, 24 Aug 2019 22:11:57: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:11:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:11:59: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:11:59: 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 @ Sat, 24 Aug 2019 22:11:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.05_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/sacCer3/SRX5431204/SRX5431204.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:12:02: 9000000 INFO @ Sat, 24 Aug 2019 22:12:02: 15000000 INFO @ Sat, 24 Aug 2019 22:12:11: 16000000 INFO @ Sat, 24 Aug 2019 22:12:12: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:12:19: 17000000 INFO @ Sat, 24 Aug 2019 22:12:22: 11000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:12:27: 18000000 INFO @ Sat, 24 Aug 2019 22:12:32: 12000000 INFO @ Sat, 24 Aug 2019 22:12:35: 19000000 INFO @ Sat, 24 Aug 2019 22:12:42: 13000000 INFO @ Sat, 24 Aug 2019 22:12:43: 20000000 INFO @ Sat, 24 Aug 2019 22:12:47: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:12:47: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:12:47: #1 total tags in treatment: 20467948 INFO @ Sat, 24 Aug 2019 22:12:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:12:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:12:48: #1 tags after filtering in treatment: 20467948 INFO @ Sat, 24 Aug 2019 22:12:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 22:12:48: #1 finished! INFO @ Sat, 24 Aug 2019 22:12:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:12:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:12:49: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:12:49: 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 @ Sat, 24 Aug 2019 22:12:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.10_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/SRX5431204/SRX5431204.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:12:51: 14000000 INFO @ Sat, 24 Aug 2019 22:13:01: 15000000 INFO @ Sat, 24 Aug 2019 22:13:10: 16000000 INFO @ Sat, 24 Aug 2019 22:13:20: 17000000 INFO @ Sat, 24 Aug 2019 22:13:29: 18000000 INFO @ Sat, 24 Aug 2019 22:13:39: 19000000 INFO @ Sat, 24 Aug 2019 22:13:49: 20000000 INFO @ Sat, 24 Aug 2019 22:13:53: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:13:53: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:13:53: #1 total tags in treatment: 20467948 INFO @ Sat, 24 Aug 2019 22:13:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:13:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:13:53: #1 tags after filtering in treatment: 20467948 INFO @ Sat, 24 Aug 2019 22:13:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 22:13:53: #1 finished! INFO @ Sat, 24 Aug 2019 22:13:53: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:13:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:13:55: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:13:55: 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 @ Sat, 24 Aug 2019 22:13:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.20_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/SRX5431204/SRX5431204.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431204/SRX5431204.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling