Job ID = 2641086 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T12:32:37 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 ) 2019-08-24T12:32:37 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 ) 2019-08-24T12:32:37 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 : 74,257,243 reads read : 74,257,243 reads written : 74,257,243 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: 00:11:44 74257243 reads; of these: 74257243 (100.00%) were unpaired; of these: 20161867 (27.15%) aligned 0 times 48458655 (65.26%) aligned exactly 1 time 5636721 (7.59%) aligned >1 times 72.85% overall alignment rate Time searching: 00:11:44 Overall time: 00:11:44 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 24 files... [bam_rmdupse_core] 46013322 / 54095376 = 0.8506 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:02:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.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 22:02:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:02:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:02:23: 1000000 INFO @ Sat, 24 Aug 2019 22:02:30: 2000000 INFO @ Sat, 24 Aug 2019 22:02:37: 3000000 INFO @ Sat, 24 Aug 2019 22:02:44: 4000000 INFO @ Sat, 24 Aug 2019 22:02:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.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 22:02:44: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:02:44: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:02:51: 5000000 INFO @ Sat, 24 Aug 2019 22:02:53: 1000000 INFO @ Sat, 24 Aug 2019 22:02:57: 6000000 INFO @ Sat, 24 Aug 2019 22:03:01: 2000000 INFO @ Sat, 24 Aug 2019 22:03:04: 7000000 INFO @ Sat, 24 Aug 2019 22:03:09: 3000000 INFO @ Sat, 24 Aug 2019 22:03:11: 8000000 INFO @ Sat, 24 Aug 2019 22:03:12: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:03:12: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:03:12: #1 total tags in treatment: 8082054 INFO @ Sat, 24 Aug 2019 22:03:12: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:03:12: #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 22:03:12: #1 tags after filtering in treatment: 8082054 INFO @ Sat, 24 Aug 2019 22:03:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 22:03:12: #1 finished! INFO @ Sat, 24 Aug 2019 22:03:12: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:03:12: #2 looking for paired plus/minus strand peaks... BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:03:12: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:03:12: 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 22:03:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.05_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/SRX5431189/SRX5431189.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:03:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.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 22:03:14: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:03:14: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:03:17: 4000000 INFO @ Sat, 24 Aug 2019 22:03:23: 1000000 INFO @ Sat, 24 Aug 2019 22:03:24: 5000000 INFO @ Sat, 24 Aug 2019 22:03:31: 2000000 INFO @ Sat, 24 Aug 2019 22:03:32: 6000000 INFO @ Sat, 24 Aug 2019 22:03:40: 7000000 INFO @ Sat, 24 Aug 2019 22:03:40: 3000000 INFO @ Sat, 24 Aug 2019 22:03:47: 8000000 INFO @ Sat, 24 Aug 2019 22:03:48: 4000000 INFO @ Sat, 24 Aug 2019 22:03:48: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:03:48: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:03:48: #1 total tags in treatment: 8082054 INFO @ Sat, 24 Aug 2019 22:03:48: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:03:48: #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 22:03:48: #1 tags after filtering in treatment: 8082054 INFO @ Sat, 24 Aug 2019 22:03:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 22:03:48: #1 finished! INFO @ Sat, 24 Aug 2019 22:03:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:03:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:03:49: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:03:49: 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 22:03:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.10_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/SRX5431189/SRX5431189.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:03:56: 5000000 INFO @ Sat, 24 Aug 2019 22:04:03: 6000000 INFO @ Sat, 24 Aug 2019 22:04:11: 7000000 INFO @ Sat, 24 Aug 2019 22:04:19: 8000000 INFO @ Sat, 24 Aug 2019 22:04:20: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:04:20: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:04:20: #1 total tags in treatment: 8082054 INFO @ Sat, 24 Aug 2019 22:04:20: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:04:20: #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 22:04:20: #1 tags after filtering in treatment: 8082054 INFO @ Sat, 24 Aug 2019 22:04:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 22:04:20: #1 finished! INFO @ Sat, 24 Aug 2019 22:04:20: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:04:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:04:20: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:04:20: 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 22:04:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.20_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/sacCer3/SRX5431189/SRX5431189.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431189/SRX5431189.20_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。