Job ID = 2641054 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T12:03:50 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 ) 2019-08-24T12:05:21 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 ) 2019-08-24T12:05:21 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 : 21,708,266 reads read : 21,708,266 reads written : 21,708,266 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: 00:07:17 21708266 reads; of these: 21708266 (100.00%) were unpaired; of these: 313355 (1.44%) aligned 0 times 19269986 (88.77%) aligned exactly 1 time 2124925 (9.79%) aligned >1 times 98.56% overall alignment rate Time searching: 00:07:17 Overall time: 00:07:17 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 12 files... [bam_rmdupse_core] 11796141 / 21394911 = 0.5514 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:29:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.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 21:29:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:29:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:29:25: 1000000 INFO @ Sat, 24 Aug 2019 21:29:35: 2000000 INFO @ Sat, 24 Aug 2019 21:29:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.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 21:29:44: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:29:44: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:29:46: 3000000 INFO @ Sat, 24 Aug 2019 21:29:58: 1000000 INFO @ Sat, 24 Aug 2019 21:29:58: 4000000 INFO @ Sat, 24 Aug 2019 21:30:08: 2000000 INFO @ Sat, 24 Aug 2019 21:30:11: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:30:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.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 21:30:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:30:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:30:18: 3000000 INFO @ Sat, 24 Aug 2019 21:30:22: 6000000 INFO @ Sat, 24 Aug 2019 21:30:26: 1000000 INFO @ Sat, 24 Aug 2019 21:30:28: 4000000 INFO @ Sat, 24 Aug 2019 21:30:33: 7000000 INFO @ Sat, 24 Aug 2019 21:30:39: 2000000 INFO @ Sat, 24 Aug 2019 21:30:40: 5000000 INFO @ Sat, 24 Aug 2019 21:30:45: 8000000 INFO @ Sat, 24 Aug 2019 21:30:52: 6000000 INFO @ Sat, 24 Aug 2019 21:30:52: 3000000 INFO @ Sat, 24 Aug 2019 21:30:56: 9000000 INFO @ Sat, 24 Aug 2019 21:31:03: #1 tag size is determined as 100 bps INFO @ Sat, 24 Aug 2019 21:31:03: #1 tag size = 100 INFO @ Sat, 24 Aug 2019 21:31:03: #1 total tags in treatment: 9598770 INFO @ Sat, 24 Aug 2019 21:31:03: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:31:03: #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 21:31:03: #1 tags after filtering in treatment: 9598770 INFO @ Sat, 24 Aug 2019 21:31:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:31:03: #1 finished! INFO @ Sat, 24 Aug 2019 21:31:03: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:31:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:31:04: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:31:04: 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 21:31:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.05_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/SRX5257249/SRX5257249.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:31:04: 7000000 INFO @ Sat, 24 Aug 2019 21:31:05: 4000000 INFO @ Sat, 24 Aug 2019 21:31:17: 8000000 INFO @ Sat, 24 Aug 2019 21:31:17: 5000000 INFO @ Sat, 24 Aug 2019 21:31:29: 6000000 INFO @ Sat, 24 Aug 2019 21:31:30: 9000000 INFO @ Sat, 24 Aug 2019 21:31:38: #1 tag size is determined as 100 bps INFO @ Sat, 24 Aug 2019 21:31:38: #1 tag size = 100 INFO @ Sat, 24 Aug 2019 21:31:38: #1 total tags in treatment: 9598770 INFO @ Sat, 24 Aug 2019 21:31:38: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:31:38: #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 21:31:38: #1 tags after filtering in treatment: 9598770 INFO @ Sat, 24 Aug 2019 21:31:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:31:38: #1 finished! INFO @ Sat, 24 Aug 2019 21:31:38: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:31:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:31:39: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:31:39: 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 21:31:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.10_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/SRX5257249/SRX5257249.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:31:41: 7000000 INFO @ Sat, 24 Aug 2019 21:31:53: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:32:04: 9000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:32:11: #1 tag size is determined as 100 bps INFO @ Sat, 24 Aug 2019 21:32:11: #1 tag size = 100 INFO @ Sat, 24 Aug 2019 21:32:11: #1 total tags in treatment: 9598770 INFO @ Sat, 24 Aug 2019 21:32:11: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:32:11: #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 21:32:11: #1 tags after filtering in treatment: 9598770 INFO @ Sat, 24 Aug 2019 21:32:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:32:11: #1 finished! INFO @ Sat, 24 Aug 2019 21:32:11: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:32:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:32:12: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:32:12: 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 21:32:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.20_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/SRX5257249/SRX5257249.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257249/SRX5257249.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling