Job ID = 2641136 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T12:30:44 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 ) 2019-08-24T12:30:44 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 : 14,288,689 reads read : 14,288,689 reads written : 14,288,689 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: 00:02:31 14288689 reads; of these: 14288689 (100.00%) were unpaired; of these: 992563 (6.95%) aligned 0 times 10768880 (75.37%) aligned exactly 1 time 2527246 (17.69%) aligned >1 times 93.05% overall alignment rate Time searching: 00:02:31 Overall time: 00:02:31 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 8 files... [bam_rmdupse_core] 4949715 / 13296126 = 0.3723 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:41:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.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 21:41:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:41:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:41:23: 1000000 INFO @ Sat, 24 Aug 2019 21:41:30: 2000000 INFO @ Sat, 24 Aug 2019 21:41:37: 3000000 INFO @ Sat, 24 Aug 2019 21:41:44: 4000000 INFO @ Sat, 24 Aug 2019 21:41:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.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 21:41:45: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:41:45: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:41:51: 5000000 INFO @ Sat, 24 Aug 2019 21:41:53: 1000000 INFO @ Sat, 24 Aug 2019 21:41:58: 6000000 INFO @ Sat, 24 Aug 2019 21:42:00: 2000000 INFO @ Sat, 24 Aug 2019 21:42:05: 7000000 INFO @ Sat, 24 Aug 2019 21:42:08: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:42:14: 8000000 INFO @ Sat, 24 Aug 2019 21:42:15: 4000000 INFO @ Sat, 24 Aug 2019 21:42:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.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 21:42:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:42:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:42:17: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:42:17: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:42:17: #1 total tags in treatment: 8346411 INFO @ Sat, 24 Aug 2019 21:42:17: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:42:17: #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 21:42:17: #1 tags after filtering in treatment: 8346411 INFO @ Sat, 24 Aug 2019 21:42:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:42:17: #1 finished! INFO @ Sat, 24 Aug 2019 21:42:17: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:42:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:42:17: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:42:17: 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 21:42:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.05_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/SRX559605/SRX559605.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:42:22: 5000000 INFO @ Sat, 24 Aug 2019 21:42:25: 1000000 INFO @ Sat, 24 Aug 2019 21:42:29: 6000000 INFO @ Sat, 24 Aug 2019 21:42:35: 2000000 INFO @ Sat, 24 Aug 2019 21:42:36: 7000000 INFO @ Sat, 24 Aug 2019 21:42:43: 8000000 INFO @ Sat, 24 Aug 2019 21:42:44: 3000000 INFO @ Sat, 24 Aug 2019 21:42:46: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:42:46: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:42:46: #1 total tags in treatment: 8346411 INFO @ Sat, 24 Aug 2019 21:42:46: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:42:46: #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 21:42:46: #1 tags after filtering in treatment: 8346411 INFO @ Sat, 24 Aug 2019 21:42:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:42:46: #1 finished! INFO @ Sat, 24 Aug 2019 21:42:46: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:42:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:42:47: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:42:47: 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 21:42:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.10_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/SRX559605/SRX559605.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:42:53: 4000000 INFO @ Sat, 24 Aug 2019 21:43:00: 5000000 INFO @ Sat, 24 Aug 2019 21:43:07: 6000000 INFO @ Sat, 24 Aug 2019 21:43:13: 7000000 INFO @ Sat, 24 Aug 2019 21:43:20: 8000000 INFO @ Sat, 24 Aug 2019 21:43:22: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:43:22: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:43:22: #1 total tags in treatment: 8346411 INFO @ Sat, 24 Aug 2019 21:43:22: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:43:22: #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 21:43:22: #1 tags after filtering in treatment: 8346411 INFO @ Sat, 24 Aug 2019 21:43:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:43:22: #1 finished! INFO @ Sat, 24 Aug 2019 21:43:22: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:43:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:43:23: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:43:23: 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 21:43:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.20_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/SRX559605/SRX559605.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX559605/SRX559605.20_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。