Job ID = 1293147 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,668,453 reads read : 32,668,453 reads written : 32,668,453 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:06:34 32668453 reads; of these: 32668453 (100.00%) were unpaired; of these: 6742700 (20.64%) aligned 0 times 22060927 (67.53%) aligned exactly 1 time 3864826 (11.83%) aligned >1 times 79.36% overall alignment rate Time searching: 00:06:34 Overall time: 00:06:34 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4182221 / 25925753 = 0.1613 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sun, 02 Jun 2019 22:26:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 22:26:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:26:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:26:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 22:26:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:26:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:26:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 22:26:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:26:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:26:49: 1000000 INFO @ Sun, 02 Jun 2019 22:26:49: 1000000 INFO @ Sun, 02 Jun 2019 22:26:52: 1000000 INFO @ Sun, 02 Jun 2019 22:26:57: 2000000 INFO @ Sun, 02 Jun 2019 22:26:57: 2000000 INFO @ Sun, 02 Jun 2019 22:27:02: 2000000 INFO @ Sun, 02 Jun 2019 22:27:05: 3000000 INFO @ Sun, 02 Jun 2019 22:27:05: 3000000 INFO @ Sun, 02 Jun 2019 22:27:12: 4000000 INFO @ Sun, 02 Jun 2019 22:27:12: 3000000 INFO @ Sun, 02 Jun 2019 22:27:13: 4000000 INFO @ Sun, 02 Jun 2019 22:27:20: 5000000 INFO @ Sun, 02 Jun 2019 22:27:20: 5000000 INFO @ Sun, 02 Jun 2019 22:27:23: 4000000 INFO @ Sun, 02 Jun 2019 22:27:28: 6000000 INFO @ Sun, 02 Jun 2019 22:27:28: 6000000 INFO @ Sun, 02 Jun 2019 22:27:33: 5000000 INFO @ Sun, 02 Jun 2019 22:27:36: 7000000 INFO @ Sun, 02 Jun 2019 22:27:36: 7000000 INFO @ Sun, 02 Jun 2019 22:27:43: 8000000 INFO @ Sun, 02 Jun 2019 22:27:44: 8000000 INFO @ Sun, 02 Jun 2019 22:27:44: 6000000 INFO @ Sun, 02 Jun 2019 22:27:51: 9000000 INFO @ Sun, 02 Jun 2019 22:27:52: 9000000 INFO @ Sun, 02 Jun 2019 22:27:54: 7000000 INFO @ Sun, 02 Jun 2019 22:27:59: 10000000 INFO @ Sun, 02 Jun 2019 22:27:59: 10000000 INFO @ Sun, 02 Jun 2019 22:28:05: 8000000 INFO @ Sun, 02 Jun 2019 22:28:06: 11000000 INFO @ Sun, 02 Jun 2019 22:28:07: 11000000 INFO @ Sun, 02 Jun 2019 22:28:14: 12000000 INFO @ Sun, 02 Jun 2019 22:28:14: 12000000 INFO @ Sun, 02 Jun 2019 22:28:17: 9000000 INFO @ Sun, 02 Jun 2019 22:28:22: 13000000 INFO @ Sun, 02 Jun 2019 22:28:22: 13000000 INFO @ Sun, 02 Jun 2019 22:28:28: 10000000 INFO @ Sun, 02 Jun 2019 22:28:29: 14000000 INFO @ Sun, 02 Jun 2019 22:28:30: 14000000 INFO @ Sun, 02 Jun 2019 22:28:37: 15000000 INFO @ Sun, 02 Jun 2019 22:28:37: 15000000 INFO @ Sun, 02 Jun 2019 22:28:39: 11000000 INFO @ Sun, 02 Jun 2019 22:28:45: 16000000 INFO @ Sun, 02 Jun 2019 22:28:46: 16000000 INFO @ Sun, 02 Jun 2019 22:28:49: 12000000 INFO @ Sun, 02 Jun 2019 22:28:54: 17000000 INFO @ Sun, 02 Jun 2019 22:28:54: 17000000 INFO @ Sun, 02 Jun 2019 22:28:59: 13000000 INFO @ Sun, 02 Jun 2019 22:29:02: 18000000 INFO @ Sun, 02 Jun 2019 22:29:02: 18000000 INFO @ Sun, 02 Jun 2019 22:29:10: 14000000 INFO @ Sun, 02 Jun 2019 22:29:10: 19000000 INFO @ Sun, 02 Jun 2019 22:29:10: 19000000 INFO @ Sun, 02 Jun 2019 22:29:18: 20000000 INFO @ Sun, 02 Jun 2019 22:29:18: 20000000 INFO @ Sun, 02 Jun 2019 22:29:22: 15000000 INFO @ Sun, 02 Jun 2019 22:29:26: 21000000 INFO @ Sun, 02 Jun 2019 22:29:27: 21000000 INFO @ Sun, 02 Jun 2019 22:29:32: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:29:32: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:29:32: #1 total tags in treatment: 21743532 INFO @ Sun, 02 Jun 2019 22:29:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:29:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:29:32: #1 tags after filtering in treatment: 21743532 INFO @ Sun, 02 Jun 2019 22:29:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:29:32: #1 finished! INFO @ Sun, 02 Jun 2019 22:29:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:29:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:29:33: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:29:33: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:29:33: #1 total tags in treatment: 21743532 INFO @ Sun, 02 Jun 2019 22:29:33: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:29:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:29:33: 16000000 INFO @ Sun, 02 Jun 2019 22:29:33: #1 tags after filtering in treatment: 21743532 INFO @ Sun, 02 Jun 2019 22:29:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:29:33: #1 finished! INFO @ Sun, 02 Jun 2019 22:29:33: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:29:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:29:34: #2 number of paired peaks: 151 WARNING @ Sun, 02 Jun 2019 22:29:34: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Sun, 02 Jun 2019 22:29:34: start model_add_line... INFO @ Sun, 02 Jun 2019 22:29:35: start X-correlation... INFO @ Sun, 02 Jun 2019 22:29:35: end of X-cor INFO @ Sun, 02 Jun 2019 22:29:35: #2 finished! INFO @ Sun, 02 Jun 2019 22:29:35: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:29:35: #2 alternative fragment length(s) may be 1,25,43,500,565,597 bps INFO @ Sun, 02 Jun 2019 22:29:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.05_model.r WARNING @ Sun, 02 Jun 2019 22:29:35: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:29:35: #2 You may need to consider one of the other alternative d(s): 1,25,43,500,565,597 WARNING @ Sun, 02 Jun 2019 22:29:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:29:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:29:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:29:35: #2 number of paired peaks: 151 WARNING @ Sun, 02 Jun 2019 22:29:35: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Sun, 02 Jun 2019 22:29:35: start model_add_line... INFO @ Sun, 02 Jun 2019 22:29:35: start X-correlation... INFO @ Sun, 02 Jun 2019 22:29:35: end of X-cor INFO @ Sun, 02 Jun 2019 22:29:35: #2 finished! INFO @ Sun, 02 Jun 2019 22:29:35: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:29:35: #2 alternative fragment length(s) may be 1,25,43,500,565,597 bps INFO @ Sun, 02 Jun 2019 22:29:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.10_model.r WARNING @ Sun, 02 Jun 2019 22:29:36: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:29:36: #2 You may need to consider one of the other alternative d(s): 1,25,43,500,565,597 WARNING @ Sun, 02 Jun 2019 22:29:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:29:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:29:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:29:45: 17000000 INFO @ Sun, 02 Jun 2019 22:29:56: 18000000 INFO @ Sun, 02 Jun 2019 22:30:06: 19000000 INFO @ Sun, 02 Jun 2019 22:30:16: 20000000 INFO @ Sun, 02 Jun 2019 22:30:21: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:30:21: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:30:26: 21000000 INFO @ Sun, 02 Jun 2019 22:30:34: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:30:34: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:30:34: #1 total tags in treatment: 21743532 INFO @ Sun, 02 Jun 2019 22:30:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:30:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:30:35: #1 tags after filtering in treatment: 21743532 INFO @ Sun, 02 Jun 2019 22:30:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:30:35: #1 finished! INFO @ Sun, 02 Jun 2019 22:30:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:30:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:30:36: #2 number of paired peaks: 151 WARNING @ Sun, 02 Jun 2019 22:30:36: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Sun, 02 Jun 2019 22:30:36: start model_add_line... INFO @ Sun, 02 Jun 2019 22:30:37: start X-correlation... INFO @ Sun, 02 Jun 2019 22:30:37: end of X-cor INFO @ Sun, 02 Jun 2019 22:30:37: #2 finished! INFO @ Sun, 02 Jun 2019 22:30:37: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:30:37: #2 alternative fragment length(s) may be 1,25,43,500,565,597 bps INFO @ Sun, 02 Jun 2019 22:30:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.20_model.r WARNING @ Sun, 02 Jun 2019 22:30:37: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:30:37: #2 You may need to consider one of the other alternative d(s): 1,25,43,500,565,597 WARNING @ Sun, 02 Jun 2019 22:30:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:30:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:30:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:30:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:30:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:30:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.05_summits.bed INFO @ Sun, 02 Jun 2019 22:30:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:30:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:30:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:30:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.10_summits.bed INFO @ Sun, 02 Jun 2019 22:30:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:31:21: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:31:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:31:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:31:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402715/SRX5402715.20_summits.bed INFO @ Sun, 02 Jun 2019 22:31:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。