Job ID = 2590081 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,771,760 reads read : 21,771,760 reads written : 21,771,760 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: 00:05:42 21771760 reads; of these: 21771760 (100.00%) were unpaired; of these: 1355886 (6.23%) aligned 0 times 17025403 (78.20%) aligned exactly 1 time 3390471 (15.57%) aligned >1 times 93.77% overall alignment rate Time searching: 00:05:42 Overall time: 00:05:42 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] 5572272 / 20415874 = 0.2729 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 @ Mon, 12 Aug 2019 19:48:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.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 @ Mon, 12 Aug 2019 19:48:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:48:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:48:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.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 @ Mon, 12 Aug 2019 19:48:30: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:48:30: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:48:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.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 @ Mon, 12 Aug 2019 19:48:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:48:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:48:37: 1000000 INFO @ Mon, 12 Aug 2019 19:48:38: 1000000 INFO @ Mon, 12 Aug 2019 19:48:41: 1000000 INFO @ Mon, 12 Aug 2019 19:48:46: 2000000 INFO @ Mon, 12 Aug 2019 19:48:47: 2000000 INFO @ Mon, 12 Aug 2019 19:48:51: 2000000 INFO @ Mon, 12 Aug 2019 19:48:54: 3000000 INFO @ Mon, 12 Aug 2019 19:48:55: 3000000 INFO @ Mon, 12 Aug 2019 19:49:01: 3000000 INFO @ Mon, 12 Aug 2019 19:49:02: 4000000 INFO @ Mon, 12 Aug 2019 19:49:03: 4000000 INFO @ Mon, 12 Aug 2019 19:49:11: 4000000 INFO @ Mon, 12 Aug 2019 19:49:11: 5000000 INFO @ Mon, 12 Aug 2019 19:49:12: 5000000 INFO @ Mon, 12 Aug 2019 19:49:19: 6000000 INFO @ Mon, 12 Aug 2019 19:49:20: 6000000 INFO @ Mon, 12 Aug 2019 19:49:20: 5000000 INFO @ Mon, 12 Aug 2019 19:49:28: 7000000 INFO @ Mon, 12 Aug 2019 19:49:28: 7000000 INFO @ Mon, 12 Aug 2019 19:49:30: 6000000 INFO @ Mon, 12 Aug 2019 19:49:36: 8000000 INFO @ Mon, 12 Aug 2019 19:49:37: 8000000 INFO @ Mon, 12 Aug 2019 19:49:40: 7000000 INFO @ Mon, 12 Aug 2019 19:49:45: 9000000 INFO @ Mon, 12 Aug 2019 19:49:46: 9000000 INFO @ Mon, 12 Aug 2019 19:49:49: 8000000 INFO @ Mon, 12 Aug 2019 19:49:54: 10000000 INFO @ Mon, 12 Aug 2019 19:49:55: 10000000 INFO @ Mon, 12 Aug 2019 19:49:59: 9000000 INFO @ Mon, 12 Aug 2019 19:50:03: 11000000 INFO @ Mon, 12 Aug 2019 19:50:04: 11000000 INFO @ Mon, 12 Aug 2019 19:50:07: 10000000 INFO @ Mon, 12 Aug 2019 19:50:12: 12000000 INFO @ Mon, 12 Aug 2019 19:50:13: 12000000 INFO @ Mon, 12 Aug 2019 19:50:16: 11000000 INFO @ Mon, 12 Aug 2019 19:50:21: 13000000 INFO @ Mon, 12 Aug 2019 19:50:22: 13000000 INFO @ Mon, 12 Aug 2019 19:50:24: 12000000 INFO @ Mon, 12 Aug 2019 19:50:29: 14000000 INFO @ Mon, 12 Aug 2019 19:50:30: 14000000 INFO @ Mon, 12 Aug 2019 19:50:34: 13000000 INFO @ Mon, 12 Aug 2019 19:50:36: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:50:36: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:50:36: #1 total tags in treatment: 14843602 INFO @ Mon, 12 Aug 2019 19:50:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:50:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:50:36: #1 tags after filtering in treatment: 14843602 INFO @ Mon, 12 Aug 2019 19:50:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:50:36: #1 finished! INFO @ Mon, 12 Aug 2019 19:50:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:50:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:50:37: #2 number of paired peaks: 307 WARNING @ Mon, 12 Aug 2019 19:50:37: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Mon, 12 Aug 2019 19:50:37: start model_add_line... INFO @ Mon, 12 Aug 2019 19:50:37: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:50:37: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:50:37: #1 total tags in treatment: 14843602 INFO @ Mon, 12 Aug 2019 19:50:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:50:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:50:37: start X-correlation... INFO @ Mon, 12 Aug 2019 19:50:37: end of X-cor INFO @ Mon, 12 Aug 2019 19:50:37: #2 finished! INFO @ Mon, 12 Aug 2019 19:50:37: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 19:50:37: #2 alternative fragment length(s) may be 1,43,546,560 bps INFO @ Mon, 12 Aug 2019 19:50:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.05_model.r WARNING @ Mon, 12 Aug 2019 19:50:37: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:50:37: #2 You may need to consider one of the other alternative d(s): 1,43,546,560 WARNING @ Mon, 12 Aug 2019 19:50:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:50:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:50:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:50:38: #1 tags after filtering in treatment: 14843602 INFO @ Mon, 12 Aug 2019 19:50:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:50:38: #1 finished! INFO @ Mon, 12 Aug 2019 19:50:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:50:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:50:39: #2 number of paired peaks: 307 WARNING @ Mon, 12 Aug 2019 19:50:39: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Mon, 12 Aug 2019 19:50:39: start model_add_line... INFO @ Mon, 12 Aug 2019 19:50:39: start X-correlation... INFO @ Mon, 12 Aug 2019 19:50:39: end of X-cor INFO @ Mon, 12 Aug 2019 19:50:39: #2 finished! INFO @ Mon, 12 Aug 2019 19:50:39: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 19:50:39: #2 alternative fragment length(s) may be 1,43,546,560 bps INFO @ Mon, 12 Aug 2019 19:50:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.10_model.r WARNING @ Mon, 12 Aug 2019 19:50:39: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:50:39: #2 You may need to consider one of the other alternative d(s): 1,43,546,560 WARNING @ Mon, 12 Aug 2019 19:50:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:50:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:50:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:50:44: 14000000 INFO @ Mon, 12 Aug 2019 19:50:52: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:50:52: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:50:52: #1 total tags in treatment: 14843602 INFO @ Mon, 12 Aug 2019 19:50:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:50:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:50:52: #1 tags after filtering in treatment: 14843602 INFO @ Mon, 12 Aug 2019 19:50:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:50:52: #1 finished! INFO @ Mon, 12 Aug 2019 19:50:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:50:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:50:53: #2 number of paired peaks: 307 WARNING @ Mon, 12 Aug 2019 19:50:53: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Mon, 12 Aug 2019 19:50:53: start model_add_line... INFO @ Mon, 12 Aug 2019 19:50:53: start X-correlation... INFO @ Mon, 12 Aug 2019 19:50:53: end of X-cor INFO @ Mon, 12 Aug 2019 19:50:53: #2 finished! INFO @ Mon, 12 Aug 2019 19:50:53: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 19:50:53: #2 alternative fragment length(s) may be 1,43,546,560 bps INFO @ Mon, 12 Aug 2019 19:50:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.20_model.r WARNING @ Mon, 12 Aug 2019 19:50:53: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:50:53: #2 You may need to consider one of the other alternative d(s): 1,43,546,560 WARNING @ Mon, 12 Aug 2019 19:50:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:50:53: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:50:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:51:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:51:15: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:51:29: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:51:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:51:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:51:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.05_summits.bed INFO @ Mon, 12 Aug 2019 19:51:31: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (807 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:51:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:51:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:51:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.10_summits.bed INFO @ Mon, 12 Aug 2019 19:51:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (497 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:51:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:51:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:51:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494923/SRX494923.20_summits.bed INFO @ Mon, 12 Aug 2019 19:51:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。