Job ID = 2589969 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,788,149 reads read : 30,788,149 reads written : 30,788,149 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: 00:06:36 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 171801 (0.56%) aligned 0 times 25273567 (82.09%) aligned exactly 1 time 5342781 (17.35%) aligned >1 times 99.44% overall alignment rate Time searching: 00:06:36 Overall time: 00:06:36 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 8 files... [bam_rmdupse_core] 4710705 / 30616348 = 0.1539 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 19:17:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.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 19:17:08: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:17:08: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:17:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.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 19:17:09: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:17:09: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:17:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.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 19:17:10: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:17:10: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:17:16: 1000000 INFO @ Mon, 12 Aug 2019 19:17:17: 1000000 INFO @ Mon, 12 Aug 2019 19:17:18: 1000000 INFO @ Mon, 12 Aug 2019 19:17:23: 2000000 INFO @ Mon, 12 Aug 2019 19:17:24: 2000000 INFO @ Mon, 12 Aug 2019 19:17:25: 2000000 INFO @ Mon, 12 Aug 2019 19:17:30: 3000000 INFO @ Mon, 12 Aug 2019 19:17:31: 3000000 INFO @ Mon, 12 Aug 2019 19:17:32: 3000000 INFO @ Mon, 12 Aug 2019 19:17:37: 4000000 INFO @ Mon, 12 Aug 2019 19:17:38: 4000000 INFO @ Mon, 12 Aug 2019 19:17:39: 4000000 INFO @ Mon, 12 Aug 2019 19:17:44: 5000000 INFO @ Mon, 12 Aug 2019 19:17:44: 5000000 INFO @ Mon, 12 Aug 2019 19:17:46: 5000000 INFO @ Mon, 12 Aug 2019 19:17:50: 6000000 INFO @ Mon, 12 Aug 2019 19:17:51: 6000000 INFO @ Mon, 12 Aug 2019 19:17:53: 6000000 INFO @ Mon, 12 Aug 2019 19:17:57: 7000000 INFO @ Mon, 12 Aug 2019 19:17:58: 7000000 INFO @ Mon, 12 Aug 2019 19:17:59: 7000000 INFO @ Mon, 12 Aug 2019 19:18:04: 8000000 INFO @ Mon, 12 Aug 2019 19:18:05: 8000000 INFO @ Mon, 12 Aug 2019 19:18:06: 8000000 INFO @ Mon, 12 Aug 2019 19:18:11: 9000000 INFO @ Mon, 12 Aug 2019 19:18:12: 9000000 INFO @ Mon, 12 Aug 2019 19:18:13: 9000000 INFO @ Mon, 12 Aug 2019 19:18:18: 10000000 INFO @ Mon, 12 Aug 2019 19:18:19: 10000000 INFO @ Mon, 12 Aug 2019 19:18:20: 10000000 INFO @ Mon, 12 Aug 2019 19:18:25: 11000000 INFO @ Mon, 12 Aug 2019 19:18:26: 11000000 INFO @ Mon, 12 Aug 2019 19:18:27: 11000000 INFO @ Mon, 12 Aug 2019 19:18:32: 12000000 INFO @ Mon, 12 Aug 2019 19:18:33: 12000000 INFO @ Mon, 12 Aug 2019 19:18:35: 12000000 INFO @ Mon, 12 Aug 2019 19:18:40: 13000000 INFO @ Mon, 12 Aug 2019 19:18:40: 13000000 INFO @ Mon, 12 Aug 2019 19:18:43: 13000000 INFO @ Mon, 12 Aug 2019 19:18:47: 14000000 INFO @ Mon, 12 Aug 2019 19:18:47: 14000000 INFO @ Mon, 12 Aug 2019 19:18:51: 14000000 INFO @ Mon, 12 Aug 2019 19:18:54: 15000000 INFO @ Mon, 12 Aug 2019 19:18:55: 15000000 INFO @ Mon, 12 Aug 2019 19:18:58: 15000000 INFO @ Mon, 12 Aug 2019 19:19:01: 16000000 INFO @ Mon, 12 Aug 2019 19:19:02: 16000000 INFO @ Mon, 12 Aug 2019 19:19:05: 16000000 INFO @ Mon, 12 Aug 2019 19:19:08: 17000000 INFO @ Mon, 12 Aug 2019 19:19:09: 17000000 INFO @ Mon, 12 Aug 2019 19:19:12: 17000000 INFO @ Mon, 12 Aug 2019 19:19:15: 18000000 INFO @ Mon, 12 Aug 2019 19:19:17: 18000000 INFO @ Mon, 12 Aug 2019 19:19:19: 18000000 INFO @ Mon, 12 Aug 2019 19:19:22: 19000000 INFO @ Mon, 12 Aug 2019 19:19:24: 19000000 INFO @ Mon, 12 Aug 2019 19:19:26: 19000000 INFO @ Mon, 12 Aug 2019 19:19:29: 20000000 INFO @ Mon, 12 Aug 2019 19:19:31: 20000000 INFO @ Mon, 12 Aug 2019 19:19:33: 20000000 INFO @ Mon, 12 Aug 2019 19:19:36: 21000000 INFO @ Mon, 12 Aug 2019 19:19:38: 21000000 INFO @ Mon, 12 Aug 2019 19:19:40: 21000000 INFO @ Mon, 12 Aug 2019 19:19:43: 22000000 INFO @ Mon, 12 Aug 2019 19:19:46: 22000000 INFO @ Mon, 12 Aug 2019 19:19:47: 22000000 INFO @ Mon, 12 Aug 2019 19:19:50: 23000000 INFO @ Mon, 12 Aug 2019 19:19:53: 23000000 INFO @ Mon, 12 Aug 2019 19:19:54: 23000000 INFO @ Mon, 12 Aug 2019 19:19:57: 24000000 INFO @ Mon, 12 Aug 2019 19:20:00: 24000000 INFO @ Mon, 12 Aug 2019 19:20:01: 24000000 INFO @ Mon, 12 Aug 2019 19:20:04: 25000000 INFO @ Mon, 12 Aug 2019 19:20:08: 25000000 INFO @ Mon, 12 Aug 2019 19:20:08: 25000000 INFO @ Mon, 12 Aug 2019 19:20:10: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 19:20:10: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 19:20:10: #1 total tags in treatment: 25905643 INFO @ Mon, 12 Aug 2019 19:20:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:20:10: #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 19:20:11: #1 tags after filtering in treatment: 25905643 INFO @ Mon, 12 Aug 2019 19:20:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:20:11: #1 finished! INFO @ Mon, 12 Aug 2019 19:20:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:20:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:20:13: #2 number of paired peaks: 133 WARNING @ Mon, 12 Aug 2019 19:20:13: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Mon, 12 Aug 2019 19:20:13: start model_add_line... INFO @ Mon, 12 Aug 2019 19:20:13: start X-correlation... INFO @ Mon, 12 Aug 2019 19:20:13: end of X-cor INFO @ Mon, 12 Aug 2019 19:20:13: #2 finished! INFO @ Mon, 12 Aug 2019 19:20:13: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 19:20:13: #2 alternative fragment length(s) may be 1,14,29,84,287,306,366,382,464,502,566 bps INFO @ Mon, 12 Aug 2019 19:20:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.10_model.r WARNING @ Mon, 12 Aug 2019 19:20:13: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:20:13: #2 You may need to consider one of the other alternative d(s): 1,14,29,84,287,306,366,382,464,502,566 WARNING @ Mon, 12 Aug 2019 19:20:13: #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 19:20:13: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:20:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:20:14: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 19:20:14: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 19:20:14: #1 total tags in treatment: 25905643 INFO @ Mon, 12 Aug 2019 19:20:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:20:14: #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 19:20:15: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 19:20:15: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 19:20:15: #1 total tags in treatment: 25905643 INFO @ Mon, 12 Aug 2019 19:20:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:20:15: #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 19:20:15: #1 tags after filtering in treatment: 25905643 INFO @ Mon, 12 Aug 2019 19:20:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:20:15: #1 finished! INFO @ Mon, 12 Aug 2019 19:20:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:20:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:20:15: #1 tags after filtering in treatment: 25905643 INFO @ Mon, 12 Aug 2019 19:20:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:20:15: #1 finished! INFO @ Mon, 12 Aug 2019 19:20:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:20:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:20:17: #2 number of paired peaks: 133 WARNING @ Mon, 12 Aug 2019 19:20:17: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Mon, 12 Aug 2019 19:20:17: start model_add_line... INFO @ Mon, 12 Aug 2019 19:20:17: start X-correlation... INFO @ Mon, 12 Aug 2019 19:20:17: end of X-cor INFO @ Mon, 12 Aug 2019 19:20:17: #2 finished! INFO @ Mon, 12 Aug 2019 19:20:17: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 19:20:17: #2 alternative fragment length(s) may be 1,14,29,84,287,306,366,382,464,502,566 bps INFO @ Mon, 12 Aug 2019 19:20:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.05_model.r WARNING @ Mon, 12 Aug 2019 19:20:17: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:20:17: #2 You may need to consider one of the other alternative d(s): 1,14,29,84,287,306,366,382,464,502,566 WARNING @ Mon, 12 Aug 2019 19:20:17: #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 19:20:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:20:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:20:17: #2 number of paired peaks: 133 WARNING @ Mon, 12 Aug 2019 19:20:17: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Mon, 12 Aug 2019 19:20:17: start model_add_line... INFO @ Mon, 12 Aug 2019 19:20:18: start X-correlation... INFO @ Mon, 12 Aug 2019 19:20:18: end of X-cor INFO @ Mon, 12 Aug 2019 19:20:18: #2 finished! INFO @ Mon, 12 Aug 2019 19:20:18: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 19:20:18: #2 alternative fragment length(s) may be 1,14,29,84,287,306,366,382,464,502,566 bps INFO @ Mon, 12 Aug 2019 19:20:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.20_model.r WARNING @ Mon, 12 Aug 2019 19:20:18: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:20:18: #2 You may need to consider one of the other alternative d(s): 1,14,29,84,287,306,366,382,464,502,566 WARNING @ Mon, 12 Aug 2019 19:20:18: #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 19:20:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:20:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:21:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:21:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:21:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:21:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:21:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:21:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.10_summits.bed INFO @ Mon, 12 Aug 2019 19:21:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:21:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:21:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:21:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.20_summits.bed INFO @ Mon, 12 Aug 2019 19:21:32: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:21:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:21:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:21:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466500/SRX466500.05_summits.bed INFO @ Mon, 12 Aug 2019 19:21:33: 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。