Job ID = 2589355 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,713,577 reads read : 28,713,577 reads written : 28,713,577 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 28713577 reads; of these: 28713577 (100.00%) were unpaired; of these: 763465 (2.66%) aligned 0 times 23454076 (81.68%) aligned exactly 1 time 4496036 (15.66%) aligned >1 times 97.34% 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: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4015375 / 27950112 = 0.1437 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 18:01:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.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 18:01:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:01:03: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:01:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.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 18:01:04: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:01:04: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:01:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.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 18:01:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:01:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:01:11: 1000000 INFO @ Mon, 12 Aug 2019 18:01:13: 1000000 INFO @ Mon, 12 Aug 2019 18:01:13: 1000000 INFO @ Mon, 12 Aug 2019 18:01:19: 2000000 INFO @ Mon, 12 Aug 2019 18:01:20: 2000000 INFO @ Mon, 12 Aug 2019 18:01:22: 2000000 INFO @ Mon, 12 Aug 2019 18:01:27: 3000000 INFO @ Mon, 12 Aug 2019 18:01:28: 3000000 INFO @ Mon, 12 Aug 2019 18:01:30: 3000000 INFO @ Mon, 12 Aug 2019 18:01:35: 4000000 INFO @ Mon, 12 Aug 2019 18:01:36: 4000000 INFO @ Mon, 12 Aug 2019 18:01:38: 4000000 INFO @ Mon, 12 Aug 2019 18:01:42: 5000000 INFO @ Mon, 12 Aug 2019 18:01:44: 5000000 INFO @ Mon, 12 Aug 2019 18:01:47: 5000000 INFO @ Mon, 12 Aug 2019 18:01:50: 6000000 INFO @ Mon, 12 Aug 2019 18:01:52: 6000000 INFO @ Mon, 12 Aug 2019 18:01:55: 6000000 INFO @ Mon, 12 Aug 2019 18:01:58: 7000000 INFO @ Mon, 12 Aug 2019 18:01:59: 7000000 INFO @ Mon, 12 Aug 2019 18:02:03: 7000000 INFO @ Mon, 12 Aug 2019 18:02:06: 8000000 INFO @ Mon, 12 Aug 2019 18:02:07: 8000000 INFO @ Mon, 12 Aug 2019 18:02:11: 8000000 INFO @ Mon, 12 Aug 2019 18:02:14: 9000000 INFO @ Mon, 12 Aug 2019 18:02:15: 9000000 INFO @ Mon, 12 Aug 2019 18:02:20: 9000000 INFO @ Mon, 12 Aug 2019 18:02:21: 10000000 INFO @ Mon, 12 Aug 2019 18:02:23: 10000000 INFO @ Mon, 12 Aug 2019 18:02:28: 10000000 INFO @ Mon, 12 Aug 2019 18:02:29: 11000000 INFO @ Mon, 12 Aug 2019 18:02:30: 11000000 INFO @ Mon, 12 Aug 2019 18:02:36: 11000000 INFO @ Mon, 12 Aug 2019 18:02:37: 12000000 INFO @ Mon, 12 Aug 2019 18:02:38: 12000000 INFO @ Mon, 12 Aug 2019 18:02:44: 12000000 INFO @ Mon, 12 Aug 2019 18:02:44: 13000000 INFO @ Mon, 12 Aug 2019 18:02:46: 13000000 INFO @ Mon, 12 Aug 2019 18:02:52: 14000000 INFO @ Mon, 12 Aug 2019 18:02:53: 13000000 INFO @ Mon, 12 Aug 2019 18:02:53: 14000000 INFO @ Mon, 12 Aug 2019 18:03:00: 15000000 INFO @ Mon, 12 Aug 2019 18:03:01: 14000000 INFO @ Mon, 12 Aug 2019 18:03:01: 15000000 INFO @ Mon, 12 Aug 2019 18:03:07: 16000000 INFO @ Mon, 12 Aug 2019 18:03:09: 16000000 INFO @ Mon, 12 Aug 2019 18:03:09: 15000000 INFO @ Mon, 12 Aug 2019 18:03:15: 17000000 INFO @ Mon, 12 Aug 2019 18:03:16: 17000000 INFO @ Mon, 12 Aug 2019 18:03:18: 16000000 INFO @ Mon, 12 Aug 2019 18:03:23: 18000000 INFO @ Mon, 12 Aug 2019 18:03:24: 18000000 INFO @ Mon, 12 Aug 2019 18:03:26: 17000000 INFO @ Mon, 12 Aug 2019 18:03:30: 19000000 INFO @ Mon, 12 Aug 2019 18:03:31: 19000000 INFO @ Mon, 12 Aug 2019 18:03:34: 18000000 INFO @ Mon, 12 Aug 2019 18:03:38: 20000000 INFO @ Mon, 12 Aug 2019 18:03:39: 20000000 INFO @ Mon, 12 Aug 2019 18:03:42: 19000000 INFO @ Mon, 12 Aug 2019 18:03:45: 21000000 INFO @ Mon, 12 Aug 2019 18:03:47: 21000000 INFO @ Mon, 12 Aug 2019 18:03:50: 20000000 INFO @ Mon, 12 Aug 2019 18:03:53: 22000000 INFO @ Mon, 12 Aug 2019 18:03:54: 22000000 INFO @ Mon, 12 Aug 2019 18:03:59: 21000000 INFO @ Mon, 12 Aug 2019 18:04:01: 23000000 INFO @ Mon, 12 Aug 2019 18:04:02: 23000000 INFO @ Mon, 12 Aug 2019 18:04:07: 22000000 INFO @ Mon, 12 Aug 2019 18:04:08: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:04:08: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:04:08: #1 total tags in treatment: 23934737 INFO @ Mon, 12 Aug 2019 18:04:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:04:08: #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 18:04:08: #1 tags after filtering in treatment: 23934737 INFO @ Mon, 12 Aug 2019 18:04:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:04:08: #1 finished! INFO @ Mon, 12 Aug 2019 18:04:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:04:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:04:09: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:04:09: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:04:09: #1 total tags in treatment: 23934737 INFO @ Mon, 12 Aug 2019 18:04:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:04:09: #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 18:04:09: #1 tags after filtering in treatment: 23934737 INFO @ Mon, 12 Aug 2019 18:04:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:04:09: #1 finished! INFO @ Mon, 12 Aug 2019 18:04:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:04:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:04:10: #2 number of paired peaks: 164 WARNING @ Mon, 12 Aug 2019 18:04:10: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Mon, 12 Aug 2019 18:04:10: start model_add_line... INFO @ Mon, 12 Aug 2019 18:04:11: start X-correlation... INFO @ Mon, 12 Aug 2019 18:04:11: end of X-cor INFO @ Mon, 12 Aug 2019 18:04:11: #2 finished! INFO @ Mon, 12 Aug 2019 18:04:11: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 18:04:11: #2 alternative fragment length(s) may be 1,22,51,542,592 bps INFO @ Mon, 12 Aug 2019 18:04:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.05_model.r WARNING @ Mon, 12 Aug 2019 18:04:11: #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 18:04:11: #2 You may need to consider one of the other alternative d(s): 1,22,51,542,592 WARNING @ Mon, 12 Aug 2019 18:04:11: #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 18:04:11: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:04:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:04:12: #2 number of paired peaks: 164 WARNING @ Mon, 12 Aug 2019 18:04:12: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Mon, 12 Aug 2019 18:04:12: start model_add_line... INFO @ Mon, 12 Aug 2019 18:04:12: start X-correlation... INFO @ Mon, 12 Aug 2019 18:04:12: end of X-cor INFO @ Mon, 12 Aug 2019 18:04:12: #2 finished! INFO @ Mon, 12 Aug 2019 18:04:12: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 18:04:12: #2 alternative fragment length(s) may be 1,22,51,542,592 bps INFO @ Mon, 12 Aug 2019 18:04:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.10_model.r WARNING @ Mon, 12 Aug 2019 18:04:12: #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 18:04:12: #2 You may need to consider one of the other alternative d(s): 1,22,51,542,592 WARNING @ Mon, 12 Aug 2019 18:04:12: #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 18:04:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:04:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:04:15: 23000000 INFO @ Mon, 12 Aug 2019 18:04:23: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:04:23: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:04:23: #1 total tags in treatment: 23934737 INFO @ Mon, 12 Aug 2019 18:04:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:04:23: #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 18:04:23: #1 tags after filtering in treatment: 23934737 INFO @ Mon, 12 Aug 2019 18:04:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:04:23: #1 finished! INFO @ Mon, 12 Aug 2019 18:04:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:04:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:04:25: #2 number of paired peaks: 164 WARNING @ Mon, 12 Aug 2019 18:04:25: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Mon, 12 Aug 2019 18:04:25: start model_add_line... INFO @ Mon, 12 Aug 2019 18:04:25: start X-correlation... INFO @ Mon, 12 Aug 2019 18:04:25: end of X-cor INFO @ Mon, 12 Aug 2019 18:04:25: #2 finished! INFO @ Mon, 12 Aug 2019 18:04:25: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 18:04:25: #2 alternative fragment length(s) may be 1,22,51,542,592 bps INFO @ Mon, 12 Aug 2019 18:04:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.20_model.r WARNING @ Mon, 12 Aug 2019 18:04:25: #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 18:04:25: #2 You may need to consider one of the other alternative d(s): 1,22,51,542,592 WARNING @ Mon, 12 Aug 2019 18:04:25: #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 18:04:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:04:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:05:00: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:05:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:05:15: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:05:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:05:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:05:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.05_summits.bed INFO @ Mon, 12 Aug 2019 18:05:22: Done! INFO @ Mon, 12 Aug 2019 18:05:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:05:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:05:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.10_summits.bed INFO @ Mon, 12 Aug 2019 18:05:22: Done! pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:05:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:05:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:05:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078708/SRX1078708.20_summits.bed INFO @ Mon, 12 Aug 2019 18:05:37: 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。