Job ID = 2591022 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,150,490 reads read : 15,150,490 reads written : 15,150,490 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: 00:04:02 15150490 reads; of these: 15150490 (100.00%) were unpaired; of these: 1051804 (6.94%) aligned 0 times 12135795 (80.10%) aligned exactly 1 time 1962891 (12.96%) aligned >1 times 93.06% overall alignment rate Time searching: 00:04:02 Overall time: 00:04:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1328360 / 14098686 = 0.0942 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 @ Tue, 13 Aug 2019 00:42:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 13 Aug 2019 00:42:49: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:42:49: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:42:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 13 Aug 2019 00:42:50: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:42:50: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:42:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 13 Aug 2019 00:42:51: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:42:51: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:42:57: 1000000 INFO @ Tue, 13 Aug 2019 00:42:59: 1000000 INFO @ Tue, 13 Aug 2019 00:42:59: 1000000 INFO @ Tue, 13 Aug 2019 00:43:06: 2000000 INFO @ Tue, 13 Aug 2019 00:43:08: 2000000 INFO @ Tue, 13 Aug 2019 00:43:09: 2000000 INFO @ Tue, 13 Aug 2019 00:43:14: 3000000 INFO @ Tue, 13 Aug 2019 00:43:17: 3000000 INFO @ Tue, 13 Aug 2019 00:43:17: 3000000 INFO @ Tue, 13 Aug 2019 00:43:23: 4000000 INFO @ Tue, 13 Aug 2019 00:43:26: 4000000 INFO @ Tue, 13 Aug 2019 00:43:26: 4000000 INFO @ Tue, 13 Aug 2019 00:43:32: 5000000 INFO @ Tue, 13 Aug 2019 00:43:34: 5000000 INFO @ Tue, 13 Aug 2019 00:43:35: 5000000 INFO @ Tue, 13 Aug 2019 00:43:41: 6000000 INFO @ Tue, 13 Aug 2019 00:43:43: 6000000 INFO @ Tue, 13 Aug 2019 00:43:44: 6000000 INFO @ Tue, 13 Aug 2019 00:43:49: 7000000 INFO @ Tue, 13 Aug 2019 00:43:53: 7000000 INFO @ Tue, 13 Aug 2019 00:43:53: 7000000 INFO @ Tue, 13 Aug 2019 00:43:57: 8000000 INFO @ Tue, 13 Aug 2019 00:44:01: 8000000 INFO @ Tue, 13 Aug 2019 00:44:02: 8000000 INFO @ Tue, 13 Aug 2019 00:44:06: 9000000 INFO @ Tue, 13 Aug 2019 00:44:09: 9000000 INFO @ Tue, 13 Aug 2019 00:44:11: 9000000 INFO @ Tue, 13 Aug 2019 00:44:14: 10000000 INFO @ Tue, 13 Aug 2019 00:44:17: 10000000 INFO @ Tue, 13 Aug 2019 00:44:20: 10000000 INFO @ Tue, 13 Aug 2019 00:44:22: 11000000 INFO @ Tue, 13 Aug 2019 00:44:26: 11000000 INFO @ Tue, 13 Aug 2019 00:44:29: 11000000 INFO @ Tue, 13 Aug 2019 00:44:31: 12000000 INFO @ Tue, 13 Aug 2019 00:44:35: 12000000 INFO @ Tue, 13 Aug 2019 00:44:37: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:44:37: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:44:37: #1 total tags in treatment: 12770326 INFO @ Tue, 13 Aug 2019 00:44:37: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:44:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:44:38: #1 tags after filtering in treatment: 12770326 INFO @ Tue, 13 Aug 2019 00:44:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:44:38: #1 finished! INFO @ Tue, 13 Aug 2019 00:44:38: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:44:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:44:38: 12000000 INFO @ Tue, 13 Aug 2019 00:44:39: #2 number of paired peaks: 113 WARNING @ Tue, 13 Aug 2019 00:44:39: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 13 Aug 2019 00:44:39: start model_add_line... INFO @ Tue, 13 Aug 2019 00:44:39: start X-correlation... INFO @ Tue, 13 Aug 2019 00:44:39: end of X-cor INFO @ Tue, 13 Aug 2019 00:44:39: #2 finished! INFO @ Tue, 13 Aug 2019 00:44:39: #2 predicted fragment length is 56 bps INFO @ Tue, 13 Aug 2019 00:44:39: #2 alternative fragment length(s) may be 2,56,78,81,107,145,527,564,572,577 bps INFO @ Tue, 13 Aug 2019 00:44:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.05_model.r WARNING @ Tue, 13 Aug 2019 00:44:39: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:44:39: #2 You may need to consider one of the other alternative d(s): 2,56,78,81,107,145,527,564,572,577 WARNING @ Tue, 13 Aug 2019 00:44:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:44:39: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:44:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:44:41: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:44:41: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:44:41: #1 total tags in treatment: 12770326 INFO @ Tue, 13 Aug 2019 00:44:41: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:44:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:44:41: #1 tags after filtering in treatment: 12770326 INFO @ Tue, 13 Aug 2019 00:44:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:44:41: #1 finished! INFO @ Tue, 13 Aug 2019 00:44:41: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:44:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:44:42: #2 number of paired peaks: 113 WARNING @ Tue, 13 Aug 2019 00:44:42: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 13 Aug 2019 00:44:42: start model_add_line... INFO @ Tue, 13 Aug 2019 00:44:42: start X-correlation... INFO @ Tue, 13 Aug 2019 00:44:42: end of X-cor INFO @ Tue, 13 Aug 2019 00:44:42: #2 finished! INFO @ Tue, 13 Aug 2019 00:44:42: #2 predicted fragment length is 56 bps INFO @ Tue, 13 Aug 2019 00:44:42: #2 alternative fragment length(s) may be 2,56,78,81,107,145,527,564,572,577 bps INFO @ Tue, 13 Aug 2019 00:44:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.20_model.r WARNING @ Tue, 13 Aug 2019 00:44:42: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:44:42: #2 You may need to consider one of the other alternative d(s): 2,56,78,81,107,145,527,564,572,577 WARNING @ Tue, 13 Aug 2019 00:44:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:44:42: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:44:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:44:45: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:44:45: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:44:45: #1 total tags in treatment: 12770326 INFO @ Tue, 13 Aug 2019 00:44:45: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:44:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:44:45: #1 tags after filtering in treatment: 12770326 INFO @ Tue, 13 Aug 2019 00:44:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:44:45: #1 finished! INFO @ Tue, 13 Aug 2019 00:44:45: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:44:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:44:46: #2 number of paired peaks: 113 WARNING @ Tue, 13 Aug 2019 00:44:46: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 13 Aug 2019 00:44:46: start model_add_line... INFO @ Tue, 13 Aug 2019 00:44:46: start X-correlation... INFO @ Tue, 13 Aug 2019 00:44:46: end of X-cor INFO @ Tue, 13 Aug 2019 00:44:46: #2 finished! INFO @ Tue, 13 Aug 2019 00:44:46: #2 predicted fragment length is 56 bps INFO @ Tue, 13 Aug 2019 00:44:46: #2 alternative fragment length(s) may be 2,56,78,81,107,145,527,564,572,577 bps INFO @ Tue, 13 Aug 2019 00:44:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.10_model.r WARNING @ Tue, 13 Aug 2019 00:44:46: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:44:46: #2 You may need to consider one of the other alternative d(s): 2,56,78,81,107,145,527,564,572,577 WARNING @ Tue, 13 Aug 2019 00:44:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:44:46: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:44:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:45:13: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:45:17: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:45:20: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:45:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:45:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:45:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.05_summits.bed INFO @ Tue, 13 Aug 2019 00:45:31: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (281 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:45:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:45:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:45:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.20_summits.bed INFO @ Tue, 13 Aug 2019 00:45:34: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (64 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:45:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:45:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:45:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661233/SRX661233.10_summits.bed INFO @ Tue, 13 Aug 2019 00:45:38: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (184 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。