Job ID = 1294379 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,753,278 reads read : 19,506,556 reads written : 9,753,278 reads 0-length : 9,753,278 spots read : 9,728,374 reads read : 19,456,748 reads written : 9,728,374 reads 0-length : 9,728,374 spots read : 9,678,707 reads read : 19,357,414 reads written : 9,678,707 reads 0-length : 9,678,707 spots read : 9,690,012 reads read : 19,380,024 reads written : 9,690,012 reads 0-length : 9,690,012 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: 00:22:15 38850371 reads; of these: 38850371 (100.00%) were unpaired; of these: 1269211 (3.27%) aligned 0 times 26694775 (68.71%) aligned exactly 1 time 10886385 (28.02%) aligned >1 times 96.73% overall alignment rate Time searching: 00:22:15 Overall time: 00:22:15 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 16 files... [bam_rmdupse_core] 25037474 / 37581160 = 0.6662 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, 03 Jun 2019 07:50:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.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 @ Mon, 03 Jun 2019 07:50:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:50:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:50:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.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 @ Mon, 03 Jun 2019 07:50:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:50:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:50:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.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 @ Mon, 03 Jun 2019 07:50:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:50:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:50:11: 1000000 INFO @ Mon, 03 Jun 2019 07:50:13: 1000000 INFO @ Mon, 03 Jun 2019 07:50:13: 1000000 INFO @ Mon, 03 Jun 2019 07:50:20: 2000000 INFO @ Mon, 03 Jun 2019 07:50:24: 2000000 INFO @ Mon, 03 Jun 2019 07:50:24: 2000000 INFO @ Mon, 03 Jun 2019 07:50:29: 3000000 INFO @ Mon, 03 Jun 2019 07:50:34: 3000000 INFO @ Mon, 03 Jun 2019 07:50:35: 3000000 INFO @ Mon, 03 Jun 2019 07:50:37: 4000000 INFO @ Mon, 03 Jun 2019 07:50:44: 4000000 INFO @ Mon, 03 Jun 2019 07:50:45: 4000000 INFO @ Mon, 03 Jun 2019 07:50:46: 5000000 INFO @ Mon, 03 Jun 2019 07:50:54: 6000000 INFO @ Mon, 03 Jun 2019 07:50:55: 5000000 INFO @ Mon, 03 Jun 2019 07:50:56: 5000000 INFO @ Mon, 03 Jun 2019 07:51:03: 7000000 INFO @ Mon, 03 Jun 2019 07:51:05: 6000000 INFO @ Mon, 03 Jun 2019 07:51:06: 6000000 INFO @ Mon, 03 Jun 2019 07:51:12: 8000000 INFO @ Mon, 03 Jun 2019 07:51:15: 7000000 INFO @ Mon, 03 Jun 2019 07:51:17: 7000000 INFO @ Mon, 03 Jun 2019 07:51:20: 9000000 INFO @ Mon, 03 Jun 2019 07:51:25: 8000000 INFO @ Mon, 03 Jun 2019 07:51:27: 8000000 INFO @ Mon, 03 Jun 2019 07:51:29: 10000000 INFO @ Mon, 03 Jun 2019 07:51:36: 9000000 INFO @ Mon, 03 Jun 2019 07:51:38: 11000000 INFO @ Mon, 03 Jun 2019 07:51:38: 9000000 INFO @ Mon, 03 Jun 2019 07:51:47: 10000000 INFO @ Mon, 03 Jun 2019 07:51:49: 12000000 INFO @ Mon, 03 Jun 2019 07:51:49: 10000000 INFO @ Mon, 03 Jun 2019 07:51:55: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 07:51:55: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 07:51:55: #1 total tags in treatment: 12543686 INFO @ Mon, 03 Jun 2019 07:51:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:51:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 07:51:55: #1 tags after filtering in treatment: 12543686 INFO @ Mon, 03 Jun 2019 07:51:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:51:55: #1 finished! INFO @ Mon, 03 Jun 2019 07:51:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:51:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:51:57: #2 number of paired peaks: 146 WARNING @ Mon, 03 Jun 2019 07:51:57: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Mon, 03 Jun 2019 07:51:57: start model_add_line... INFO @ Mon, 03 Jun 2019 07:51:57: start X-correlation... INFO @ Mon, 03 Jun 2019 07:51:57: end of X-cor INFO @ Mon, 03 Jun 2019 07:51:57: #2 finished! INFO @ Mon, 03 Jun 2019 07:51:57: #2 predicted fragment length is 81 bps INFO @ Mon, 03 Jun 2019 07:51:57: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 03 Jun 2019 07:51:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.10_model.r WARNING @ Mon, 03 Jun 2019 07:51:57: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:51:57: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Mon, 03 Jun 2019 07:51:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 07:51:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:51:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:51:58: 11000000 INFO @ Mon, 03 Jun 2019 07:52:01: 11000000 INFO @ Mon, 03 Jun 2019 07:52:09: 12000000 INFO @ Mon, 03 Jun 2019 07:52:12: 12000000 INFO @ Mon, 03 Jun 2019 07:52:15: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 07:52:15: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 07:52:15: #1 total tags in treatment: 12543686 INFO @ Mon, 03 Jun 2019 07:52:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:52:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 07:52:15: #1 tags after filtering in treatment: 12543686 INFO @ Mon, 03 Jun 2019 07:52:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:52:15: #1 finished! INFO @ Mon, 03 Jun 2019 07:52:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:52:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:52:16: #2 number of paired peaks: 146 WARNING @ Mon, 03 Jun 2019 07:52:16: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Mon, 03 Jun 2019 07:52:16: start model_add_line... INFO @ Mon, 03 Jun 2019 07:52:16: start X-correlation... INFO @ Mon, 03 Jun 2019 07:52:16: end of X-cor INFO @ Mon, 03 Jun 2019 07:52:16: #2 finished! INFO @ Mon, 03 Jun 2019 07:52:16: #2 predicted fragment length is 81 bps INFO @ Mon, 03 Jun 2019 07:52:16: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 03 Jun 2019 07:52:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.05_model.r WARNING @ Mon, 03 Jun 2019 07:52:16: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:52:16: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Mon, 03 Jun 2019 07:52:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 07:52:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:52:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:52:17: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 07:52:17: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 07:52:17: #1 total tags in treatment: 12543686 INFO @ Mon, 03 Jun 2019 07:52:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:52:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 07:52:18: #1 tags after filtering in treatment: 12543686 INFO @ Mon, 03 Jun 2019 07:52:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:52:18: #1 finished! INFO @ Mon, 03 Jun 2019 07:52:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:52:19: #2 number of paired peaks: 146 WARNING @ Mon, 03 Jun 2019 07:52:19: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Mon, 03 Jun 2019 07:52:19: start model_add_line... INFO @ Mon, 03 Jun 2019 07:52:19: start X-correlation... INFO @ Mon, 03 Jun 2019 07:52:19: end of X-cor INFO @ Mon, 03 Jun 2019 07:52:19: #2 finished! INFO @ Mon, 03 Jun 2019 07:52:19: #2 predicted fragment length is 81 bps INFO @ Mon, 03 Jun 2019 07:52:19: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 03 Jun 2019 07:52:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.20_model.r WARNING @ Mon, 03 Jun 2019 07:52:19: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:52:19: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Mon, 03 Jun 2019 07:52:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 07:52:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:52:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:52:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:52:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:52:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:52:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.10_summits.bed INFO @ Mon, 03 Jun 2019 07:52:52: Done! INFO @ Mon, 03 Jun 2019 07:52:52: #3 Call peaks for each chromosome... pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1613 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:52:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:53:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:53:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:53:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.05_summits.bed INFO @ Mon, 03 Jun 2019 07:53:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5859 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:53:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:53:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:53:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2870712/SRX2870712.20_summits.bed INFO @ Mon, 03 Jun 2019 07:53:14: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (525 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。