Job ID = 4178578 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,521,637 reads read : 35,043,274 reads written : 17,521,637 reads 0-length : 17,521,637 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: 00:05:49 17521637 reads; of these: 17521637 (100.00%) were unpaired; of these: 2685963 (15.33%) aligned 0 times 10879437 (62.09%) aligned exactly 1 time 3956237 (22.58%) aligned >1 times 84.67% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 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] 4745283 / 14835674 = 0.3199 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:22:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.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 @ Thu, 05 Dec 2019 13:22:29: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:22:29: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:22:39: 1000000 INFO @ Thu, 05 Dec 2019 13:22:48: 2000000 INFO @ Thu, 05 Dec 2019 13:22:57: 3000000 INFO @ Thu, 05 Dec 2019 13:22:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.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 @ Thu, 05 Dec 2019 13:22:58: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:22:58: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:23:07: 4000000 INFO @ Thu, 05 Dec 2019 13:23:08: 1000000 INFO @ Thu, 05 Dec 2019 13:23:16: 5000000 INFO @ Thu, 05 Dec 2019 13:23:17: 2000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:23:26: 6000000 INFO @ Thu, 05 Dec 2019 13:23:26: 3000000 INFO @ Thu, 05 Dec 2019 13:23:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.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 @ Thu, 05 Dec 2019 13:23:28: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:23:28: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:23:35: 7000000 INFO @ Thu, 05 Dec 2019 13:23:35: 4000000 INFO @ Thu, 05 Dec 2019 13:23:38: 1000000 INFO @ Thu, 05 Dec 2019 13:23:44: 8000000 INFO @ Thu, 05 Dec 2019 13:23:44: 5000000 INFO @ Thu, 05 Dec 2019 13:23:49: 2000000 INFO @ Thu, 05 Dec 2019 13:23:53: 9000000 INFO @ Thu, 05 Dec 2019 13:23:54: 6000000 INFO @ Thu, 05 Dec 2019 13:23:59: 3000000 INFO @ Thu, 05 Dec 2019 13:24:03: 10000000 INFO @ Thu, 05 Dec 2019 13:24:03: 7000000 INFO @ Thu, 05 Dec 2019 13:24:04: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:24:04: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:24:04: #1 total tags in treatment: 10090391 INFO @ Thu, 05 Dec 2019 13:24:04: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:24:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:24:04: #1 tags after filtering in treatment: 10090391 INFO @ Thu, 05 Dec 2019 13:24:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:24:04: #1 finished! INFO @ Thu, 05 Dec 2019 13:24:04: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:24:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:24:05: #2 number of paired peaks: 163 WARNING @ Thu, 05 Dec 2019 13:24:05: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Thu, 05 Dec 2019 13:24:05: start model_add_line... INFO @ Thu, 05 Dec 2019 13:24:05: start X-correlation... INFO @ Thu, 05 Dec 2019 13:24:05: end of X-cor INFO @ Thu, 05 Dec 2019 13:24:05: #2 finished! INFO @ Thu, 05 Dec 2019 13:24:05: #2 predicted fragment length is 51 bps INFO @ Thu, 05 Dec 2019 13:24:05: #2 alternative fragment length(s) may be 4,51,539 bps INFO @ Thu, 05 Dec 2019 13:24:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.05_model.r WARNING @ Thu, 05 Dec 2019 13:24:05: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:24:05: #2 You may need to consider one of the other alternative d(s): 4,51,539 WARNING @ Thu, 05 Dec 2019 13:24:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:24:05: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:24:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:24:09: 4000000 INFO @ Thu, 05 Dec 2019 13:24:11: 8000000 INFO @ Thu, 05 Dec 2019 13:24:18: 5000000 INFO @ Thu, 05 Dec 2019 13:24:20: 9000000 INFO @ Thu, 05 Dec 2019 13:24:27: 6000000 INFO @ Thu, 05 Dec 2019 13:24:30: 10000000 INFO @ Thu, 05 Dec 2019 13:24:31: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:24:31: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:24:31: #1 total tags in treatment: 10090391 INFO @ Thu, 05 Dec 2019 13:24:31: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:24:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:24:32: #1 tags after filtering in treatment: 10090391 INFO @ Thu, 05 Dec 2019 13:24:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:24:32: #1 finished! INFO @ Thu, 05 Dec 2019 13:24:32: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:24:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:24:33: #2 number of paired peaks: 163 WARNING @ Thu, 05 Dec 2019 13:24:33: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Thu, 05 Dec 2019 13:24:33: start model_add_line... INFO @ Thu, 05 Dec 2019 13:24:33: start X-correlation... INFO @ Thu, 05 Dec 2019 13:24:33: end of X-cor INFO @ Thu, 05 Dec 2019 13:24:33: #2 finished! INFO @ Thu, 05 Dec 2019 13:24:33: #2 predicted fragment length is 51 bps INFO @ Thu, 05 Dec 2019 13:24:33: #2 alternative fragment length(s) may be 4,51,539 bps INFO @ Thu, 05 Dec 2019 13:24:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.10_model.r WARNING @ Thu, 05 Dec 2019 13:24:33: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:24:33: #2 You may need to consider one of the other alternative d(s): 4,51,539 WARNING @ Thu, 05 Dec 2019 13:24:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:24:33: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:24:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:24:34: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:24:39: 7000000 INFO @ Thu, 05 Dec 2019 13:24:48: 8000000 INFO @ Thu, 05 Dec 2019 13:24:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:24:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:24:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.05_summits.bed INFO @ Thu, 05 Dec 2019 13:24:49: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1321 records, 4 fields): 85 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:24:57: 9000000 INFO @ Thu, 05 Dec 2019 13:25:02: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:25:06: 10000000 INFO @ Thu, 05 Dec 2019 13:25:07: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:25:07: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:25:07: #1 total tags in treatment: 10090391 INFO @ Thu, 05 Dec 2019 13:25:07: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:25:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:25:08: #1 tags after filtering in treatment: 10090391 INFO @ Thu, 05 Dec 2019 13:25:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:25:08: #1 finished! INFO @ Thu, 05 Dec 2019 13:25:08: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:25:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:25:09: #2 number of paired peaks: 163 WARNING @ Thu, 05 Dec 2019 13:25:09: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Thu, 05 Dec 2019 13:25:09: start model_add_line... INFO @ Thu, 05 Dec 2019 13:25:09: start X-correlation... INFO @ Thu, 05 Dec 2019 13:25:09: end of X-cor INFO @ Thu, 05 Dec 2019 13:25:09: #2 finished! INFO @ Thu, 05 Dec 2019 13:25:09: #2 predicted fragment length is 51 bps INFO @ Thu, 05 Dec 2019 13:25:09: #2 alternative fragment length(s) may be 4,51,539 bps INFO @ Thu, 05 Dec 2019 13:25:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.20_model.r WARNING @ Thu, 05 Dec 2019 13:25:09: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:25:09: #2 You may need to consider one of the other alternative d(s): 4,51,539 WARNING @ Thu, 05 Dec 2019 13:25:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:25:09: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:25:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:25:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:25:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:25:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.10_summits.bed INFO @ Thu, 05 Dec 2019 13:25:17: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1013 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:25:38: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:25:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:25:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:25:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827842/SRX5827842.20_summits.bed INFO @ Thu, 05 Dec 2019 13:25:54: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (631 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。