Job ID = 1294790 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,757,525 reads read : 11,757,525 reads written : 11,757,525 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:05:25 11757525 reads; of these: 11757525 (100.00%) were unpaired; of these: 440135 (3.74%) aligned 0 times 7992114 (67.97%) aligned exactly 1 time 3325276 (28.28%) aligned >1 times 96.26% overall alignment rate Time searching: 00:05:25 Overall time: 00:05:25 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] 1087463 / 11317390 = 0.0961 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 10:16:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.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 10:16:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:16:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:16:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.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 10:16:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:16:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:16:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.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 10:16:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:16:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:16:33: 1000000 INFO @ Mon, 03 Jun 2019 10:16:33: 1000000 INFO @ Mon, 03 Jun 2019 10:16:35: 1000000 INFO @ Mon, 03 Jun 2019 10:16:42: 2000000 INFO @ Mon, 03 Jun 2019 10:16:42: 2000000 INFO @ Mon, 03 Jun 2019 10:16:46: 2000000 INFO @ Mon, 03 Jun 2019 10:16:52: 3000000 INFO @ Mon, 03 Jun 2019 10:16:52: 3000000 INFO @ Mon, 03 Jun 2019 10:16:56: 3000000 INFO @ Mon, 03 Jun 2019 10:17:01: 4000000 INFO @ Mon, 03 Jun 2019 10:17:01: 4000000 INFO @ Mon, 03 Jun 2019 10:17:07: 4000000 INFO @ Mon, 03 Jun 2019 10:17:10: 5000000 INFO @ Mon, 03 Jun 2019 10:17:10: 5000000 INFO @ Mon, 03 Jun 2019 10:17:18: 5000000 INFO @ Mon, 03 Jun 2019 10:17:20: 6000000 INFO @ Mon, 03 Jun 2019 10:17:20: 6000000 INFO @ Mon, 03 Jun 2019 10:17:28: 6000000 INFO @ Mon, 03 Jun 2019 10:17:29: 7000000 INFO @ Mon, 03 Jun 2019 10:17:29: 7000000 INFO @ Mon, 03 Jun 2019 10:17:38: 8000000 INFO @ Mon, 03 Jun 2019 10:17:38: 8000000 INFO @ Mon, 03 Jun 2019 10:17:39: 7000000 INFO @ Mon, 03 Jun 2019 10:17:47: 9000000 INFO @ Mon, 03 Jun 2019 10:17:47: 9000000 INFO @ Mon, 03 Jun 2019 10:17:49: 8000000 INFO @ Mon, 03 Jun 2019 10:17:57: 10000000 INFO @ Mon, 03 Jun 2019 10:17:57: 10000000 INFO @ Mon, 03 Jun 2019 10:17:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:17:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:17:59: #1 total tags in treatment: 10229927 INFO @ Mon, 03 Jun 2019 10:17:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:17:59: #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 10:17:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:17:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:17:59: #1 total tags in treatment: 10229927 INFO @ Mon, 03 Jun 2019 10:17:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:17:59: #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 10:17:59: #1 tags after filtering in treatment: 10229927 INFO @ Mon, 03 Jun 2019 10:17:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:17:59: #1 finished! INFO @ Mon, 03 Jun 2019 10:17:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:17:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:17:59: #1 tags after filtering in treatment: 10229927 INFO @ Mon, 03 Jun 2019 10:17:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:17:59: #1 finished! INFO @ Mon, 03 Jun 2019 10:17:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:17:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:17:59: 9000000 INFO @ Mon, 03 Jun 2019 10:18:00: #2 number of paired peaks: 420 WARNING @ Mon, 03 Jun 2019 10:18:00: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Mon, 03 Jun 2019 10:18:00: start model_add_line... INFO @ Mon, 03 Jun 2019 10:18:00: #2 number of paired peaks: 420 WARNING @ Mon, 03 Jun 2019 10:18:00: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Mon, 03 Jun 2019 10:18:00: start model_add_line... INFO @ Mon, 03 Jun 2019 10:18:00: start X-correlation... INFO @ Mon, 03 Jun 2019 10:18:00: end of X-cor INFO @ Mon, 03 Jun 2019 10:18:00: #2 finished! INFO @ Mon, 03 Jun 2019 10:18:00: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 10:18:00: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 10:18:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.10_model.r WARNING @ Mon, 03 Jun 2019 10:18:00: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:18:00: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 10:18:00: #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 10:18:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:18:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:18:00: start X-correlation... INFO @ Mon, 03 Jun 2019 10:18:00: end of X-cor INFO @ Mon, 03 Jun 2019 10:18:00: #2 finished! INFO @ Mon, 03 Jun 2019 10:18:00: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 10:18:00: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 10:18:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.20_model.r WARNING @ Mon, 03 Jun 2019 10:18:00: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:18:00: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 10:18:00: #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 10:18:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:18:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:18:10: 10000000 INFO @ Mon, 03 Jun 2019 10:18:12: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:18:12: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:18:12: #1 total tags in treatment: 10229927 INFO @ Mon, 03 Jun 2019 10:18:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:18:12: #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 10:18:12: #1 tags after filtering in treatment: 10229927 INFO @ Mon, 03 Jun 2019 10:18:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:18:12: #1 finished! INFO @ Mon, 03 Jun 2019 10:18:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:18:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:18:13: #2 number of paired peaks: 420 WARNING @ Mon, 03 Jun 2019 10:18:13: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Mon, 03 Jun 2019 10:18:13: start model_add_line... INFO @ Mon, 03 Jun 2019 10:18:13: start X-correlation... INFO @ Mon, 03 Jun 2019 10:18:13: end of X-cor INFO @ Mon, 03 Jun 2019 10:18:13: #2 finished! INFO @ Mon, 03 Jun 2019 10:18:13: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 10:18:13: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 10:18:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.05_model.r WARNING @ Mon, 03 Jun 2019 10:18:13: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:18:13: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 10:18:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 10:18:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:18:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:18:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:18:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:18:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:18:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:18:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:18:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.20_summits.bed INFO @ Mon, 03 Jun 2019 10:18:42: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1026 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:18:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:18:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:18:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.10_summits.bed INFO @ Mon, 03 Jun 2019 10:18:43: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1601 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:18:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:18:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:18:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287880/SRX287880.05_summits.bed INFO @ Mon, 03 Jun 2019 10:18:56: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2410 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。