Job ID = 1294169 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,988,242 reads read : 10,988,242 reads written : 10,988,242 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: 00:03:57 10988242 reads; of these: 10988242 (100.00%) were unpaired; of these: 3540934 (32.22%) aligned 0 times 4175849 (38.00%) aligned exactly 1 time 3271459 (29.77%) aligned >1 times 67.78% overall alignment rate Time searching: 00:03:57 Overall time: 00:03:57 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_rmdupse_core] 2127392 / 7447308 = 0.2857 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 05:18:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.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 05:18:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:18:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:18:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.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 05:18:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:18:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:18:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.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 05:18:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:18:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:18:47: 1000000 INFO @ Mon, 03 Jun 2019 05:18:47: 1000000 INFO @ Mon, 03 Jun 2019 05:18:48: 1000000 INFO @ Mon, 03 Jun 2019 05:18:56: 2000000 INFO @ Mon, 03 Jun 2019 05:18:56: 2000000 INFO @ Mon, 03 Jun 2019 05:18:57: 2000000 INFO @ Mon, 03 Jun 2019 05:19:04: 3000000 INFO @ Mon, 03 Jun 2019 05:19:04: 3000000 INFO @ Mon, 03 Jun 2019 05:19:05: 3000000 INFO @ Mon, 03 Jun 2019 05:19:12: 4000000 INFO @ Mon, 03 Jun 2019 05:19:12: 4000000 INFO @ Mon, 03 Jun 2019 05:19:14: 4000000 INFO @ Mon, 03 Jun 2019 05:19:21: 5000000 INFO @ Mon, 03 Jun 2019 05:19:21: 5000000 INFO @ Mon, 03 Jun 2019 05:19:22: 5000000 INFO @ Mon, 03 Jun 2019 05:19:23: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:19:23: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:19:23: #1 total tags in treatment: 5319916 INFO @ Mon, 03 Jun 2019 05:19:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:19:23: #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 05:19:23: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:19:23: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:19:23: #1 total tags in treatment: 5319916 INFO @ Mon, 03 Jun 2019 05:19:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:19:23: #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 05:19:24: #1 tags after filtering in treatment: 5319916 INFO @ Mon, 03 Jun 2019 05:19:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:19:24: #1 finished! INFO @ Mon, 03 Jun 2019 05:19:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:19:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:19:24: #1 tags after filtering in treatment: 5319916 INFO @ Mon, 03 Jun 2019 05:19:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:19:24: #1 finished! INFO @ Mon, 03 Jun 2019 05:19:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:19:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:19:24: #2 number of paired peaks: 634 WARNING @ Mon, 03 Jun 2019 05:19:24: Fewer paired peaks (634) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 634 pairs to build model! INFO @ Mon, 03 Jun 2019 05:19:24: start model_add_line... INFO @ Mon, 03 Jun 2019 05:19:24: #2 number of paired peaks: 634 WARNING @ Mon, 03 Jun 2019 05:19:24: Fewer paired peaks (634) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 634 pairs to build model! INFO @ Mon, 03 Jun 2019 05:19:24: start model_add_line... INFO @ Mon, 03 Jun 2019 05:19:24: start X-correlation... INFO @ Mon, 03 Jun 2019 05:19:24: start X-correlation... INFO @ Mon, 03 Jun 2019 05:19:24: end of X-cor INFO @ Mon, 03 Jun 2019 05:19:24: #2 finished! INFO @ Mon, 03 Jun 2019 05:19:24: #2 predicted fragment length is 55 bps INFO @ Mon, 03 Jun 2019 05:19:24: #2 alternative fragment length(s) may be 55 bps INFO @ Mon, 03 Jun 2019 05:19:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.20_model.r WARNING @ Mon, 03 Jun 2019 05:19:24: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:19:24: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Mon, 03 Jun 2019 05:19:24: #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 05:19:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:19:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:19:24: end of X-cor INFO @ Mon, 03 Jun 2019 05:19:24: #2 finished! INFO @ Mon, 03 Jun 2019 05:19:24: #2 predicted fragment length is 55 bps INFO @ Mon, 03 Jun 2019 05:19:24: #2 alternative fragment length(s) may be 55 bps INFO @ Mon, 03 Jun 2019 05:19:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.05_model.r WARNING @ Mon, 03 Jun 2019 05:19:24: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:19:24: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Mon, 03 Jun 2019 05:19:24: #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 05:19:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:19:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:19:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:19:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:19:25: #1 total tags in treatment: 5319916 INFO @ Mon, 03 Jun 2019 05:19:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:19:25: #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 05:19:25: #1 tags after filtering in treatment: 5319916 INFO @ Mon, 03 Jun 2019 05:19:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:19:25: #1 finished! INFO @ Mon, 03 Jun 2019 05:19:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:19:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:19:25: #2 number of paired peaks: 634 WARNING @ Mon, 03 Jun 2019 05:19:25: Fewer paired peaks (634) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 634 pairs to build model! INFO @ Mon, 03 Jun 2019 05:19:25: start model_add_line... INFO @ Mon, 03 Jun 2019 05:19:25: start X-correlation... INFO @ Mon, 03 Jun 2019 05:19:26: end of X-cor INFO @ Mon, 03 Jun 2019 05:19:26: #2 finished! INFO @ Mon, 03 Jun 2019 05:19:26: #2 predicted fragment length is 55 bps INFO @ Mon, 03 Jun 2019 05:19:26: #2 alternative fragment length(s) may be 55 bps INFO @ Mon, 03 Jun 2019 05:19:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.10_model.r WARNING @ Mon, 03 Jun 2019 05:19:26: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:19:26: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Mon, 03 Jun 2019 05:19:26: #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 05:19:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:19:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:19:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:19:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:19:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:19:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:19:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:19:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.20_summits.bed INFO @ Mon, 03 Jun 2019 05:19:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:19:48: Done! INFO @ Mon, 03 Jun 2019 05:19:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:19:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.05_summits.bed INFO @ Mon, 03 Jun 2019 05:19:48: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (356 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2503 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:19:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:19:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:19:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193629/SRX193629.10_summits.bed INFO @ Mon, 03 Jun 2019 05:19:49: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (819 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。