Job ID = 1295494 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,649,545 reads read : 31,649,545 reads written : 31,649,545 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: 00:11:52 31649545 reads; of these: 31649545 (100.00%) were unpaired; of these: 25121626 (79.37%) aligned 0 times 4688105 (14.81%) aligned exactly 1 time 1839814 (5.81%) aligned >1 times 20.63% overall alignment rate Time searching: 00:11:52 Overall time: 00:11:52 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] 2287590 / 6527919 = 0.3504 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 14:17:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.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 14:17:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:17:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:17:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.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 14:17:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:17:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:17:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.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 14:17:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:17:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:17:25: 1000000 INFO @ Mon, 03 Jun 2019 14:17:25: 1000000 INFO @ Mon, 03 Jun 2019 14:17:27: 1000000 INFO @ Mon, 03 Jun 2019 14:17:37: 2000000 INFO @ Mon, 03 Jun 2019 14:17:37: 2000000 INFO @ Mon, 03 Jun 2019 14:17:42: 2000000 INFO @ Mon, 03 Jun 2019 14:17:49: 3000000 INFO @ Mon, 03 Jun 2019 14:17:49: 3000000 INFO @ Mon, 03 Jun 2019 14:17:57: 3000000 INFO @ Mon, 03 Jun 2019 14:18:00: 4000000 INFO @ Mon, 03 Jun 2019 14:18:00: 4000000 INFO @ Mon, 03 Jun 2019 14:18:03: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 14:18:03: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 14:18:03: #1 total tags in treatment: 4240329 INFO @ Mon, 03 Jun 2019 14:18:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:18:03: #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 14:18:03: #1 tags after filtering in treatment: 4240329 INFO @ Mon, 03 Jun 2019 14:18:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:18:03: #1 finished! INFO @ Mon, 03 Jun 2019 14:18:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:18:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:18:03: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 14:18:03: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 14:18:03: #1 total tags in treatment: 4240329 INFO @ Mon, 03 Jun 2019 14:18:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:18:03: #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 14:18:03: #2 number of paired peaks: 556 WARNING @ Mon, 03 Jun 2019 14:18:03: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Mon, 03 Jun 2019 14:18:03: start model_add_line... INFO @ Mon, 03 Jun 2019 14:18:03: #1 tags after filtering in treatment: 4240329 INFO @ Mon, 03 Jun 2019 14:18:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:18:03: #1 finished! INFO @ Mon, 03 Jun 2019 14:18:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:18:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:18:03: start X-correlation... INFO @ Mon, 03 Jun 2019 14:18:03: end of X-cor INFO @ Mon, 03 Jun 2019 14:18:03: #2 finished! INFO @ Mon, 03 Jun 2019 14:18:03: #2 predicted fragment length is 81 bps INFO @ Mon, 03 Jun 2019 14:18:03: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 03 Jun 2019 14:18:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.10_model.r WARNING @ Mon, 03 Jun 2019 14:18:03: #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 14:18:03: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Mon, 03 Jun 2019 14:18:03: #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 14:18:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:18:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:18:04: #2 number of paired peaks: 556 WARNING @ Mon, 03 Jun 2019 14:18:04: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Mon, 03 Jun 2019 14:18:04: start model_add_line... INFO @ Mon, 03 Jun 2019 14:18:04: start X-correlation... INFO @ Mon, 03 Jun 2019 14:18:04: end of X-cor INFO @ Mon, 03 Jun 2019 14:18:04: #2 finished! INFO @ Mon, 03 Jun 2019 14:18:04: #2 predicted fragment length is 81 bps INFO @ Mon, 03 Jun 2019 14:18:04: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 03 Jun 2019 14:18:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.05_model.r WARNING @ Mon, 03 Jun 2019 14:18:04: #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 14:18:04: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Mon, 03 Jun 2019 14:18:04: #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 14:18:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:18:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:18:11: 4000000 INFO @ Mon, 03 Jun 2019 14:18:15: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 14:18:15: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 14:18:15: #1 total tags in treatment: 4240329 INFO @ Mon, 03 Jun 2019 14:18:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:18:15: #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 14:18:15: #1 tags after filtering in treatment: 4240329 INFO @ Mon, 03 Jun 2019 14:18:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:18:15: #1 finished! INFO @ Mon, 03 Jun 2019 14:18:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:18:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:18:15: #2 number of paired peaks: 556 WARNING @ Mon, 03 Jun 2019 14:18:15: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Mon, 03 Jun 2019 14:18:15: start model_add_line... INFO @ Mon, 03 Jun 2019 14:18:15: start X-correlation... INFO @ Mon, 03 Jun 2019 14:18:15: end of X-cor INFO @ Mon, 03 Jun 2019 14:18:15: #2 finished! INFO @ Mon, 03 Jun 2019 14:18:15: #2 predicted fragment length is 81 bps INFO @ Mon, 03 Jun 2019 14:18:15: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 03 Jun 2019 14:18:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.20_model.r WARNING @ Mon, 03 Jun 2019 14:18:15: #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 14:18:15: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Mon, 03 Jun 2019 14:18:15: #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 14:18:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:18:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:18:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:18:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:18:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:18:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:18:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.10_summits.bed INFO @ Mon, 03 Jun 2019 14:18:23: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1780 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:18:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:18:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:18:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.05_summits.bed INFO @ Mon, 03 Jun 2019 14:18:23: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3231 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:18:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:18:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:18:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:18:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX348462/SRX348462.20_summits.bed INFO @ Mon, 03 Jun 2019 14:18:35: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (559 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。