Job ID = 1293686 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,077,117 reads read : 7,077,117 reads written : 7,077,117 spots read : 2,770,491 reads read : 2,770,491 reads written : 2,770,491 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: 00:01:23 9847608 reads; of these: 9847608 (100.00%) were unpaired; of these: 7074463 (71.84%) aligned 0 times 2256262 (22.91%) aligned exactly 1 time 516883 (5.25%) aligned >1 times 28.16% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 436734 / 2773145 = 0.1575 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 01:34:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.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 01:34:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:34:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:34:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.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 01:34:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.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 01:34:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:34:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:34:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:34:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:35:04: 1000000 INFO @ Mon, 03 Jun 2019 01:35:06: 1000000 INFO @ Mon, 03 Jun 2019 01:35:07: 1000000 INFO @ Mon, 03 Jun 2019 01:35:11: 2000000 INFO @ Mon, 03 Jun 2019 01:35:13: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 01:35:13: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 01:35:13: #1 total tags in treatment: 2336411 INFO @ Mon, 03 Jun 2019 01:35:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:35:13: #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 01:35:13: #1 tags after filtering in treatment: 2336411 INFO @ Mon, 03 Jun 2019 01:35:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:35:13: #1 finished! INFO @ Mon, 03 Jun 2019 01:35:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:35:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:35:14: #2 number of paired peaks: 389 WARNING @ Mon, 03 Jun 2019 01:35:14: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Mon, 03 Jun 2019 01:35:14: start model_add_line... INFO @ Mon, 03 Jun 2019 01:35:14: start X-correlation... INFO @ Mon, 03 Jun 2019 01:35:14: end of X-cor INFO @ Mon, 03 Jun 2019 01:35:14: #2 finished! INFO @ Mon, 03 Jun 2019 01:35:14: #2 predicted fragment length is 71 bps INFO @ Mon, 03 Jun 2019 01:35:14: #2 alternative fragment length(s) may be 71 bps INFO @ Mon, 03 Jun 2019 01:35:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.10_model.r WARNING @ Mon, 03 Jun 2019 01:35:14: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:35:14: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Mon, 03 Jun 2019 01:35:14: #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 01:35:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:35:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:35:14: 2000000 INFO @ Mon, 03 Jun 2019 01:35:16: 2000000 INFO @ Mon, 03 Jun 2019 01:35:17: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 01:35:17: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 01:35:17: #1 total tags in treatment: 2336411 INFO @ Mon, 03 Jun 2019 01:35:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:35:17: #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 01:35:17: #1 tags after filtering in treatment: 2336411 INFO @ Mon, 03 Jun 2019 01:35:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:35:17: #1 finished! INFO @ Mon, 03 Jun 2019 01:35:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:35:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:35:17: #2 number of paired peaks: 389 WARNING @ Mon, 03 Jun 2019 01:35:17: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Mon, 03 Jun 2019 01:35:17: start model_add_line... INFO @ Mon, 03 Jun 2019 01:35:17: start X-correlation... INFO @ Mon, 03 Jun 2019 01:35:17: end of X-cor INFO @ Mon, 03 Jun 2019 01:35:17: #2 finished! INFO @ Mon, 03 Jun 2019 01:35:17: #2 predicted fragment length is 71 bps INFO @ Mon, 03 Jun 2019 01:35:17: #2 alternative fragment length(s) may be 71 bps INFO @ Mon, 03 Jun 2019 01:35:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.20_model.r WARNING @ Mon, 03 Jun 2019 01:35:17: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:35:17: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Mon, 03 Jun 2019 01:35:17: #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 01:35:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:35:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:35:19: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 01:35:19: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 01:35:19: #1 total tags in treatment: 2336411 INFO @ Mon, 03 Jun 2019 01:35:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:35:19: #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 01:35:19: #1 tags after filtering in treatment: 2336411 INFO @ Mon, 03 Jun 2019 01:35:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:35:19: #1 finished! INFO @ Mon, 03 Jun 2019 01:35:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:35:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:35:19: #2 number of paired peaks: 389 WARNING @ Mon, 03 Jun 2019 01:35:19: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Mon, 03 Jun 2019 01:35:19: start model_add_line... INFO @ Mon, 03 Jun 2019 01:35:19: start X-correlation... INFO @ Mon, 03 Jun 2019 01:35:19: end of X-cor INFO @ Mon, 03 Jun 2019 01:35:19: #2 finished! INFO @ Mon, 03 Jun 2019 01:35:19: #2 predicted fragment length is 71 bps INFO @ Mon, 03 Jun 2019 01:35:19: #2 alternative fragment length(s) may be 71 bps INFO @ Mon, 03 Jun 2019 01:35:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.05_model.r WARNING @ Mon, 03 Jun 2019 01:35:19: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:35:19: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Mon, 03 Jun 2019 01:35:19: #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 01:35:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:35:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:35:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:35:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:35:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:35:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:35:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.10_summits.bed INFO @ Mon, 03 Jun 2019 01:35:24: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (206 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:35:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:35:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:35:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:35:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.20_summits.bed INFO @ Mon, 03 Jun 2019 01:35:28: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (69 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:35:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:35:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:35:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX109550/SRX109550.05_summits.bed INFO @ Mon, 03 Jun 2019 01:35:30: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (667 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。