Job ID = 1295566 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,673,564 reads read : 32,673,564 reads written : 32,673,564 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: 00:10:47 32673564 reads; of these: 32673564 (100.00%) were unpaired; of these: 12904563 (39.50%) aligned 0 times 12521973 (38.32%) aligned exactly 1 time 7247028 (22.18%) aligned >1 times 60.50% overall alignment rate Time searching: 00:10:47 Overall time: 00:10:47 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] 9478094 / 19769001 = 0.4794 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 14:48:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.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 14:48:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:48:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:48:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.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 14:48:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:48:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:48:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.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 14:48:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:48:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:48:40: 1000000 INFO @ Mon, 03 Jun 2019 14:48:40: 1000000 INFO @ Mon, 03 Jun 2019 14:48:40: 1000000 INFO @ Mon, 03 Jun 2019 14:48:48: 2000000 INFO @ Mon, 03 Jun 2019 14:48:48: 2000000 INFO @ Mon, 03 Jun 2019 14:48:48: 2000000 INFO @ Mon, 03 Jun 2019 14:48:55: 3000000 INFO @ Mon, 03 Jun 2019 14:48:55: 3000000 INFO @ Mon, 03 Jun 2019 14:48:55: 3000000 INFO @ Mon, 03 Jun 2019 14:49:02: 4000000 INFO @ Mon, 03 Jun 2019 14:49:03: 4000000 INFO @ Mon, 03 Jun 2019 14:49:03: 4000000 INFO @ Mon, 03 Jun 2019 14:49:10: 5000000 INFO @ Mon, 03 Jun 2019 14:49:10: 5000000 INFO @ Mon, 03 Jun 2019 14:49:10: 5000000 INFO @ Mon, 03 Jun 2019 14:49:17: 6000000 INFO @ Mon, 03 Jun 2019 14:49:18: 6000000 INFO @ Mon, 03 Jun 2019 14:49:18: 6000000 INFO @ Mon, 03 Jun 2019 14:49:25: 7000000 INFO @ Mon, 03 Jun 2019 14:49:26: 7000000 INFO @ Mon, 03 Jun 2019 14:49:26: 7000000 INFO @ Mon, 03 Jun 2019 14:49:32: 8000000 INFO @ Mon, 03 Jun 2019 14:49:34: 8000000 INFO @ Mon, 03 Jun 2019 14:49:34: 8000000 INFO @ Mon, 03 Jun 2019 14:49:39: 9000000 INFO @ Mon, 03 Jun 2019 14:49:41: 9000000 INFO @ Mon, 03 Jun 2019 14:49:41: 9000000 INFO @ Mon, 03 Jun 2019 14:49:46: 10000000 INFO @ Mon, 03 Jun 2019 14:49:48: 10000000 INFO @ Mon, 03 Jun 2019 14:49:49: 10000000 INFO @ Mon, 03 Jun 2019 14:49:49: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 14:49:49: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 14:49:49: #1 total tags in treatment: 10290907 INFO @ Mon, 03 Jun 2019 14:49:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:49:49: #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 14:49:49: #1 tags after filtering in treatment: 10290906 INFO @ Mon, 03 Jun 2019 14:49:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:49:49: #1 finished! INFO @ Mon, 03 Jun 2019 14:49:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:49:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:49:50: #2 number of paired peaks: 1568 INFO @ Mon, 03 Jun 2019 14:49:50: start model_add_line... INFO @ Mon, 03 Jun 2019 14:49:50: start X-correlation... INFO @ Mon, 03 Jun 2019 14:49:50: end of X-cor INFO @ Mon, 03 Jun 2019 14:49:50: #2 finished! INFO @ Mon, 03 Jun 2019 14:49:50: #2 predicted fragment length is 36 bps INFO @ Mon, 03 Jun 2019 14:49:50: #2 alternative fragment length(s) may be 36 bps INFO @ Mon, 03 Jun 2019 14:49:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.10_model.r WARNING @ Mon, 03 Jun 2019 14:49:50: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:49:50: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Mon, 03 Jun 2019 14:49:50: #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 14:49:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:49:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:49:51: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 14:49:51: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 14:49:51: #1 total tags in treatment: 10290907 INFO @ Mon, 03 Jun 2019 14:49:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:49:51: #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 14:49:51: #1 tags after filtering in treatment: 10290906 INFO @ Mon, 03 Jun 2019 14:49:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:49:51: #1 finished! INFO @ Mon, 03 Jun 2019 14:49:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:49:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:49:51: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 14:49:51: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 14:49:51: #1 total tags in treatment: 10290907 INFO @ Mon, 03 Jun 2019 14:49:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:49:51: #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 14:49:51: #1 tags after filtering in treatment: 10290906 INFO @ Mon, 03 Jun 2019 14:49:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:49:51: #1 finished! INFO @ Mon, 03 Jun 2019 14:49:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:49:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:49:52: #2 number of paired peaks: 1568 INFO @ Mon, 03 Jun 2019 14:49:52: start model_add_line... INFO @ Mon, 03 Jun 2019 14:49:52: start X-correlation... INFO @ Mon, 03 Jun 2019 14:49:52: end of X-cor INFO @ Mon, 03 Jun 2019 14:49:52: #2 finished! INFO @ Mon, 03 Jun 2019 14:49:52: #2 predicted fragment length is 36 bps INFO @ Mon, 03 Jun 2019 14:49:52: #2 alternative fragment length(s) may be 36 bps INFO @ Mon, 03 Jun 2019 14:49:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.05_model.r WARNING @ Mon, 03 Jun 2019 14:49:52: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:49:52: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Mon, 03 Jun 2019 14:49:52: #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 14:49:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:49:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:49:52: #2 number of paired peaks: 1568 INFO @ Mon, 03 Jun 2019 14:49:52: start model_add_line... INFO @ Mon, 03 Jun 2019 14:49:52: start X-correlation... INFO @ Mon, 03 Jun 2019 14:49:52: end of X-cor INFO @ Mon, 03 Jun 2019 14:49:52: #2 finished! INFO @ Mon, 03 Jun 2019 14:49:52: #2 predicted fragment length is 36 bps INFO @ Mon, 03 Jun 2019 14:49:52: #2 alternative fragment length(s) may be 36 bps INFO @ Mon, 03 Jun 2019 14:49:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.20_model.r WARNING @ Mon, 03 Jun 2019 14:49:52: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:49:52: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Mon, 03 Jun 2019 14:49:52: #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 14:49:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:49:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:50:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:50:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:50:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:50:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:50:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:50:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.10_summits.bed INFO @ Mon, 03 Jun 2019 14:50:33: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4150 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:50:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:50:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:50:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.05_summits.bed INFO @ Mon, 03 Jun 2019 14:50:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:50:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:50:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX367040/SRX367040.20_summits.bed INFO @ Mon, 03 Jun 2019 14:50:35: Done! INFO @ Mon, 03 Jun 2019 14:50:35: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1166 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8449 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。