Job ID = 1295799 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,010,113 reads read : 14,010,113 reads written : 14,010,113 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: 00:05:18 14010113 reads; of these: 14010113 (100.00%) were unpaired; of these: 4267431 (30.46%) aligned 0 times 6911915 (49.34%) aligned exactly 1 time 2830767 (20.21%) aligned >1 times 69.54% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 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] 1459209 / 9742682 = 0.1498 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 15:50:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.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 15:50:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:50:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:50:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.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 15:50:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:50:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:50:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.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 15:50:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:50:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:50:24: 1000000 INFO @ Mon, 03 Jun 2019 15:50:25: 1000000 INFO @ Mon, 03 Jun 2019 15:50:26: 1000000 INFO @ Mon, 03 Jun 2019 15:50:32: 2000000 INFO @ Mon, 03 Jun 2019 15:50:33: 2000000 INFO @ Mon, 03 Jun 2019 15:50:36: 2000000 INFO @ Mon, 03 Jun 2019 15:50:39: 3000000 INFO @ Mon, 03 Jun 2019 15:50:41: 3000000 INFO @ Mon, 03 Jun 2019 15:50:45: 3000000 INFO @ Mon, 03 Jun 2019 15:50:47: 4000000 INFO @ Mon, 03 Jun 2019 15:50:49: 4000000 INFO @ Mon, 03 Jun 2019 15:50:54: 4000000 INFO @ Mon, 03 Jun 2019 15:50:54: 5000000 INFO @ Mon, 03 Jun 2019 15:50:56: 5000000 INFO @ Mon, 03 Jun 2019 15:51:02: 6000000 INFO @ Mon, 03 Jun 2019 15:51:03: 5000000 INFO @ Mon, 03 Jun 2019 15:51:04: 6000000 INFO @ Mon, 03 Jun 2019 15:51:10: 7000000 INFO @ Mon, 03 Jun 2019 15:51:12: 6000000 INFO @ Mon, 03 Jun 2019 15:51:12: 7000000 INFO @ Mon, 03 Jun 2019 15:51:18: 8000000 INFO @ Mon, 03 Jun 2019 15:51:20: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:51:20: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:51:20: #1 total tags in treatment: 8283473 INFO @ Mon, 03 Jun 2019 15:51:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:51:20: #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 15:51:21: #1 tags after filtering in treatment: 8283473 INFO @ Mon, 03 Jun 2019 15:51:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:51:21: #1 finished! INFO @ Mon, 03 Jun 2019 15:51:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:51:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:51:21: 8000000 INFO @ Mon, 03 Jun 2019 15:51:21: 7000000 INFO @ Mon, 03 Jun 2019 15:51:21: #2 number of paired peaks: 540 WARNING @ Mon, 03 Jun 2019 15:51:21: Fewer paired peaks (540) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 540 pairs to build model! INFO @ Mon, 03 Jun 2019 15:51:21: start model_add_line... INFO @ Mon, 03 Jun 2019 15:51:21: start X-correlation... INFO @ Mon, 03 Jun 2019 15:51:22: end of X-cor INFO @ Mon, 03 Jun 2019 15:51:22: #2 finished! INFO @ Mon, 03 Jun 2019 15:51:22: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 15:51:22: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 15:51:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.20_model.r WARNING @ Mon, 03 Jun 2019 15:51:22: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:51:22: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 15:51:22: #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 15:51:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:51:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:51:23: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:51:23: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:51:23: #1 total tags in treatment: 8283473 INFO @ Mon, 03 Jun 2019 15:51:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:51:23: #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 15:51:23: #1 tags after filtering in treatment: 8283473 INFO @ Mon, 03 Jun 2019 15:51:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:51:23: #1 finished! INFO @ Mon, 03 Jun 2019 15:51:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:51:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:51:24: #2 number of paired peaks: 540 WARNING @ Mon, 03 Jun 2019 15:51:24: Fewer paired peaks (540) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 540 pairs to build model! INFO @ Mon, 03 Jun 2019 15:51:24: start model_add_line... INFO @ Mon, 03 Jun 2019 15:51:24: start X-correlation... INFO @ Mon, 03 Jun 2019 15:51:24: end of X-cor INFO @ Mon, 03 Jun 2019 15:51:24: #2 finished! INFO @ Mon, 03 Jun 2019 15:51:24: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 15:51:24: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 15:51:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.05_model.r WARNING @ Mon, 03 Jun 2019 15:51:24: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:51:24: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 15:51:24: #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 15:51:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:51:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:51:31: 8000000 INFO @ Mon, 03 Jun 2019 15:51:33: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:51:33: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:51:33: #1 total tags in treatment: 8283473 INFO @ Mon, 03 Jun 2019 15:51:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:51:33: #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 15:51:33: #1 tags after filtering in treatment: 8283473 INFO @ Mon, 03 Jun 2019 15:51:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:51:33: #1 finished! INFO @ Mon, 03 Jun 2019 15:51:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:51:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:51:34: #2 number of paired peaks: 540 WARNING @ Mon, 03 Jun 2019 15:51:34: Fewer paired peaks (540) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 540 pairs to build model! INFO @ Mon, 03 Jun 2019 15:51:34: start model_add_line... INFO @ Mon, 03 Jun 2019 15:51:34: start X-correlation... INFO @ Mon, 03 Jun 2019 15:51:34: end of X-cor INFO @ Mon, 03 Jun 2019 15:51:34: #2 finished! INFO @ Mon, 03 Jun 2019 15:51:34: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 15:51:34: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 15:51:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.10_model.r WARNING @ Mon, 03 Jun 2019 15:51:34: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:51:34: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 15:51:34: #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 15:51:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:51:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:51:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:51:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:51:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:51:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:51:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.20_summits.bed INFO @ Mon, 03 Jun 2019 15:51:57: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (818 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:51:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:52:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:52:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:52:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.05_summits.bed INFO @ Mon, 03 Jun 2019 15:52:01: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1512 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:52:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:52:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:52:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4563525/SRX4563525.10_summits.bed INFO @ Mon, 03 Jun 2019 15:52:10: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1043 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。