Job ID = 1294094 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,492,092 reads read : 32,492,092 reads written : 32,492,092 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: 00:09:39 32492092 reads; of these: 32492092 (100.00%) were unpaired; of these: 2171833 (6.68%) aligned 0 times 24482379 (75.35%) aligned exactly 1 time 5837880 (17.97%) aligned >1 times 93.32% overall alignment rate Time searching: 00:09:39 Overall time: 00:09:39 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] 16655665 / 30320259 = 0.5493 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 05:22:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.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 05:22:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:22:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:22:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.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 05:22:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:22:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:22:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.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 05:22:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:22:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:22:48: 1000000 INFO @ Mon, 03 Jun 2019 05:22:48: 1000000 INFO @ Mon, 03 Jun 2019 05:22:50: 1000000 INFO @ Mon, 03 Jun 2019 05:22:56: 2000000 INFO @ Mon, 03 Jun 2019 05:22:56: 2000000 INFO @ Mon, 03 Jun 2019 05:23:00: 2000000 INFO @ Mon, 03 Jun 2019 05:23:04: 3000000 INFO @ Mon, 03 Jun 2019 05:23:04: 3000000 INFO @ Mon, 03 Jun 2019 05:23:11: 3000000 INFO @ Mon, 03 Jun 2019 05:23:12: 4000000 INFO @ Mon, 03 Jun 2019 05:23:13: 4000000 INFO @ Mon, 03 Jun 2019 05:23:20: 5000000 INFO @ Mon, 03 Jun 2019 05:23:21: 5000000 INFO @ Mon, 03 Jun 2019 05:23:21: 4000000 INFO @ Mon, 03 Jun 2019 05:23:28: 6000000 INFO @ Mon, 03 Jun 2019 05:23:29: 6000000 INFO @ Mon, 03 Jun 2019 05:23:31: 5000000 INFO @ Mon, 03 Jun 2019 05:23:35: 7000000 INFO @ Mon, 03 Jun 2019 05:23:38: 7000000 INFO @ Mon, 03 Jun 2019 05:23:41: 6000000 INFO @ Mon, 03 Jun 2019 05:23:43: 8000000 INFO @ Mon, 03 Jun 2019 05:23:46: 8000000 INFO @ Mon, 03 Jun 2019 05:23:51: 9000000 INFO @ Mon, 03 Jun 2019 05:23:51: 7000000 INFO @ Mon, 03 Jun 2019 05:23:54: 9000000 INFO @ Mon, 03 Jun 2019 05:23:59: 10000000 INFO @ Mon, 03 Jun 2019 05:24:01: 8000000 INFO @ Mon, 03 Jun 2019 05:24:02: 10000000 INFO @ Mon, 03 Jun 2019 05:24:07: 11000000 INFO @ Mon, 03 Jun 2019 05:24:10: 11000000 INFO @ Mon, 03 Jun 2019 05:24:11: 9000000 INFO @ Mon, 03 Jun 2019 05:24:14: 12000000 INFO @ Mon, 03 Jun 2019 05:24:18: 12000000 INFO @ Mon, 03 Jun 2019 05:24:22: 10000000 INFO @ Mon, 03 Jun 2019 05:24:22: 13000000 INFO @ Mon, 03 Jun 2019 05:24:26: 13000000 INFO @ Mon, 03 Jun 2019 05:24:27: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:24:27: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:24:27: #1 total tags in treatment: 13664594 INFO @ Mon, 03 Jun 2019 05:24:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:24:27: #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 05:24:27: #1 tags after filtering in treatment: 13664594 INFO @ Mon, 03 Jun 2019 05:24:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:24:27: #1 finished! INFO @ Mon, 03 Jun 2019 05:24:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:24:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:24:28: #2 number of paired peaks: 360 WARNING @ Mon, 03 Jun 2019 05:24:28: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Mon, 03 Jun 2019 05:24:28: start model_add_line... INFO @ Mon, 03 Jun 2019 05:24:29: start X-correlation... INFO @ Mon, 03 Jun 2019 05:24:29: end of X-cor INFO @ Mon, 03 Jun 2019 05:24:29: #2 finished! INFO @ Mon, 03 Jun 2019 05:24:29: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 05:24:29: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 05:24:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.05_model.r WARNING @ Mon, 03 Jun 2019 05:24:29: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:24:29: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 05:24:29: #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 05:24:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:24:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:24:31: 11000000 INFO @ Mon, 03 Jun 2019 05:24:31: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:24:31: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:24:31: #1 total tags in treatment: 13664594 INFO @ Mon, 03 Jun 2019 05:24:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:24:31: #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 05:24:32: #1 tags after filtering in treatment: 13664594 INFO @ Mon, 03 Jun 2019 05:24:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:24:32: #1 finished! INFO @ Mon, 03 Jun 2019 05:24:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:24:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:24:33: #2 number of paired peaks: 360 WARNING @ Mon, 03 Jun 2019 05:24:33: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Mon, 03 Jun 2019 05:24:33: start model_add_line... INFO @ Mon, 03 Jun 2019 05:24:33: start X-correlation... INFO @ Mon, 03 Jun 2019 05:24:33: end of X-cor INFO @ Mon, 03 Jun 2019 05:24:33: #2 finished! INFO @ Mon, 03 Jun 2019 05:24:33: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 05:24:33: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 05:24:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.20_model.r WARNING @ Mon, 03 Jun 2019 05:24:33: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:24:33: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 05:24:33: #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 05:24:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:24:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:24:41: 12000000 INFO @ Mon, 03 Jun 2019 05:24:50: 13000000 INFO @ Mon, 03 Jun 2019 05:24:56: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:24:56: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:24:56: #1 total tags in treatment: 13664594 INFO @ Mon, 03 Jun 2019 05:24:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:24:56: #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 05:24:57: #1 tags after filtering in treatment: 13664594 INFO @ Mon, 03 Jun 2019 05:24:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:24:57: #1 finished! INFO @ Mon, 03 Jun 2019 05:24:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:24:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:24:58: #2 number of paired peaks: 360 WARNING @ Mon, 03 Jun 2019 05:24:58: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Mon, 03 Jun 2019 05:24:58: start model_add_line... INFO @ Mon, 03 Jun 2019 05:24:58: start X-correlation... INFO @ Mon, 03 Jun 2019 05:24:58: end of X-cor INFO @ Mon, 03 Jun 2019 05:24:58: #2 finished! INFO @ Mon, 03 Jun 2019 05:24:58: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 05:24:58: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 05:24:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.10_model.r WARNING @ Mon, 03 Jun 2019 05:24:58: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:24:58: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 05:24:58: #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 05:24:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:24:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:25:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:25:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:25:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:25:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:25:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.05_summits.bed INFO @ Mon, 03 Jun 2019 05:25:23: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (15046 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:25:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:25:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:25:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.20_summits.bed INFO @ Mon, 03 Jun 2019 05:25:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2037 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:25:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:25:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:25:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:25:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX183883/SRX183883.10_summits.bed INFO @ Mon, 03 Jun 2019 05:25:54: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5781 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。