Job ID = 1294529 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,101,770 reads read : 24,101,770 reads written : 24,101,770 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: 00:10:04 24101770 reads; of these: 24101770 (100.00%) were unpaired; of these: 1437594 (5.96%) aligned 0 times 17009937 (70.58%) aligned exactly 1 time 5654239 (23.46%) aligned >1 times 94.04% overall alignment rate Time searching: 00:10:04 Overall time: 00:10:04 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 12 files... [bam_rmdupse_core] 3332229 / 22664176 = 0.1470 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 09:11:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.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 09:11:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:11:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:11:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.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 09:11:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:11:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:11:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.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 09:11:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:11:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:11:40: 1000000 INFO @ Mon, 03 Jun 2019 09:11:41: 1000000 INFO @ Mon, 03 Jun 2019 09:11:42: 1000000 INFO @ Mon, 03 Jun 2019 09:11:48: 2000000 INFO @ Mon, 03 Jun 2019 09:11:52: 2000000 INFO @ Mon, 03 Jun 2019 09:11:52: 2000000 INFO @ Mon, 03 Jun 2019 09:11:58: 3000000 INFO @ Mon, 03 Jun 2019 09:12:01: 3000000 INFO @ Mon, 03 Jun 2019 09:12:02: 3000000 INFO @ Mon, 03 Jun 2019 09:12:06: 4000000 INFO @ Mon, 03 Jun 2019 09:12:12: 4000000 INFO @ Mon, 03 Jun 2019 09:12:12: 4000000 INFO @ Mon, 03 Jun 2019 09:12:15: 5000000 INFO @ Mon, 03 Jun 2019 09:12:21: 5000000 INFO @ Mon, 03 Jun 2019 09:12:22: 5000000 INFO @ Mon, 03 Jun 2019 09:12:23: 6000000 INFO @ Mon, 03 Jun 2019 09:12:29: 6000000 INFO @ Mon, 03 Jun 2019 09:12:30: 6000000 INFO @ Mon, 03 Jun 2019 09:12:31: 7000000 INFO @ Mon, 03 Jun 2019 09:12:38: 7000000 INFO @ Mon, 03 Jun 2019 09:12:39: 8000000 INFO @ Mon, 03 Jun 2019 09:12:40: 7000000 INFO @ Mon, 03 Jun 2019 09:12:47: 8000000 INFO @ Mon, 03 Jun 2019 09:12:47: 9000000 INFO @ Mon, 03 Jun 2019 09:12:49: 8000000 INFO @ Mon, 03 Jun 2019 09:12:55: 9000000 INFO @ Mon, 03 Jun 2019 09:12:55: 10000000 INFO @ Mon, 03 Jun 2019 09:12:58: 9000000 INFO @ Mon, 03 Jun 2019 09:13:04: 11000000 INFO @ Mon, 03 Jun 2019 09:13:05: 10000000 INFO @ Mon, 03 Jun 2019 09:13:07: 10000000 INFO @ Mon, 03 Jun 2019 09:13:11: 12000000 INFO @ Mon, 03 Jun 2019 09:13:13: 11000000 INFO @ Mon, 03 Jun 2019 09:13:16: 11000000 INFO @ Mon, 03 Jun 2019 09:13:19: 13000000 INFO @ Mon, 03 Jun 2019 09:13:21: 12000000 INFO @ Mon, 03 Jun 2019 09:13:24: 12000000 INFO @ Mon, 03 Jun 2019 09:13:28: 14000000 INFO @ Mon, 03 Jun 2019 09:13:29: 13000000 INFO @ Mon, 03 Jun 2019 09:13:33: 13000000 INFO @ Mon, 03 Jun 2019 09:13:36: 15000000 INFO @ Mon, 03 Jun 2019 09:13:37: 14000000 INFO @ Mon, 03 Jun 2019 09:13:42: 14000000 INFO @ Mon, 03 Jun 2019 09:13:44: 16000000 INFO @ Mon, 03 Jun 2019 09:13:45: 15000000 INFO @ Mon, 03 Jun 2019 09:13:50: 15000000 INFO @ Mon, 03 Jun 2019 09:13:52: 17000000 INFO @ Mon, 03 Jun 2019 09:13:53: 16000000 INFO @ Mon, 03 Jun 2019 09:13:58: 16000000 INFO @ Mon, 03 Jun 2019 09:14:00: 18000000 INFO @ Mon, 03 Jun 2019 09:14:01: 17000000 INFO @ Mon, 03 Jun 2019 09:14:07: 17000000 INFO @ Mon, 03 Jun 2019 09:14:07: 19000000 INFO @ Mon, 03 Jun 2019 09:14:09: 18000000 INFO @ Mon, 03 Jun 2019 09:14:11: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:14:11: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:14:11: #1 total tags in treatment: 19331947 INFO @ Mon, 03 Jun 2019 09:14:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:14:11: #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 09:14:11: #1 tags after filtering in treatment: 19331947 INFO @ Mon, 03 Jun 2019 09:14:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:14:11: #1 finished! INFO @ Mon, 03 Jun 2019 09:14:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:14:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:14:13: #2 number of paired peaks: 101 WARNING @ Mon, 03 Jun 2019 09:14:13: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Mon, 03 Jun 2019 09:14:13: start model_add_line... INFO @ Mon, 03 Jun 2019 09:14:13: start X-correlation... INFO @ Mon, 03 Jun 2019 09:14:13: end of X-cor INFO @ Mon, 03 Jun 2019 09:14:13: #2 finished! INFO @ Mon, 03 Jun 2019 09:14:13: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 09:14:13: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 09:14:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.10_model.r WARNING @ Mon, 03 Jun 2019 09:14:13: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:14:13: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 09:14:13: #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 09:14:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:14:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:14:15: 18000000 INFO @ Mon, 03 Jun 2019 09:14:17: 19000000 INFO @ Mon, 03 Jun 2019 09:14:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:14:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:14:20: #1 total tags in treatment: 19331947 INFO @ Mon, 03 Jun 2019 09:14:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:14:20: #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 09:14:21: #1 tags after filtering in treatment: 19331947 INFO @ Mon, 03 Jun 2019 09:14:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:14:21: #1 finished! INFO @ Mon, 03 Jun 2019 09:14:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:14:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:14:22: #2 number of paired peaks: 101 WARNING @ Mon, 03 Jun 2019 09:14:22: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Mon, 03 Jun 2019 09:14:22: start model_add_line... INFO @ Mon, 03 Jun 2019 09:14:22: start X-correlation... INFO @ Mon, 03 Jun 2019 09:14:22: end of X-cor INFO @ Mon, 03 Jun 2019 09:14:22: #2 finished! INFO @ Mon, 03 Jun 2019 09:14:22: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 09:14:22: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 09:14:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.20_model.r WARNING @ Mon, 03 Jun 2019 09:14:22: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:14:22: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 09:14:22: #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 09:14:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:14:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:14:23: 19000000 INFO @ Mon, 03 Jun 2019 09:14:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:14:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:14:26: #1 total tags in treatment: 19331947 INFO @ Mon, 03 Jun 2019 09:14:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:14:26: #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 09:14:27: #1 tags after filtering in treatment: 19331947 INFO @ Mon, 03 Jun 2019 09:14:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:14:27: #1 finished! INFO @ Mon, 03 Jun 2019 09:14:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:14:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:14:28: #2 number of paired peaks: 101 WARNING @ Mon, 03 Jun 2019 09:14:28: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Mon, 03 Jun 2019 09:14:28: start model_add_line... INFO @ Mon, 03 Jun 2019 09:14:28: start X-correlation... INFO @ Mon, 03 Jun 2019 09:14:28: end of X-cor INFO @ Mon, 03 Jun 2019 09:14:28: #2 finished! INFO @ Mon, 03 Jun 2019 09:14:28: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 09:14:28: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 09:14:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.05_model.r WARNING @ Mon, 03 Jun 2019 09:14:28: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:14:28: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 09:14:28: #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 09:14:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:14:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:15:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:15:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:15:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:15:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:15:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:15:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.10_summits.bed INFO @ Mon, 03 Jun 2019 09:15:25: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1721 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:15:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:15:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:15:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.20_summits.bed INFO @ Mon, 03 Jun 2019 09:15:34: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1253 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:15:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:15:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:15:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287721/SRX287721.05_summits.bed INFO @ Mon, 03 Jun 2019 09:15:39: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2073 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。