Job ID = 1293283 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,585,231 reads read : 25,585,231 reads written : 25,585,231 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: 00:08:10 25585231 reads; of these: 25585231 (100.00%) were unpaired; of these: 864042 (3.38%) aligned 0 times 18613307 (72.75%) aligned exactly 1 time 6107882 (23.87%) aligned >1 times 96.62% overall alignment rate Time searching: 00:08:10 Overall time: 00:08:10 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] 9148792 / 24721189 = 0.3701 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 @ Sun, 02 Jun 2019 23:00:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.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 @ Sun, 02 Jun 2019 23:00:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:00:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:00:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.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 @ Sun, 02 Jun 2019 23:00:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:00:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:00:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.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 @ Sun, 02 Jun 2019 23:00:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:00:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:00:18: 1000000 INFO @ Sun, 02 Jun 2019 23:00:19: 1000000 INFO @ Sun, 02 Jun 2019 23:00:21: 1000000 INFO @ Sun, 02 Jun 2019 23:00:26: 2000000 INFO @ Sun, 02 Jun 2019 23:00:28: 2000000 INFO @ Sun, 02 Jun 2019 23:00:32: 2000000 INFO @ Sun, 02 Jun 2019 23:00:34: 3000000 INFO @ Sun, 02 Jun 2019 23:00:38: 3000000 INFO @ Sun, 02 Jun 2019 23:00:42: 3000000 INFO @ Sun, 02 Jun 2019 23:00:43: 4000000 INFO @ Sun, 02 Jun 2019 23:00:47: 4000000 INFO @ Sun, 02 Jun 2019 23:00:51: 5000000 INFO @ Sun, 02 Jun 2019 23:00:53: 4000000 INFO @ Sun, 02 Jun 2019 23:00:56: 5000000 INFO @ Sun, 02 Jun 2019 23:01:00: 6000000 INFO @ Sun, 02 Jun 2019 23:01:05: 5000000 INFO @ Sun, 02 Jun 2019 23:01:06: 6000000 INFO @ Sun, 02 Jun 2019 23:01:08: 7000000 INFO @ Sun, 02 Jun 2019 23:01:15: 7000000 INFO @ Sun, 02 Jun 2019 23:01:15: 6000000 INFO @ Sun, 02 Jun 2019 23:01:16: 8000000 INFO @ Sun, 02 Jun 2019 23:01:23: 9000000 INFO @ Sun, 02 Jun 2019 23:01:24: 8000000 INFO @ Sun, 02 Jun 2019 23:01:26: 7000000 INFO @ Sun, 02 Jun 2019 23:01:31: 10000000 INFO @ Sun, 02 Jun 2019 23:01:33: 9000000 INFO @ Sun, 02 Jun 2019 23:01:37: 8000000 INFO @ Sun, 02 Jun 2019 23:01:39: 11000000 INFO @ Sun, 02 Jun 2019 23:01:42: 10000000 INFO @ Sun, 02 Jun 2019 23:01:47: 12000000 INFO @ Sun, 02 Jun 2019 23:01:48: 9000000 INFO @ Sun, 02 Jun 2019 23:01:51: 11000000 INFO @ Sun, 02 Jun 2019 23:01:55: 13000000 INFO @ Sun, 02 Jun 2019 23:01:59: 10000000 INFO @ Sun, 02 Jun 2019 23:02:01: 12000000 INFO @ Sun, 02 Jun 2019 23:02:03: 14000000 INFO @ Sun, 02 Jun 2019 23:02:09: 13000000 INFO @ Sun, 02 Jun 2019 23:02:10: 11000000 INFO @ Sun, 02 Jun 2019 23:02:11: 15000000 INFO @ Sun, 02 Jun 2019 23:02:16: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:02:16: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:02:16: #1 total tags in treatment: 15572397 INFO @ Sun, 02 Jun 2019 23:02:16: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:02:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:02:16: #1 tags after filtering in treatment: 15572397 INFO @ Sun, 02 Jun 2019 23:02:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:02:16: #1 finished! INFO @ Sun, 02 Jun 2019 23:02:16: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:02:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:02:17: #2 number of paired peaks: 374 WARNING @ Sun, 02 Jun 2019 23:02:17: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Sun, 02 Jun 2019 23:02:17: start model_add_line... INFO @ Sun, 02 Jun 2019 23:02:17: start X-correlation... INFO @ Sun, 02 Jun 2019 23:02:18: end of X-cor INFO @ Sun, 02 Jun 2019 23:02:18: #2 finished! INFO @ Sun, 02 Jun 2019 23:02:18: #2 predicted fragment length is 40 bps INFO @ Sun, 02 Jun 2019 23:02:18: #2 alternative fragment length(s) may be 40 bps INFO @ Sun, 02 Jun 2019 23:02:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.10_model.r WARNING @ Sun, 02 Jun 2019 23:02:18: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:02:18: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Sun, 02 Jun 2019 23:02:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:02:18: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:02:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:02:18: 14000000 INFO @ Sun, 02 Jun 2019 23:02:20: 12000000 INFO @ Sun, 02 Jun 2019 23:02:27: 15000000 INFO @ Sun, 02 Jun 2019 23:02:31: 13000000 INFO @ Sun, 02 Jun 2019 23:02:32: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:02:32: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:02:32: #1 total tags in treatment: 15572397 INFO @ Sun, 02 Jun 2019 23:02:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:02:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:02:32: #1 tags after filtering in treatment: 15572397 INFO @ Sun, 02 Jun 2019 23:02:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:02:32: #1 finished! INFO @ Sun, 02 Jun 2019 23:02:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:02:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:02:34: #2 number of paired peaks: 374 WARNING @ Sun, 02 Jun 2019 23:02:34: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Sun, 02 Jun 2019 23:02:34: start model_add_line... INFO @ Sun, 02 Jun 2019 23:02:34: start X-correlation... INFO @ Sun, 02 Jun 2019 23:02:34: end of X-cor INFO @ Sun, 02 Jun 2019 23:02:34: #2 finished! INFO @ Sun, 02 Jun 2019 23:02:34: #2 predicted fragment length is 40 bps INFO @ Sun, 02 Jun 2019 23:02:34: #2 alternative fragment length(s) may be 40 bps INFO @ Sun, 02 Jun 2019 23:02:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.05_model.r WARNING @ Sun, 02 Jun 2019 23:02:34: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:02:34: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Sun, 02 Jun 2019 23:02:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:02:34: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:02:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:02:40: 14000000 INFO @ Sun, 02 Jun 2019 23:02:50: 15000000 INFO @ Sun, 02 Jun 2019 23:02:56: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:02:56: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:02:56: #1 total tags in treatment: 15572397 INFO @ Sun, 02 Jun 2019 23:02:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:02:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:02:56: #1 tags after filtering in treatment: 15572397 INFO @ Sun, 02 Jun 2019 23:02:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:02:56: #1 finished! INFO @ Sun, 02 Jun 2019 23:02:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:02:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:02:58: #2 number of paired peaks: 374 WARNING @ Sun, 02 Jun 2019 23:02:58: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Sun, 02 Jun 2019 23:02:58: start model_add_line... INFO @ Sun, 02 Jun 2019 23:02:58: start X-correlation... INFO @ Sun, 02 Jun 2019 23:02:58: end of X-cor INFO @ Sun, 02 Jun 2019 23:02:58: #2 finished! INFO @ Sun, 02 Jun 2019 23:02:58: #2 predicted fragment length is 40 bps INFO @ Sun, 02 Jun 2019 23:02:58: #2 alternative fragment length(s) may be 40 bps INFO @ Sun, 02 Jun 2019 23:02:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.20_model.r WARNING @ Sun, 02 Jun 2019 23:02:58: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:02:58: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Sun, 02 Jun 2019 23:02:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:02:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:02:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:02:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:03:16: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:03:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:03:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:03:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.10_summits.bed INFO @ Sun, 02 Jun 2019 23:03:19: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (1395 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:03:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:03:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:03:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.05_summits.bed INFO @ Sun, 02 Jun 2019 23:03:38: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1758 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:03:40: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:04:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:04:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:04:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011419/ERX011419.20_summits.bed INFO @ Sun, 02 Jun 2019 23:04:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (948 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。