Job ID = 1293743 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,160,753 reads read : 13,160,753 reads written : 13,160,753 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: 00:10:02 13160753 reads; of these: 13160753 (100.00%) were unpaired; of these: 749996 (5.70%) aligned 0 times 4089638 (31.07%) aligned exactly 1 time 8321119 (63.23%) aligned >1 times 94.30% overall alignment rate Time searching: 00:10:02 Overall time: 00:10:02 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] 2916730 / 12410757 = 0.2350 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 02:20:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.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 02:20:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:20:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:20:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.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 02:20:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:20:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:20:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.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 02:20:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:20:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:20:38: 1000000 INFO @ Mon, 03 Jun 2019 02:20:39: 1000000 INFO @ Mon, 03 Jun 2019 02:20:40: 1000000 INFO @ Mon, 03 Jun 2019 02:20:48: 2000000 INFO @ Mon, 03 Jun 2019 02:20:50: 2000000 INFO @ Mon, 03 Jun 2019 02:20:52: 2000000 INFO @ Mon, 03 Jun 2019 02:20:58: 3000000 INFO @ Mon, 03 Jun 2019 02:21:00: 3000000 INFO @ Mon, 03 Jun 2019 02:21:04: 3000000 INFO @ Mon, 03 Jun 2019 02:21:08: 4000000 INFO @ Mon, 03 Jun 2019 02:21:10: 4000000 INFO @ Mon, 03 Jun 2019 02:21:15: 4000000 INFO @ Mon, 03 Jun 2019 02:21:17: 5000000 INFO @ Mon, 03 Jun 2019 02:21:20: 5000000 INFO @ Mon, 03 Jun 2019 02:21:27: 5000000 INFO @ Mon, 03 Jun 2019 02:21:27: 6000000 INFO @ Mon, 03 Jun 2019 02:21:29: 6000000 INFO @ Mon, 03 Jun 2019 02:21:37: 7000000 INFO @ Mon, 03 Jun 2019 02:21:37: 6000000 INFO @ Mon, 03 Jun 2019 02:21:39: 7000000 INFO @ Mon, 03 Jun 2019 02:21:46: 8000000 INFO @ Mon, 03 Jun 2019 02:21:48: 7000000 INFO @ Mon, 03 Jun 2019 02:21:48: 8000000 INFO @ Mon, 03 Jun 2019 02:21:56: 9000000 INFO @ Mon, 03 Jun 2019 02:21:58: 9000000 INFO @ Mon, 03 Jun 2019 02:21:59: 8000000 INFO @ Mon, 03 Jun 2019 02:22:01: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 02:22:01: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 02:22:01: #1 total tags in treatment: 9494027 INFO @ Mon, 03 Jun 2019 02:22:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:22:01: #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 02:22:01: #1 tags after filtering in treatment: 9494027 INFO @ Mon, 03 Jun 2019 02:22:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:22:01: #1 finished! INFO @ Mon, 03 Jun 2019 02:22:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:22:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:22:02: #2 number of paired peaks: 1081 INFO @ Mon, 03 Jun 2019 02:22:02: start model_add_line... INFO @ Mon, 03 Jun 2019 02:22:02: start X-correlation... INFO @ Mon, 03 Jun 2019 02:22:03: end of X-cor INFO @ Mon, 03 Jun 2019 02:22:03: #2 finished! INFO @ Mon, 03 Jun 2019 02:22:03: #2 predicted fragment length is 92 bps INFO @ Mon, 03 Jun 2019 02:22:03: #2 alternative fragment length(s) may be 3,92 bps INFO @ Mon, 03 Jun 2019 02:22:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.20_model.r WARNING @ Mon, 03 Jun 2019 02:22:03: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:22:03: #2 You may need to consider one of the other alternative d(s): 3,92 WARNING @ Mon, 03 Jun 2019 02:22:03: #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 02:22:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:22:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:22:03: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 02:22:03: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 02:22:03: #1 total tags in treatment: 9494027 INFO @ Mon, 03 Jun 2019 02:22:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:22:03: #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 02:22:04: #1 tags after filtering in treatment: 9494027 INFO @ Mon, 03 Jun 2019 02:22:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:22:04: #1 finished! INFO @ Mon, 03 Jun 2019 02:22:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:22:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:22:04: #2 number of paired peaks: 1081 INFO @ Mon, 03 Jun 2019 02:22:04: start model_add_line... INFO @ Mon, 03 Jun 2019 02:22:05: start X-correlation... INFO @ Mon, 03 Jun 2019 02:22:05: end of X-cor INFO @ Mon, 03 Jun 2019 02:22:05: #2 finished! INFO @ Mon, 03 Jun 2019 02:22:05: #2 predicted fragment length is 92 bps INFO @ Mon, 03 Jun 2019 02:22:05: #2 alternative fragment length(s) may be 3,92 bps INFO @ Mon, 03 Jun 2019 02:22:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.10_model.r WARNING @ Mon, 03 Jun 2019 02:22:05: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:22:05: #2 You may need to consider one of the other alternative d(s): 3,92 WARNING @ Mon, 03 Jun 2019 02:22:05: #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 02:22:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:22:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:22:11: 9000000 INFO @ Mon, 03 Jun 2019 02:22:17: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 02:22:17: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 02:22:17: #1 total tags in treatment: 9494027 INFO @ Mon, 03 Jun 2019 02:22:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:22:17: #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 02:22:17: #1 tags after filtering in treatment: 9494027 INFO @ Mon, 03 Jun 2019 02:22:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:22:17: #1 finished! INFO @ Mon, 03 Jun 2019 02:22:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:22:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:22:18: #2 number of paired peaks: 1081 INFO @ Mon, 03 Jun 2019 02:22:18: start model_add_line... INFO @ Mon, 03 Jun 2019 02:22:18: start X-correlation... INFO @ Mon, 03 Jun 2019 02:22:18: end of X-cor INFO @ Mon, 03 Jun 2019 02:22:18: #2 finished! INFO @ Mon, 03 Jun 2019 02:22:18: #2 predicted fragment length is 92 bps INFO @ Mon, 03 Jun 2019 02:22:18: #2 alternative fragment length(s) may be 3,92 bps INFO @ Mon, 03 Jun 2019 02:22:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.05_model.r WARNING @ Mon, 03 Jun 2019 02:22:18: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:22:18: #2 You may need to consider one of the other alternative d(s): 3,92 WARNING @ Mon, 03 Jun 2019 02:22:18: #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 02:22:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:22:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:22:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:22:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:22:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:22:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:22:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.20_summits.bed INFO @ Mon, 03 Jun 2019 02:22:43: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (276 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:22:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:22:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:22:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.10_summits.bed INFO @ Mon, 03 Jun 2019 02:22:45: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1844 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:22:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:22:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:23:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:23:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1120689/SRX1120689.05_summits.bed INFO @ Mon, 03 Jun 2019 02:23:00: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7793 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。