Job ID = 1293644 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,186,803 reads read : 3,186,803 reads written : 3,186,803 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: 00:01:31 3186803 reads; of these: 3186803 (100.00%) were unpaired; of these: 123309 (3.87%) aligned 0 times 1948117 (61.13%) aligned exactly 1 time 1115377 (35.00%) aligned >1 times 96.13% overall alignment rate Time searching: 00:01:31 Overall time: 00:01:31 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] 767708 / 3063494 = 0.2506 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 01:15:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.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 01:15:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:15:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:15:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.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 01:15:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:15:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:15:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.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 01:15:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:15:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:15:41: 1000000 INFO @ Mon, 03 Jun 2019 01:15:42: 1000000 INFO @ Mon, 03 Jun 2019 01:15:44: 1000000 INFO @ Mon, 03 Jun 2019 01:15:48: 2000000 INFO @ Mon, 03 Jun 2019 01:15:50: 2000000 INFO @ Mon, 03 Jun 2019 01:15:50: #1 tag size is determined as 33 bps INFO @ Mon, 03 Jun 2019 01:15:50: #1 tag size = 33 INFO @ Mon, 03 Jun 2019 01:15:50: #1 total tags in treatment: 2295786 INFO @ Mon, 03 Jun 2019 01:15:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:15:50: #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 01:15:50: #1 tags after filtering in treatment: 2295786 INFO @ Mon, 03 Jun 2019 01:15:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:15:50: #1 finished! INFO @ Mon, 03 Jun 2019 01:15:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:15:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:15:51: #2 number of paired peaks: 759 WARNING @ Mon, 03 Jun 2019 01:15:51: Fewer paired peaks (759) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 759 pairs to build model! INFO @ Mon, 03 Jun 2019 01:15:51: start model_add_line... INFO @ Mon, 03 Jun 2019 01:15:51: start X-correlation... INFO @ Mon, 03 Jun 2019 01:15:51: end of X-cor INFO @ Mon, 03 Jun 2019 01:15:51: #2 finished! INFO @ Mon, 03 Jun 2019 01:15:51: #2 predicted fragment length is 34 bps INFO @ Mon, 03 Jun 2019 01:15:51: #2 alternative fragment length(s) may be 34 bps INFO @ Mon, 03 Jun 2019 01:15:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.10_model.r WARNING @ Mon, 03 Jun 2019 01:15:51: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:15:51: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Mon, 03 Jun 2019 01:15:51: #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 01:15:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:15:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:15:52: #1 tag size is determined as 33 bps INFO @ Mon, 03 Jun 2019 01:15:52: #1 tag size = 33 INFO @ Mon, 03 Jun 2019 01:15:52: #1 total tags in treatment: 2295786 INFO @ Mon, 03 Jun 2019 01:15:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:15:52: #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 01:15:52: #1 tags after filtering in treatment: 2295786 INFO @ Mon, 03 Jun 2019 01:15:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:15:52: #1 finished! INFO @ Mon, 03 Jun 2019 01:15:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:15:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:15:52: #2 number of paired peaks: 759 WARNING @ Mon, 03 Jun 2019 01:15:52: Fewer paired peaks (759) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 759 pairs to build model! INFO @ Mon, 03 Jun 2019 01:15:52: start model_add_line... INFO @ Mon, 03 Jun 2019 01:15:52: start X-correlation... INFO @ Mon, 03 Jun 2019 01:15:52: end of X-cor INFO @ Mon, 03 Jun 2019 01:15:52: #2 finished! INFO @ Mon, 03 Jun 2019 01:15:52: #2 predicted fragment length is 34 bps INFO @ Mon, 03 Jun 2019 01:15:52: #2 alternative fragment length(s) may be 34 bps INFO @ Mon, 03 Jun 2019 01:15:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.05_model.r WARNING @ Mon, 03 Jun 2019 01:15:52: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:15:52: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Mon, 03 Jun 2019 01:15:52: #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 01:15:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:15:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:15:55: 2000000 INFO @ Mon, 03 Jun 2019 01:15:58: #1 tag size is determined as 33 bps INFO @ Mon, 03 Jun 2019 01:15:58: #1 tag size = 33 INFO @ Mon, 03 Jun 2019 01:15:58: #1 total tags in treatment: 2295786 INFO @ Mon, 03 Jun 2019 01:15:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:15:58: #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 01:15:58: #1 tags after filtering in treatment: 2295786 INFO @ Mon, 03 Jun 2019 01:15:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:15:58: #1 finished! INFO @ Mon, 03 Jun 2019 01:15:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:15:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:15:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:15:58: #2 number of paired peaks: 759 WARNING @ Mon, 03 Jun 2019 01:15:58: Fewer paired peaks (759) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 759 pairs to build model! INFO @ Mon, 03 Jun 2019 01:15:58: start model_add_line... INFO @ Mon, 03 Jun 2019 01:15:58: start X-correlation... INFO @ Mon, 03 Jun 2019 01:15:58: end of X-cor INFO @ Mon, 03 Jun 2019 01:15:58: #2 finished! INFO @ Mon, 03 Jun 2019 01:15:58: #2 predicted fragment length is 34 bps INFO @ Mon, 03 Jun 2019 01:15:58: #2 alternative fragment length(s) may be 34 bps INFO @ Mon, 03 Jun 2019 01:15:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.20_model.r WARNING @ Mon, 03 Jun 2019 01:15:58: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:15:58: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Mon, 03 Jun 2019 01:15:58: #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 01:15:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:15:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:15:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:16:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:16:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:16:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.10_summits.bed INFO @ Mon, 03 Jun 2019 01:16:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (959 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:16:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:16:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:16:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.05_summits.bed INFO @ Mon, 03 Jun 2019 01:16:03: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1451 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:16:05: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 01:16:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:16:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:16:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032417/SRX1032417.20_summits.bed INFO @ Mon, 03 Jun 2019 01:16:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (456 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。