Job ID = 1294014 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,000,265 reads read : 17,000,265 reads written : 17,000,265 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: 00:02:03 17000265 reads; of these: 17000265 (100.00%) were unpaired; of these: 14709452 (86.52%) aligned 0 times 1468878 (8.64%) aligned exactly 1 time 821935 (4.83%) aligned >1 times 13.48% overall alignment rate Time searching: 00:02:03 Overall time: 00:02:03 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] 1437309 / 2290813 = 0.6274 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 04:07:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.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 04:07:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:07:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:07:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.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 04:07:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:07:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:07:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.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 04:07:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:07:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:07:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:07:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:07:53: #1 total tags in treatment: 853504 INFO @ Mon, 03 Jun 2019 04:07:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:07:53: #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 04:07:53: #1 tags after filtering in treatment: 853504 INFO @ Mon, 03 Jun 2019 04:07:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:07:53: #1 finished! INFO @ Mon, 03 Jun 2019 04:07:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:07:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:07:53: #2 number of paired peaks: 2040 INFO @ Mon, 03 Jun 2019 04:07:53: start model_add_line... INFO @ Mon, 03 Jun 2019 04:07:53: start X-correlation... INFO @ Mon, 03 Jun 2019 04:07:53: end of X-cor INFO @ Mon, 03 Jun 2019 04:07:53: #2 finished! INFO @ Mon, 03 Jun 2019 04:07:53: #2 predicted fragment length is 81 bps INFO @ Mon, 03 Jun 2019 04:07:53: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 03 Jun 2019 04:07:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.10_model.r WARNING @ Mon, 03 Jun 2019 04:07:54: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:07:54: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Mon, 03 Jun 2019 04:07:54: #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 04:07:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:07:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:07:54: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:07:54: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:07:54: #1 total tags in treatment: 853504 INFO @ Mon, 03 Jun 2019 04:07:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:07:54: #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 04:07:54: #1 tags after filtering in treatment: 853504 INFO @ Mon, 03 Jun 2019 04:07:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:07:54: #1 finished! INFO @ Mon, 03 Jun 2019 04:07:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:07:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:07:54: #2 number of paired peaks: 2040 INFO @ Mon, 03 Jun 2019 04:07:54: start model_add_line... INFO @ Mon, 03 Jun 2019 04:07:54: start X-correlation... INFO @ Mon, 03 Jun 2019 04:07:54: end of X-cor INFO @ Mon, 03 Jun 2019 04:07:54: #2 finished! INFO @ Mon, 03 Jun 2019 04:07:54: #2 predicted fragment length is 81 bps INFO @ Mon, 03 Jun 2019 04:07:54: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 03 Jun 2019 04:07:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.20_model.r WARNING @ Mon, 03 Jun 2019 04:07:54: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:07:54: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Mon, 03 Jun 2019 04:07:54: #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 04:07:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:07:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:07:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:07:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:07:55: #1 total tags in treatment: 853504 INFO @ Mon, 03 Jun 2019 04:07:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:07:55: #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 04:07:55: #1 tags after filtering in treatment: 853504 INFO @ Mon, 03 Jun 2019 04:07:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:07:55: #1 finished! INFO @ Mon, 03 Jun 2019 04:07:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:07:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:07:55: #2 number of paired peaks: 2040 INFO @ Mon, 03 Jun 2019 04:07:55: start model_add_line... INFO @ Mon, 03 Jun 2019 04:07:55: start X-correlation... INFO @ Mon, 03 Jun 2019 04:07:55: end of X-cor INFO @ Mon, 03 Jun 2019 04:07:55: #2 finished! INFO @ Mon, 03 Jun 2019 04:07:55: #2 predicted fragment length is 81 bps INFO @ Mon, 03 Jun 2019 04:07:55: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 03 Jun 2019 04:07:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.05_model.r WARNING @ Mon, 03 Jun 2019 04:07:55: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:07:55: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Mon, 03 Jun 2019 04:07:55: #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 04:07:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:07:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:07:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:07:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:07:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:07:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:07:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.10_summits.bed INFO @ Mon, 03 Jun 2019 04:07:58: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1061 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:07:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:07:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:07:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.20_summits.bed INFO @ Mon, 03 Jun 2019 04:07:58: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (510 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 04:07:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:08:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:08:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:08:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX170985/SRX170985.05_summits.bed INFO @ Mon, 03 Jun 2019 04:08:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1649 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。