Job ID = 1294240 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,163,368 reads read : 9,163,368 reads written : 9,163,368 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:52 9163368 reads; of these: 9163368 (100.00%) were unpaired; of these: 3955737 (43.17%) aligned 0 times 3636366 (39.68%) aligned exactly 1 time 1571265 (17.15%) aligned >1 times 56.83% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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] 1934158 / 5207631 = 0.3714 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 05:49:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.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 05:49:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:49:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:49:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.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 05:49:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:49:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:49:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.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 05:49:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:49:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:50:04: 1000000 INFO @ Mon, 03 Jun 2019 05:50:05: 1000000 INFO @ Mon, 03 Jun 2019 05:50:05: 1000000 INFO @ Mon, 03 Jun 2019 05:50:12: 2000000 INFO @ Mon, 03 Jun 2019 05:50:15: 2000000 INFO @ Mon, 03 Jun 2019 05:50:16: 2000000 INFO @ Mon, 03 Jun 2019 05:50:20: 3000000 INFO @ Mon, 03 Jun 2019 05:50:22: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:50:22: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:50:22: #1 total tags in treatment: 3273473 INFO @ Mon, 03 Jun 2019 05:50:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:50:22: #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 05:50:22: #1 tags after filtering in treatment: 3273473 INFO @ Mon, 03 Jun 2019 05:50:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:50:22: #1 finished! INFO @ Mon, 03 Jun 2019 05:50:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:50:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:50:23: #2 number of paired peaks: 825 WARNING @ Mon, 03 Jun 2019 05:50:23: Fewer paired peaks (825) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 825 pairs to build model! INFO @ Mon, 03 Jun 2019 05:50:23: start model_add_line... INFO @ Mon, 03 Jun 2019 05:50:23: start X-correlation... INFO @ Mon, 03 Jun 2019 05:50:23: end of X-cor INFO @ Mon, 03 Jun 2019 05:50:23: #2 finished! INFO @ Mon, 03 Jun 2019 05:50:23: #2 predicted fragment length is 58 bps INFO @ Mon, 03 Jun 2019 05:50:23: #2 alternative fragment length(s) may be 58,133,172,404,517,560 bps INFO @ Mon, 03 Jun 2019 05:50:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.05_model.r WARNING @ Mon, 03 Jun 2019 05:50:23: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:50:23: #2 You may need to consider one of the other alternative d(s): 58,133,172,404,517,560 WARNING @ Mon, 03 Jun 2019 05:50:23: #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 05:50:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:50:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:50:25: 3000000 INFO @ Mon, 03 Jun 2019 05:50:26: 3000000 INFO @ Mon, 03 Jun 2019 05:50:27: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:50:27: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:50:27: #1 total tags in treatment: 3273473 INFO @ Mon, 03 Jun 2019 05:50:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:50:27: #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 05:50:27: #1 tags after filtering in treatment: 3273473 INFO @ Mon, 03 Jun 2019 05:50:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:50:27: #1 finished! INFO @ Mon, 03 Jun 2019 05:50:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:50:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:50:28: #2 number of paired peaks: 825 WARNING @ Mon, 03 Jun 2019 05:50:28: Fewer paired peaks (825) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 825 pairs to build model! INFO @ Mon, 03 Jun 2019 05:50:28: start model_add_line... INFO @ Mon, 03 Jun 2019 05:50:28: start X-correlation... INFO @ Mon, 03 Jun 2019 05:50:28: end of X-cor INFO @ Mon, 03 Jun 2019 05:50:28: #2 finished! INFO @ Mon, 03 Jun 2019 05:50:28: #2 predicted fragment length is 58 bps INFO @ Mon, 03 Jun 2019 05:50:28: #2 alternative fragment length(s) may be 58,133,172,404,517,560 bps INFO @ Mon, 03 Jun 2019 05:50:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.10_model.r WARNING @ Mon, 03 Jun 2019 05:50:28: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:50:28: #2 You may need to consider one of the other alternative d(s): 58,133,172,404,517,560 WARNING @ Mon, 03 Jun 2019 05:50:28: #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 05:50:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:50:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:50:28: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:50:28: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:50:28: #1 total tags in treatment: 3273473 INFO @ Mon, 03 Jun 2019 05:50:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:50:28: #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 05:50:28: #1 tags after filtering in treatment: 3273473 INFO @ Mon, 03 Jun 2019 05:50:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:50:28: #1 finished! INFO @ Mon, 03 Jun 2019 05:50:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:50:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:50:29: #2 number of paired peaks: 825 WARNING @ Mon, 03 Jun 2019 05:50:29: Fewer paired peaks (825) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 825 pairs to build model! INFO @ Mon, 03 Jun 2019 05:50:29: start model_add_line... INFO @ Mon, 03 Jun 2019 05:50:29: start X-correlation... INFO @ Mon, 03 Jun 2019 05:50:29: end of X-cor INFO @ Mon, 03 Jun 2019 05:50:29: #2 finished! INFO @ Mon, 03 Jun 2019 05:50:29: #2 predicted fragment length is 58 bps INFO @ Mon, 03 Jun 2019 05:50:29: #2 alternative fragment length(s) may be 58,133,172,404,517,560 bps INFO @ Mon, 03 Jun 2019 05:50:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.20_model.r WARNING @ Mon, 03 Jun 2019 05:50:29: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:50:29: #2 You may need to consider one of the other alternative d(s): 58,133,172,404,517,560 WARNING @ Mon, 03 Jun 2019 05:50:29: #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 05:50:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:50:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:50:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:50:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:50:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:50:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:50:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.05_summits.bed INFO @ Mon, 03 Jun 2019 05:50:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1089 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:50:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:50:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:50:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:50:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.10_summits.bed INFO @ Mon, 03 Jun 2019 05:50:43: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (365 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:50:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:50:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:50:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX202128/SRX202128.20_summits.bed INFO @ Mon, 03 Jun 2019 05:50:44: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (116 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。