Job ID = 1306693 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,996,115 reads read : 5,996,115 reads written : 5,996,115 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: 00:02:29 5996115 reads; of these: 5996115 (100.00%) were unpaired; of these: 317548 (5.30%) aligned 0 times 3450688 (57.55%) aligned exactly 1 time 2227879 (37.16%) aligned >1 times 94.70% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 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] 994157 / 5678567 = 0.1751 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 21:57:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.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 21:57:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:57:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:57:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.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 21:57:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:57:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:57:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.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 21:57:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:57:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:57:31: 1000000 INFO @ Mon, 03 Jun 2019 21:57:32: 1000000 INFO @ Mon, 03 Jun 2019 21:57:33: 1000000 INFO @ Mon, 03 Jun 2019 21:57:39: 2000000 INFO @ Mon, 03 Jun 2019 21:57:40: 2000000 INFO @ Mon, 03 Jun 2019 21:57:43: 2000000 INFO @ Mon, 03 Jun 2019 21:57:47: 3000000 INFO @ Mon, 03 Jun 2019 21:57:48: 3000000 INFO @ Mon, 03 Jun 2019 21:57:53: 3000000 INFO @ Mon, 03 Jun 2019 21:57:54: 4000000 INFO @ Mon, 03 Jun 2019 21:57:56: 4000000 INFO @ Mon, 03 Jun 2019 21:57:59: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:57:59: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:57:59: #1 total tags in treatment: 4684410 INFO @ Mon, 03 Jun 2019 21:57:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:57:59: #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 21:57:59: #1 tags after filtering in treatment: 4684410 INFO @ Mon, 03 Jun 2019 21:57:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:57:59: #1 finished! INFO @ Mon, 03 Jun 2019 21:57:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:57:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:58:00: #2 number of paired peaks: 400 WARNING @ Mon, 03 Jun 2019 21:58:00: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Mon, 03 Jun 2019 21:58:00: start model_add_line... INFO @ Mon, 03 Jun 2019 21:58:00: start X-correlation... INFO @ Mon, 03 Jun 2019 21:58:00: end of X-cor INFO @ Mon, 03 Jun 2019 21:58:00: #2 finished! INFO @ Mon, 03 Jun 2019 21:58:00: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 21:58:00: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 21:58:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.05_model.r WARNING @ Mon, 03 Jun 2019 21:58:00: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:58:00: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 21:58:00: #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 21:58:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:58:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:58:02: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:58:02: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:58:02: #1 total tags in treatment: 4684410 INFO @ Mon, 03 Jun 2019 21:58:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:58:02: #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 21:58:02: #1 tags after filtering in treatment: 4684410 INFO @ Mon, 03 Jun 2019 21:58:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:58:02: #1 finished! INFO @ Mon, 03 Jun 2019 21:58:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:58:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:58:02: #2 number of paired peaks: 400 WARNING @ Mon, 03 Jun 2019 21:58:02: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Mon, 03 Jun 2019 21:58:02: start model_add_line... INFO @ Mon, 03 Jun 2019 21:58:02: start X-correlation... INFO @ Mon, 03 Jun 2019 21:58:02: end of X-cor INFO @ Mon, 03 Jun 2019 21:58:02: #2 finished! INFO @ Mon, 03 Jun 2019 21:58:02: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 21:58:02: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 21:58:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.10_model.r WARNING @ Mon, 03 Jun 2019 21:58:02: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:58:02: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 21:58:02: #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 21:58:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:58:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:58:02: 4000000 INFO @ Mon, 03 Jun 2019 21:58:08: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:58:08: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:58:08: #1 total tags in treatment: 4684410 INFO @ Mon, 03 Jun 2019 21:58:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:58:08: #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 21:58:09: #1 tags after filtering in treatment: 4684410 INFO @ Mon, 03 Jun 2019 21:58:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:58:09: #1 finished! INFO @ Mon, 03 Jun 2019 21:58:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:58:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:58:09: #2 number of paired peaks: 400 WARNING @ Mon, 03 Jun 2019 21:58:09: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Mon, 03 Jun 2019 21:58:09: start model_add_line... INFO @ Mon, 03 Jun 2019 21:58:09: start X-correlation... INFO @ Mon, 03 Jun 2019 21:58:09: end of X-cor INFO @ Mon, 03 Jun 2019 21:58:09: #2 finished! INFO @ Mon, 03 Jun 2019 21:58:09: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 21:58:09: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 21:58:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.20_model.r WARNING @ Mon, 03 Jun 2019 21:58:09: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:58:09: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 21:58:09: #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 21:58:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:58:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:58:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:58:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:58:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.05_peaks.xls INFO @ Mon, 03 Jun 2019 21:58:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:58:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.05_summits.bed INFO @ Mon, 03 Jun 2019 21:58:20: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1165 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:58:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.10_peaks.xls INFO @ Mon, 03 Jun 2019 21:58:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:58:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.10_summits.bed INFO @ Mon, 03 Jun 2019 21:58:23: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (833 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:58:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:58:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.20_peaks.xls INFO @ Mon, 03 Jun 2019 21:58:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:58:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507381/SRX507381.20_summits.bed INFO @ Mon, 03 Jun 2019 21:58:30: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (415 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。