Job ID = 1293762 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,383,971 reads read : 10,383,971 reads written : 10,383,971 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:06 10383971 reads; of these: 10383971 (100.00%) were unpaired; of these: 2478343 (23.87%) aligned 0 times 6273282 (60.41%) aligned exactly 1 time 1632346 (15.72%) aligned >1 times 76.13% overall alignment rate Time searching: 00:04:07 Overall time: 00:04:07 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] 3573410 / 7905628 = 0.4520 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 02:17:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.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 02:17:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:17:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:17:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.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 02:17:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:17:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:17:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.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 02:17:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:17:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:18:02: 1000000 INFO @ Mon, 03 Jun 2019 02:18:04: 1000000 INFO @ Mon, 03 Jun 2019 02:18:04: 1000000 INFO @ Mon, 03 Jun 2019 02:18:10: 2000000 INFO @ Mon, 03 Jun 2019 02:18:13: 2000000 INFO @ Mon, 03 Jun 2019 02:18:13: 2000000 INFO @ Mon, 03 Jun 2019 02:18:18: 3000000 INFO @ Mon, 03 Jun 2019 02:18:22: 3000000 INFO @ Mon, 03 Jun 2019 02:18:22: 3000000 INFO @ Mon, 03 Jun 2019 02:18:26: 4000000 INFO @ Mon, 03 Jun 2019 02:18:29: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 02:18:29: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 02:18:29: #1 total tags in treatment: 4332218 INFO @ Mon, 03 Jun 2019 02:18:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:18:29: #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 02:18:29: #1 tags after filtering in treatment: 4332218 INFO @ Mon, 03 Jun 2019 02:18:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:18:29: #1 finished! INFO @ Mon, 03 Jun 2019 02:18:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:18:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:18:29: #2 number of paired peaks: 259 WARNING @ Mon, 03 Jun 2019 02:18:29: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Mon, 03 Jun 2019 02:18:29: start model_add_line... INFO @ Mon, 03 Jun 2019 02:18:29: start X-correlation... INFO @ Mon, 03 Jun 2019 02:18:29: end of X-cor INFO @ Mon, 03 Jun 2019 02:18:29: #2 finished! INFO @ Mon, 03 Jun 2019 02:18:29: #2 predicted fragment length is 77 bps INFO @ Mon, 03 Jun 2019 02:18:29: #2 alternative fragment length(s) may be 77 bps INFO @ Mon, 03 Jun 2019 02:18:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.05_model.r WARNING @ Mon, 03 Jun 2019 02:18:29: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:18:29: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Mon, 03 Jun 2019 02:18:29: #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 02:18:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:18:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:18:31: 4000000 INFO @ Mon, 03 Jun 2019 02:18:31: 4000000 INFO @ Mon, 03 Jun 2019 02:18:34: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 02:18:34: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 02:18:34: #1 total tags in treatment: 4332218 INFO @ Mon, 03 Jun 2019 02:18:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:18:34: #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 02:18:34: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 02:18:34: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 02:18:34: #1 total tags in treatment: 4332218 INFO @ Mon, 03 Jun 2019 02:18:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:18:34: #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 02:18:34: #1 tags after filtering in treatment: 4332218 INFO @ Mon, 03 Jun 2019 02:18:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:18:34: #1 finished! INFO @ Mon, 03 Jun 2019 02:18:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:18:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:18:34: #1 tags after filtering in treatment: 4332218 INFO @ Mon, 03 Jun 2019 02:18:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:18:34: #1 finished! INFO @ Mon, 03 Jun 2019 02:18:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:18:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:18:34: #2 number of paired peaks: 259 WARNING @ Mon, 03 Jun 2019 02:18:34: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Mon, 03 Jun 2019 02:18:34: start model_add_line... INFO @ Mon, 03 Jun 2019 02:18:34: start X-correlation... INFO @ Mon, 03 Jun 2019 02:18:34: #2 number of paired peaks: 259 WARNING @ Mon, 03 Jun 2019 02:18:34: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Mon, 03 Jun 2019 02:18:34: start model_add_line... INFO @ Mon, 03 Jun 2019 02:18:34: end of X-cor INFO @ Mon, 03 Jun 2019 02:18:34: #2 finished! INFO @ Mon, 03 Jun 2019 02:18:34: #2 predicted fragment length is 77 bps INFO @ Mon, 03 Jun 2019 02:18:34: #2 alternative fragment length(s) may be 77 bps INFO @ Mon, 03 Jun 2019 02:18:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.20_model.r WARNING @ Mon, 03 Jun 2019 02:18:34: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:18:34: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Mon, 03 Jun 2019 02:18:34: #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 02:18:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:18:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:18:34: start X-correlation... INFO @ Mon, 03 Jun 2019 02:18:34: end of X-cor INFO @ Mon, 03 Jun 2019 02:18:34: #2 finished! INFO @ Mon, 03 Jun 2019 02:18:34: #2 predicted fragment length is 77 bps INFO @ Mon, 03 Jun 2019 02:18:34: #2 alternative fragment length(s) may be 77 bps INFO @ Mon, 03 Jun 2019 02:18:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.10_model.r WARNING @ Mon, 03 Jun 2019 02:18:34: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:18:34: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Mon, 03 Jun 2019 02:18:34: #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 02:18:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:18:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:18:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:18:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:18:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:18:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:18:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:18:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.05_summits.bed INFO @ Mon, 03 Jun 2019 02:18:49: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (390 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:18:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:18:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:18:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.20_summits.bed INFO @ Mon, 03 Jun 2019 02:18:54: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:18:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:18:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:18:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1120704/SRX1120704.10_summits.bed INFO @ Mon, 03 Jun 2019 02:18:54: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (268 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。