Job ID = 1295521 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,094,683 reads read : 14,094,683 reads written : 14,094,683 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: 00:05:31 14094683 reads; of these: 14094683 (100.00%) were unpaired; of these: 1164235 (8.26%) aligned 0 times 9253533 (65.65%) aligned exactly 1 time 3676915 (26.09%) aligned >1 times 91.74% overall alignment rate Time searching: 00:05:31 Overall time: 00:05:31 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1955956 / 12930448 = 0.1513 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 14:14:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.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 14:14:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:14:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:14:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.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 14:14:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:14:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:14:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.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 14:14:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:14:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:14:43: 1000000 INFO @ Mon, 03 Jun 2019 14:14:45: 1000000 INFO @ Mon, 03 Jun 2019 14:14:46: 1000000 INFO @ Mon, 03 Jun 2019 14:14:51: 2000000 INFO @ Mon, 03 Jun 2019 14:14:53: 2000000 INFO @ Mon, 03 Jun 2019 14:14:56: 2000000 INFO @ Mon, 03 Jun 2019 14:14:59: 3000000 INFO @ Mon, 03 Jun 2019 14:15:02: 3000000 INFO @ Mon, 03 Jun 2019 14:15:05: 3000000 INFO @ Mon, 03 Jun 2019 14:15:07: 4000000 INFO @ Mon, 03 Jun 2019 14:15:11: 4000000 INFO @ Mon, 03 Jun 2019 14:15:15: 5000000 INFO @ Mon, 03 Jun 2019 14:15:15: 4000000 INFO @ Mon, 03 Jun 2019 14:15:20: 5000000 INFO @ Mon, 03 Jun 2019 14:15:23: 6000000 INFO @ Mon, 03 Jun 2019 14:15:26: 5000000 INFO @ Mon, 03 Jun 2019 14:15:29: 6000000 INFO @ Mon, 03 Jun 2019 14:15:31: 7000000 INFO @ Mon, 03 Jun 2019 14:15:36: 6000000 INFO @ Mon, 03 Jun 2019 14:15:38: 7000000 INFO @ Mon, 03 Jun 2019 14:15:38: 8000000 INFO @ Mon, 03 Jun 2019 14:15:45: 7000000 INFO @ Mon, 03 Jun 2019 14:15:46: 9000000 INFO @ Mon, 03 Jun 2019 14:15:47: 8000000 INFO @ Mon, 03 Jun 2019 14:15:53: 10000000 INFO @ Mon, 03 Jun 2019 14:15:55: 8000000 INFO @ Mon, 03 Jun 2019 14:15:56: 9000000 INFO @ Mon, 03 Jun 2019 14:16:00: #1 tag size is determined as 46 bps INFO @ Mon, 03 Jun 2019 14:16:00: #1 tag size = 46 INFO @ Mon, 03 Jun 2019 14:16:00: #1 total tags in treatment: 10974492 INFO @ Mon, 03 Jun 2019 14:16:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:16:00: #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 14:16:00: #1 tags after filtering in treatment: 10974492 INFO @ Mon, 03 Jun 2019 14:16:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:16:00: #1 finished! INFO @ Mon, 03 Jun 2019 14:16:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:16:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:16:01: #2 number of paired peaks: 562 WARNING @ Mon, 03 Jun 2019 14:16:01: Fewer paired peaks (562) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 562 pairs to build model! INFO @ Mon, 03 Jun 2019 14:16:01: start model_add_line... INFO @ Mon, 03 Jun 2019 14:16:01: start X-correlation... INFO @ Mon, 03 Jun 2019 14:16:02: end of X-cor INFO @ Mon, 03 Jun 2019 14:16:02: #2 finished! INFO @ Mon, 03 Jun 2019 14:16:02: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 14:16:02: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 14:16:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.10_model.r WARNING @ Mon, 03 Jun 2019 14:16:02: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:16:02: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 14:16:02: #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 14:16:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:16:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:16:05: 10000000 INFO @ Mon, 03 Jun 2019 14:16:05: 9000000 INFO @ Mon, 03 Jun 2019 14:16:13: #1 tag size is determined as 46 bps INFO @ Mon, 03 Jun 2019 14:16:13: #1 tag size = 46 INFO @ Mon, 03 Jun 2019 14:16:13: #1 total tags in treatment: 10974492 INFO @ Mon, 03 Jun 2019 14:16:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:16:13: #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 14:16:14: #1 tags after filtering in treatment: 10974492 INFO @ Mon, 03 Jun 2019 14:16:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:16:14: #1 finished! INFO @ Mon, 03 Jun 2019 14:16:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:16:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:16:15: #2 number of paired peaks: 562 WARNING @ Mon, 03 Jun 2019 14:16:15: Fewer paired peaks (562) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 562 pairs to build model! INFO @ Mon, 03 Jun 2019 14:16:15: start model_add_line... INFO @ Mon, 03 Jun 2019 14:16:15: start X-correlation... INFO @ Mon, 03 Jun 2019 14:16:15: end of X-cor INFO @ Mon, 03 Jun 2019 14:16:15: #2 finished! INFO @ Mon, 03 Jun 2019 14:16:15: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 14:16:15: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 14:16:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.05_model.r WARNING @ Mon, 03 Jun 2019 14:16:15: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:16:15: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 14:16:15: #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 14:16:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:16:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:16:16: 10000000 INFO @ Mon, 03 Jun 2019 14:16:25: #1 tag size is determined as 46 bps INFO @ Mon, 03 Jun 2019 14:16:25: #1 tag size = 46 INFO @ Mon, 03 Jun 2019 14:16:25: #1 total tags in treatment: 10974492 INFO @ Mon, 03 Jun 2019 14:16:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:16:25: #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 14:16:26: #1 tags after filtering in treatment: 10974492 INFO @ Mon, 03 Jun 2019 14:16:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:16:26: #1 finished! INFO @ Mon, 03 Jun 2019 14:16:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:16:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:16:27: #2 number of paired peaks: 562 WARNING @ Mon, 03 Jun 2019 14:16:27: Fewer paired peaks (562) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 562 pairs to build model! INFO @ Mon, 03 Jun 2019 14:16:27: start model_add_line... INFO @ Mon, 03 Jun 2019 14:16:27: start X-correlation... INFO @ Mon, 03 Jun 2019 14:16:27: end of X-cor INFO @ Mon, 03 Jun 2019 14:16:27: #2 finished! INFO @ Mon, 03 Jun 2019 14:16:27: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 14:16:27: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 14:16:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.20_model.r WARNING @ Mon, 03 Jun 2019 14:16:27: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:16:27: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 14:16:27: #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 14:16:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:16:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:16:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:16:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:16:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:16:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:16:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.10_summits.bed INFO @ Mon, 03 Jun 2019 14:16:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1709 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:16:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:17:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:17:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:17:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.05_summits.bed INFO @ Mon, 03 Jun 2019 14:17:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2770 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:17:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:17:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:17:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX359796/SRX359796.20_summits.bed INFO @ Mon, 03 Jun 2019 14:17:14: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (998 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。