Job ID = 2589379 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,405,441 reads read : 9,405,441 reads written : 9,405,441 rm: cannot remove ‘[DSE]RR*’: 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: 00:02:45 9405441 reads; of these: 9405441 (100.00%) were unpaired; of these: 154181 (1.64%) aligned 0 times 7688890 (81.75%) aligned exactly 1 time 1562370 (16.61%) aligned >1 times 98.36% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 744319 / 9251260 = 0.0805 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, 12 Aug 2019 17:44:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 17:44:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:44:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:44:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 17:44:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:44:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:44:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 17:44:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:44:03: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:44:08: 1000000 INFO @ Mon, 12 Aug 2019 17:44:09: 1000000 INFO @ Mon, 12 Aug 2019 17:44:12: 1000000 INFO @ Mon, 12 Aug 2019 17:44:16: 2000000 INFO @ Mon, 12 Aug 2019 17:44:17: 2000000 INFO @ Mon, 12 Aug 2019 17:44:22: 2000000 INFO @ Mon, 12 Aug 2019 17:44:25: 3000000 INFO @ Mon, 12 Aug 2019 17:44:25: 3000000 INFO @ Mon, 12 Aug 2019 17:44:31: 3000000 INFO @ Mon, 12 Aug 2019 17:44:33: 4000000 INFO @ Mon, 12 Aug 2019 17:44:35: 4000000 INFO @ Mon, 12 Aug 2019 17:44:40: 5000000 INFO @ Mon, 12 Aug 2019 17:44:41: 4000000 INFO @ Mon, 12 Aug 2019 17:44:44: 5000000 INFO @ Mon, 12 Aug 2019 17:44:48: 6000000 INFO @ Mon, 12 Aug 2019 17:44:50: 5000000 INFO @ Mon, 12 Aug 2019 17:44:52: 6000000 INFO @ Mon, 12 Aug 2019 17:44:55: 7000000 INFO @ Mon, 12 Aug 2019 17:44:59: 6000000 INFO @ Mon, 12 Aug 2019 17:44:59: 7000000 INFO @ Mon, 12 Aug 2019 17:45:03: 8000000 INFO @ Mon, 12 Aug 2019 17:45:06: 8000000 INFO @ Mon, 12 Aug 2019 17:45:06: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:45:06: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:45:06: #1 total tags in treatment: 8506941 INFO @ Mon, 12 Aug 2019 17:45:06: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:45:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:45:07: #1 tags after filtering in treatment: 8506941 INFO @ Mon, 12 Aug 2019 17:45:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:45:07: #1 finished! INFO @ Mon, 12 Aug 2019 17:45:07: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:45:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:45:07: #2 number of paired peaks: 415 WARNING @ Mon, 12 Aug 2019 17:45:07: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Mon, 12 Aug 2019 17:45:07: start model_add_line... INFO @ Mon, 12 Aug 2019 17:45:07: start X-correlation... INFO @ Mon, 12 Aug 2019 17:45:07: end of X-cor INFO @ Mon, 12 Aug 2019 17:45:07: #2 finished! INFO @ Mon, 12 Aug 2019 17:45:07: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 17:45:07: #2 alternative fragment length(s) may be 3,50,555 bps INFO @ Mon, 12 Aug 2019 17:45:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.10_model.r WARNING @ Mon, 12 Aug 2019 17:45:07: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:45:07: #2 You may need to consider one of the other alternative d(s): 3,50,555 WARNING @ Mon, 12 Aug 2019 17:45:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:45:07: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:45:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:45:08: 7000000 INFO @ Mon, 12 Aug 2019 17:45:10: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:45:10: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:45:10: #1 total tags in treatment: 8506941 INFO @ Mon, 12 Aug 2019 17:45:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:45:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:45:10: #1 tags after filtering in treatment: 8506941 INFO @ Mon, 12 Aug 2019 17:45:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:45:10: #1 finished! INFO @ Mon, 12 Aug 2019 17:45:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:45:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:45:11: #2 number of paired peaks: 415 WARNING @ Mon, 12 Aug 2019 17:45:11: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Mon, 12 Aug 2019 17:45:11: start model_add_line... INFO @ Mon, 12 Aug 2019 17:45:11: start X-correlation... INFO @ Mon, 12 Aug 2019 17:45:11: end of X-cor INFO @ Mon, 12 Aug 2019 17:45:11: #2 finished! INFO @ Mon, 12 Aug 2019 17:45:11: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 17:45:11: #2 alternative fragment length(s) may be 3,50,555 bps INFO @ Mon, 12 Aug 2019 17:45:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.05_model.r WARNING @ Mon, 12 Aug 2019 17:45:11: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:45:11: #2 You may need to consider one of the other alternative d(s): 3,50,555 WARNING @ Mon, 12 Aug 2019 17:45:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:45:11: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:45:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:45:16: 8000000 INFO @ Mon, 12 Aug 2019 17:45:21: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:45:21: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:45:21: #1 total tags in treatment: 8506941 INFO @ Mon, 12 Aug 2019 17:45:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:45:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:45:21: #1 tags after filtering in treatment: 8506941 INFO @ Mon, 12 Aug 2019 17:45:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:45:21: #1 finished! INFO @ Mon, 12 Aug 2019 17:45:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:45:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:45:22: #2 number of paired peaks: 415 WARNING @ Mon, 12 Aug 2019 17:45:22: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Mon, 12 Aug 2019 17:45:22: start model_add_line... INFO @ Mon, 12 Aug 2019 17:45:22: start X-correlation... INFO @ Mon, 12 Aug 2019 17:45:22: end of X-cor INFO @ Mon, 12 Aug 2019 17:45:22: #2 finished! INFO @ Mon, 12 Aug 2019 17:45:22: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 17:45:22: #2 alternative fragment length(s) may be 3,50,555 bps INFO @ Mon, 12 Aug 2019 17:45:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.20_model.r WARNING @ Mon, 12 Aug 2019 17:45:22: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:45:22: #2 You may need to consider one of the other alternative d(s): 3,50,555 WARNING @ Mon, 12 Aug 2019 17:45:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:45:22: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:45:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:45:31: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:45:34: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:45:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:45:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:45:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.10_summits.bed INFO @ Mon, 12 Aug 2019 17:45:42: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (414 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:45:45: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:45:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:45:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:45:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.05_summits.bed INFO @ Mon, 12 Aug 2019 17:45:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (651 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:45:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:45:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:45:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078730/SRX1078730.20_summits.bed INFO @ Mon, 12 Aug 2019 17:45:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。