Job ID = 2590028 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,727,987 reads read : 10,727,987 reads written : 10,727,987 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1198404.sra.cache’: 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: 00:02:10 10727987 reads; of these: 10727987 (100.00%) were unpaired; of these: 2100053 (19.58%) aligned 0 times 7379840 (68.79%) aligned exactly 1 time 1248094 (11.63%) aligned >1 times 80.42% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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] 1364242 / 8627934 = 0.1581 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 19:10:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.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 19:10:39: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:10:39: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:10:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.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 19:10:39: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:10:39: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:10:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.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 19:10:40: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:10:40: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:10:46: 1000000 INFO @ Mon, 12 Aug 2019 19:10:48: 1000000 INFO @ Mon, 12 Aug 2019 19:10:48: 1000000 INFO @ Mon, 12 Aug 2019 19:10:54: 2000000 INFO @ Mon, 12 Aug 2019 19:10:55: 2000000 INFO @ Mon, 12 Aug 2019 19:10:57: 2000000 INFO @ Mon, 12 Aug 2019 19:11:01: 3000000 INFO @ Mon, 12 Aug 2019 19:11:02: 3000000 INFO @ Mon, 12 Aug 2019 19:11:05: 3000000 INFO @ Mon, 12 Aug 2019 19:11:08: 4000000 INFO @ Mon, 12 Aug 2019 19:11:09: 4000000 INFO @ Mon, 12 Aug 2019 19:11:14: 4000000 INFO @ Mon, 12 Aug 2019 19:11:15: 5000000 INFO @ Mon, 12 Aug 2019 19:11:16: 5000000 INFO @ Mon, 12 Aug 2019 19:11:22: 6000000 INFO @ Mon, 12 Aug 2019 19:11:22: 5000000 INFO @ Mon, 12 Aug 2019 19:11:23: 6000000 INFO @ Mon, 12 Aug 2019 19:11:29: 7000000 INFO @ Mon, 12 Aug 2019 19:11:30: 7000000 INFO @ Mon, 12 Aug 2019 19:11:31: 6000000 INFO @ Mon, 12 Aug 2019 19:11:31: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:11:31: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:11:31: #1 total tags in treatment: 7263692 INFO @ Mon, 12 Aug 2019 19:11:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:11:31: #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 19:11:31: #1 tags after filtering in treatment: 7263692 INFO @ Mon, 12 Aug 2019 19:11:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:11:31: #1 finished! INFO @ Mon, 12 Aug 2019 19:11:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:11:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:11:32: #2 number of paired peaks: 299 WARNING @ Mon, 12 Aug 2019 19:11:32: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Mon, 12 Aug 2019 19:11:32: start model_add_line... INFO @ Mon, 12 Aug 2019 19:11:32: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:11:32: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:11:32: #1 total tags in treatment: 7263692 INFO @ Mon, 12 Aug 2019 19:11:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:11:32: #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 19:11:32: start X-correlation... INFO @ Mon, 12 Aug 2019 19:11:32: end of X-cor INFO @ Mon, 12 Aug 2019 19:11:32: #2 finished! INFO @ Mon, 12 Aug 2019 19:11:32: #2 predicted fragment length is 42 bps INFO @ Mon, 12 Aug 2019 19:11:32: #2 alternative fragment length(s) may be 3,42,578 bps INFO @ Mon, 12 Aug 2019 19:11:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.10_model.r WARNING @ Mon, 12 Aug 2019 19:11:32: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:11:32: #2 You may need to consider one of the other alternative d(s): 3,42,578 WARNING @ Mon, 12 Aug 2019 19:11:32: #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 19:11:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:11:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:11:32: #1 tags after filtering in treatment: 7263692 INFO @ Mon, 12 Aug 2019 19:11:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:11:32: #1 finished! INFO @ Mon, 12 Aug 2019 19:11:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:11:33: #2 number of paired peaks: 299 WARNING @ Mon, 12 Aug 2019 19:11:33: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Mon, 12 Aug 2019 19:11:33: start model_add_line... INFO @ Mon, 12 Aug 2019 19:11:33: start X-correlation... INFO @ Mon, 12 Aug 2019 19:11:33: end of X-cor INFO @ Mon, 12 Aug 2019 19:11:33: #2 finished! INFO @ Mon, 12 Aug 2019 19:11:33: #2 predicted fragment length is 42 bps INFO @ Mon, 12 Aug 2019 19:11:33: #2 alternative fragment length(s) may be 3,42,578 bps INFO @ Mon, 12 Aug 2019 19:11:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.20_model.r WARNING @ Mon, 12 Aug 2019 19:11:33: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:11:33: #2 You may need to consider one of the other alternative d(s): 3,42,578 WARNING @ Mon, 12 Aug 2019 19:11:33: #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 19:11:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:11:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:11:39: 7000000 INFO @ Mon, 12 Aug 2019 19:11:41: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:11:41: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:11:41: #1 total tags in treatment: 7263692 INFO @ Mon, 12 Aug 2019 19:11:41: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:11:41: #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 19:11:41: #1 tags after filtering in treatment: 7263692 INFO @ Mon, 12 Aug 2019 19:11:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:11:41: #1 finished! INFO @ Mon, 12 Aug 2019 19:11:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:11:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:11:42: #2 number of paired peaks: 299 WARNING @ Mon, 12 Aug 2019 19:11:42: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Mon, 12 Aug 2019 19:11:42: start model_add_line... INFO @ Mon, 12 Aug 2019 19:11:42: start X-correlation... INFO @ Mon, 12 Aug 2019 19:11:42: end of X-cor INFO @ Mon, 12 Aug 2019 19:11:42: #2 finished! INFO @ Mon, 12 Aug 2019 19:11:42: #2 predicted fragment length is 42 bps INFO @ Mon, 12 Aug 2019 19:11:42: #2 alternative fragment length(s) may be 3,42,578 bps INFO @ Mon, 12 Aug 2019 19:11:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.05_model.r WARNING @ Mon, 12 Aug 2019 19:11:42: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:11:42: #2 You may need to consider one of the other alternative d(s): 3,42,578 WARNING @ Mon, 12 Aug 2019 19:11:42: #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 19:11:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:11:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:11:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:11:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:12:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:12:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:12:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.10_summits.bed INFO @ Mon, 12 Aug 2019 19:12:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (264 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:12:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:12:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:12:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.20_summits.bed INFO @ Mon, 12 Aug 2019 19:12:02: Done! INFO @ Mon, 12 Aug 2019 19:12:02: #3 Call peaks for each chromosome... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (89 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:12:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:12:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:12:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494872/SRX494872.05_summits.bed INFO @ Mon, 12 Aug 2019 19:12:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (484 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。