Job ID = 2589879 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,599,163 reads read : 7,599,163 reads written : 7,599,163 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947514.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: 00:01:29 7599163 reads; of these: 7599163 (100.00%) were unpaired; of these: 44012 (0.58%) aligned 0 times 6306310 (82.99%) aligned exactly 1 time 1248841 (16.43%) aligned >1 times 99.42% overall alignment rate Time searching: 00:01:29 Overall time: 00:01:29 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 488685 / 7555151 = 0.0647 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 18:43:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.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 18:43:07: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:43:07: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:43:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.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 18:43:08: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:43:08: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:43:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.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 18:43:09: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:43:09: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:43:14: 1000000 INFO @ Mon, 12 Aug 2019 18:43:15: 1000000 INFO @ Mon, 12 Aug 2019 18:43:17: 1000000 INFO @ Mon, 12 Aug 2019 18:43:20: 2000000 INFO @ Mon, 12 Aug 2019 18:43:21: 2000000 INFO @ Mon, 12 Aug 2019 18:43:24: 2000000 INFO @ Mon, 12 Aug 2019 18:43:27: 3000000 INFO @ Mon, 12 Aug 2019 18:43:28: 3000000 INFO @ Mon, 12 Aug 2019 18:43:31: 3000000 INFO @ Mon, 12 Aug 2019 18:43:34: 4000000 INFO @ Mon, 12 Aug 2019 18:43:35: 4000000 INFO @ Mon, 12 Aug 2019 18:43:38: 4000000 INFO @ Mon, 12 Aug 2019 18:43:42: 5000000 INFO @ Mon, 12 Aug 2019 18:43:43: 5000000 INFO @ Mon, 12 Aug 2019 18:43:44: 5000000 INFO @ Mon, 12 Aug 2019 18:43:48: 6000000 INFO @ Mon, 12 Aug 2019 18:43:49: 6000000 INFO @ Mon, 12 Aug 2019 18:43:51: 6000000 INFO @ Mon, 12 Aug 2019 18:43:55: 7000000 INFO @ Mon, 12 Aug 2019 18:43:55: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:43:55: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:43:55: #1 total tags in treatment: 7066466 INFO @ Mon, 12 Aug 2019 18:43:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:43:55: #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 18:43:55: #1 tags after filtering in treatment: 7066466 INFO @ Mon, 12 Aug 2019 18:43:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:43:55: #1 finished! INFO @ Mon, 12 Aug 2019 18:43:55: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:43:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:43:56: 7000000 INFO @ Mon, 12 Aug 2019 18:43:56: #2 number of paired peaks: 410 WARNING @ Mon, 12 Aug 2019 18:43:56: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Mon, 12 Aug 2019 18:43:56: start model_add_line... INFO @ Mon, 12 Aug 2019 18:43:56: start X-correlation... INFO @ Mon, 12 Aug 2019 18:43:56: end of X-cor INFO @ Mon, 12 Aug 2019 18:43:56: #2 finished! INFO @ Mon, 12 Aug 2019 18:43:56: #2 predicted fragment length is 31 bps INFO @ Mon, 12 Aug 2019 18:43:56: #2 alternative fragment length(s) may be 3,31,558,587 bps INFO @ Mon, 12 Aug 2019 18:43:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.05_model.r WARNING @ Mon, 12 Aug 2019 18:43:56: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:43:56: #2 You may need to consider one of the other alternative d(s): 3,31,558,587 WARNING @ Mon, 12 Aug 2019 18:43:56: #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 18:43:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:43:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:43:56: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:43:56: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:43:56: #1 total tags in treatment: 7066466 INFO @ Mon, 12 Aug 2019 18:43:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:43:56: #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 18:43:56: #1 tags after filtering in treatment: 7066466 INFO @ Mon, 12 Aug 2019 18:43:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:43:56: #1 finished! INFO @ Mon, 12 Aug 2019 18:43:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:43:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:43:57: #2 number of paired peaks: 410 WARNING @ Mon, 12 Aug 2019 18:43:57: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Mon, 12 Aug 2019 18:43:57: start model_add_line... INFO @ Mon, 12 Aug 2019 18:43:57: start X-correlation... INFO @ Mon, 12 Aug 2019 18:43:57: end of X-cor INFO @ Mon, 12 Aug 2019 18:43:57: #2 finished! INFO @ Mon, 12 Aug 2019 18:43:57: #2 predicted fragment length is 31 bps INFO @ Mon, 12 Aug 2019 18:43:57: #2 alternative fragment length(s) may be 3,31,558,587 bps INFO @ Mon, 12 Aug 2019 18:43:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.10_model.r WARNING @ Mon, 12 Aug 2019 18:43:57: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:43:57: #2 You may need to consider one of the other alternative d(s): 3,31,558,587 WARNING @ Mon, 12 Aug 2019 18:43:57: #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 18:43:57: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:43:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:43:58: 7000000 INFO @ Mon, 12 Aug 2019 18:43:58: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:43:58: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:43:58: #1 total tags in treatment: 7066466 INFO @ Mon, 12 Aug 2019 18:43:58: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:43:58: #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 18:43:59: #1 tags after filtering in treatment: 7066466 INFO @ Mon, 12 Aug 2019 18:43:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:43:59: #1 finished! INFO @ Mon, 12 Aug 2019 18:43:59: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:43:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:43:59: #2 number of paired peaks: 410 WARNING @ Mon, 12 Aug 2019 18:43:59: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Mon, 12 Aug 2019 18:43:59: start model_add_line... INFO @ Mon, 12 Aug 2019 18:43:59: start X-correlation... INFO @ Mon, 12 Aug 2019 18:43:59: end of X-cor INFO @ Mon, 12 Aug 2019 18:43:59: #2 finished! INFO @ Mon, 12 Aug 2019 18:43:59: #2 predicted fragment length is 31 bps INFO @ Mon, 12 Aug 2019 18:43:59: #2 alternative fragment length(s) may be 3,31,558,587 bps INFO @ Mon, 12 Aug 2019 18:43:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.20_model.r WARNING @ Mon, 12 Aug 2019 18:43:59: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:43:59: #2 You may need to consider one of the other alternative d(s): 3,31,558,587 WARNING @ Mon, 12 Aug 2019 18:43:59: #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 18:43:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:43:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:44:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:44:17: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:44:19: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:44:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:44:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:44:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.05_summits.bed INFO @ Mon, 12 Aug 2019 18:44:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (556 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:44:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:44:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:44:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.10_summits.bed INFO @ Mon, 12 Aug 2019 18:44:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (254 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:44:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:44:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:44:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331279/SRX331279.20_summits.bed INFO @ Mon, 12 Aug 2019 18:44:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (75 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。