Job ID = 2589750 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,151,012 reads read : 8,151,012 reads written : 8,151,012 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947356.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: 00:01:27 8151012 reads; of these: 8151012 (100.00%) were unpaired; of these: 66636 (0.82%) aligned 0 times 6796534 (83.38%) aligned exactly 1 time 1287842 (15.80%) aligned >1 times 99.18% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 838181 / 8084376 = 0.1037 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 18:25:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.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 18:25:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:25:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:25:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.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 18:25:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:25:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:25:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.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 18:25:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:25:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:26:05: 1000000 INFO @ Mon, 12 Aug 2019 18:26:07: 1000000 INFO @ Mon, 12 Aug 2019 18:26:08: 1000000 INFO @ Mon, 12 Aug 2019 18:26:12: 2000000 INFO @ Mon, 12 Aug 2019 18:26:15: 2000000 INFO @ Mon, 12 Aug 2019 18:26:16: 2000000 INFO @ Mon, 12 Aug 2019 18:26:19: 3000000 INFO @ Mon, 12 Aug 2019 18:26:23: 3000000 INFO @ Mon, 12 Aug 2019 18:26:24: 3000000 INFO @ Mon, 12 Aug 2019 18:26:26: 4000000 INFO @ Mon, 12 Aug 2019 18:26:31: 4000000 INFO @ Mon, 12 Aug 2019 18:26:32: 4000000 INFO @ Mon, 12 Aug 2019 18:26:33: 5000000 INFO @ Mon, 12 Aug 2019 18:26:39: 5000000 INFO @ Mon, 12 Aug 2019 18:26:40: 5000000 INFO @ Mon, 12 Aug 2019 18:26:40: 6000000 INFO @ Mon, 12 Aug 2019 18:26:47: 6000000 INFO @ Mon, 12 Aug 2019 18:26:47: 7000000 INFO @ Mon, 12 Aug 2019 18:26:48: 6000000 INFO @ Mon, 12 Aug 2019 18:26:49: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:26:49: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:26:49: #1 total tags in treatment: 7246195 INFO @ Mon, 12 Aug 2019 18:26:49: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:26:49: #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 18:26:49: #1 tags after filtering in treatment: 7246195 INFO @ Mon, 12 Aug 2019 18:26:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:26:49: #1 finished! INFO @ Mon, 12 Aug 2019 18:26:49: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:26:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:26:50: #2 number of paired peaks: 373 WARNING @ Mon, 12 Aug 2019 18:26:50: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Mon, 12 Aug 2019 18:26:50: start model_add_line... INFO @ Mon, 12 Aug 2019 18:26:50: start X-correlation... INFO @ Mon, 12 Aug 2019 18:26:50: end of X-cor INFO @ Mon, 12 Aug 2019 18:26:50: #2 finished! INFO @ Mon, 12 Aug 2019 18:26:50: #2 predicted fragment length is 31 bps INFO @ Mon, 12 Aug 2019 18:26:50: #2 alternative fragment length(s) may be 2,31,509,525,545,571 bps INFO @ Mon, 12 Aug 2019 18:26:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.05_model.r WARNING @ Mon, 12 Aug 2019 18:26:50: #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 18:26:50: #2 You may need to consider one of the other alternative d(s): 2,31,509,525,545,571 WARNING @ Mon, 12 Aug 2019 18:26:50: #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 18:26:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:26:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:26:55: 7000000 INFO @ Mon, 12 Aug 2019 18:26:56: 7000000 INFO @ Mon, 12 Aug 2019 18:26:57: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:26:57: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:26:57: #1 total tags in treatment: 7246195 INFO @ Mon, 12 Aug 2019 18:26:57: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:26:57: #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 18:26:57: #1 tags after filtering in treatment: 7246195 INFO @ Mon, 12 Aug 2019 18:26:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:26:57: #1 finished! INFO @ Mon, 12 Aug 2019 18:26:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:26:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:26:58: #2 number of paired peaks: 373 WARNING @ Mon, 12 Aug 2019 18:26:58: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Mon, 12 Aug 2019 18:26:58: start model_add_line... INFO @ Mon, 12 Aug 2019 18:26:58: start X-correlation... INFO @ Mon, 12 Aug 2019 18:26:58: end of X-cor INFO @ Mon, 12 Aug 2019 18:26:58: #2 finished! INFO @ Mon, 12 Aug 2019 18:26:58: #2 predicted fragment length is 31 bps INFO @ Mon, 12 Aug 2019 18:26:58: #2 alternative fragment length(s) may be 2,31,509,525,545,571 bps INFO @ Mon, 12 Aug 2019 18:26:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.10_model.r WARNING @ Mon, 12 Aug 2019 18:26:58: #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 18:26:58: #2 You may need to consider one of the other alternative d(s): 2,31,509,525,545,571 WARNING @ Mon, 12 Aug 2019 18:26:58: #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 18:26:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:26:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:26:58: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:26:58: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:26:58: #1 total tags in treatment: 7246195 INFO @ Mon, 12 Aug 2019 18:26:58: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:26:58: #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 18:26:58: #1 tags after filtering in treatment: 7246195 INFO @ Mon, 12 Aug 2019 18:26:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:26:58: #1 finished! INFO @ Mon, 12 Aug 2019 18:26:58: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:26:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:26:59: #2 number of paired peaks: 373 WARNING @ Mon, 12 Aug 2019 18:26:59: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Mon, 12 Aug 2019 18:26:59: start model_add_line... INFO @ Mon, 12 Aug 2019 18:26:59: start X-correlation... INFO @ Mon, 12 Aug 2019 18:26:59: end of X-cor INFO @ Mon, 12 Aug 2019 18:26:59: #2 finished! INFO @ Mon, 12 Aug 2019 18:26:59: #2 predicted fragment length is 31 bps INFO @ Mon, 12 Aug 2019 18:26:59: #2 alternative fragment length(s) may be 2,31,509,525,545,571 bps INFO @ Mon, 12 Aug 2019 18:26:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.20_model.r WARNING @ Mon, 12 Aug 2019 18:26:59: #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 18:26:59: #2 You may need to consider one of the other alternative d(s): 2,31,509,525,545,571 WARNING @ Mon, 12 Aug 2019 18:26:59: #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 18:26:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:26:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:27:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:27:18: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:27:19: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:27:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:27:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:27:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.05_summits.bed INFO @ Mon, 12 Aug 2019 18:27:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (564 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:27:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:27:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:27:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.10_summits.bed INFO @ Mon, 12 Aug 2019 18:27:28: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (260 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:27:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:27:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:27:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331125/SRX331125.20_summits.bed INFO @ Mon, 12 Aug 2019 18:27:28: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (70 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。