Job ID = 2589741 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,281,031 reads read : 6,281,031 reads written : 6,281,031 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947348.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: 00:01:16 6281031 reads; of these: 6281031 (100.00%) were unpaired; of these: 264591 (4.21%) aligned 0 times 5047319 (80.36%) aligned exactly 1 time 969121 (15.43%) aligned >1 times 95.79% overall alignment rate Time searching: 00:01:16 Overall time: 00:01:16 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] 367146 / 6016440 = 0.0610 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 18:24:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.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 18:24:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:24:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:24:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.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 18:24:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:24:03: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:24:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.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 18:24:04: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:24:04: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:24:10: 1000000 INFO @ Mon, 12 Aug 2019 18:24:11: 1000000 INFO @ Mon, 12 Aug 2019 18:24:11: 1000000 INFO @ Mon, 12 Aug 2019 18:24:16: 2000000 INFO @ Mon, 12 Aug 2019 18:24:17: 2000000 INFO @ Mon, 12 Aug 2019 18:24:19: 2000000 INFO @ Mon, 12 Aug 2019 18:24:23: 3000000 INFO @ Mon, 12 Aug 2019 18:24:24: 3000000 INFO @ Mon, 12 Aug 2019 18:24:26: 3000000 INFO @ Mon, 12 Aug 2019 18:24:29: 4000000 INFO @ Mon, 12 Aug 2019 18:24:30: 4000000 INFO @ Mon, 12 Aug 2019 18:24:33: 4000000 INFO @ Mon, 12 Aug 2019 18:24:35: 5000000 INFO @ Mon, 12 Aug 2019 18:24:36: 5000000 INFO @ Mon, 12 Aug 2019 18:24:39: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:24:39: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:24:39: #1 total tags in treatment: 5649294 INFO @ Mon, 12 Aug 2019 18:24:39: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:24:39: #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 18:24:39: #1 tags after filtering in treatment: 5649294 INFO @ Mon, 12 Aug 2019 18:24:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:24:39: #1 finished! INFO @ Mon, 12 Aug 2019 18:24:39: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:24:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:24:40: 5000000 INFO @ Mon, 12 Aug 2019 18:24:40: #2 number of paired peaks: 356 WARNING @ Mon, 12 Aug 2019 18:24:40: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Mon, 12 Aug 2019 18:24:40: start model_add_line... INFO @ Mon, 12 Aug 2019 18:24:40: start X-correlation... INFO @ Mon, 12 Aug 2019 18:24:40: end of X-cor INFO @ Mon, 12 Aug 2019 18:24:40: #2 finished! INFO @ Mon, 12 Aug 2019 18:24:40: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 18:24:40: #2 alternative fragment length(s) may be 3,30,596 bps INFO @ Mon, 12 Aug 2019 18:24:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.05_model.r WARNING @ Mon, 12 Aug 2019 18:24:40: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:24:40: #2 You may need to consider one of the other alternative d(s): 3,30,596 WARNING @ Mon, 12 Aug 2019 18:24:40: #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 18:24:40: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:24:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:24:40: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:24:40: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:24:40: #1 total tags in treatment: 5649294 INFO @ Mon, 12 Aug 2019 18:24:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:24:40: #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 18:24:40: #1 tags after filtering in treatment: 5649294 INFO @ Mon, 12 Aug 2019 18:24:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:24:40: #1 finished! INFO @ Mon, 12 Aug 2019 18:24:40: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:24:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:24:41: #2 number of paired peaks: 356 WARNING @ Mon, 12 Aug 2019 18:24:41: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Mon, 12 Aug 2019 18:24:41: start model_add_line... INFO @ Mon, 12 Aug 2019 18:24:41: start X-correlation... INFO @ Mon, 12 Aug 2019 18:24:41: end of X-cor INFO @ Mon, 12 Aug 2019 18:24:41: #2 finished! INFO @ Mon, 12 Aug 2019 18:24:41: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 18:24:41: #2 alternative fragment length(s) may be 3,30,596 bps INFO @ Mon, 12 Aug 2019 18:24:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.20_model.r WARNING @ Mon, 12 Aug 2019 18:24:41: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:24:41: #2 You may need to consider one of the other alternative d(s): 3,30,596 WARNING @ Mon, 12 Aug 2019 18:24:41: #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 18:24:41: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:24:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:24:44: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:24:44: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:24:44: #1 total tags in treatment: 5649294 INFO @ Mon, 12 Aug 2019 18:24:44: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:24:44: #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 18:24:44: #1 tags after filtering in treatment: 5649294 INFO @ Mon, 12 Aug 2019 18:24:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:24:44: #1 finished! INFO @ Mon, 12 Aug 2019 18:24:44: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:24:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:24:45: #2 number of paired peaks: 356 WARNING @ Mon, 12 Aug 2019 18:24:45: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Mon, 12 Aug 2019 18:24:45: start model_add_line... INFO @ Mon, 12 Aug 2019 18:24:45: start X-correlation... INFO @ Mon, 12 Aug 2019 18:24:45: end of X-cor INFO @ Mon, 12 Aug 2019 18:24:45: #2 finished! INFO @ Mon, 12 Aug 2019 18:24:45: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 18:24:45: #2 alternative fragment length(s) may be 3,30,596 bps INFO @ Mon, 12 Aug 2019 18:24:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.10_model.r WARNING @ Mon, 12 Aug 2019 18:24:45: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:24:45: #2 You may need to consider one of the other alternative d(s): 3,30,596 WARNING @ Mon, 12 Aug 2019 18:24:45: #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 18:24:45: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:24:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:24:56: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:24:57: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:25:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:25:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:25:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:25:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.05_summits.bed INFO @ Mon, 12 Aug 2019 18:25:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (480 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:25:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:25:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:25:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.20_summits.bed INFO @ Mon, 12 Aug 2019 18:25:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (57 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:25:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:25:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:25:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331117/SRX331117.10_summits.bed INFO @ Mon, 12 Aug 2019 18:25:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (223 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。