Job ID = 2590027 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,047,878 reads read : 16,047,878 reads written : 16,047,878 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: 00:03:02 16047878 reads; of these: 16047878 (100.00%) were unpaired; of these: 1451996 (9.05%) aligned 0 times 12365453 (77.05%) aligned exactly 1 time 2230429 (13.90%) aligned >1 times 90.95% overall alignment rate Time searching: 00:03:03 Overall time: 00:03:03 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] 1646097 / 14595882 = 0.1128 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 19:26:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.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 19:26:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:26:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:26:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.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 19:26:06: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:26:06: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:26:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.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 19:26:07: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:26:07: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:26:12: 1000000 INFO @ Mon, 12 Aug 2019 19:26:13: 1000000 INFO @ Mon, 12 Aug 2019 19:26:15: 1000000 INFO @ Mon, 12 Aug 2019 19:26:19: 2000000 INFO @ Mon, 12 Aug 2019 19:26:20: 2000000 INFO @ Mon, 12 Aug 2019 19:26:23: 2000000 INFO @ Mon, 12 Aug 2019 19:26:26: 3000000 INFO @ Mon, 12 Aug 2019 19:26:27: 3000000 INFO @ Mon, 12 Aug 2019 19:26:30: 3000000 INFO @ Mon, 12 Aug 2019 19:26:33: 4000000 INFO @ Mon, 12 Aug 2019 19:26:34: 4000000 INFO @ Mon, 12 Aug 2019 19:26:38: 4000000 INFO @ Mon, 12 Aug 2019 19:26:40: 5000000 INFO @ Mon, 12 Aug 2019 19:26:41: 5000000 INFO @ Mon, 12 Aug 2019 19:26:45: 5000000 INFO @ Mon, 12 Aug 2019 19:26:47: 6000000 INFO @ Mon, 12 Aug 2019 19:26:48: 6000000 INFO @ Mon, 12 Aug 2019 19:26:53: 6000000 INFO @ Mon, 12 Aug 2019 19:26:54: 7000000 INFO @ Mon, 12 Aug 2019 19:26:55: 7000000 INFO @ Mon, 12 Aug 2019 19:27:00: 7000000 INFO @ Mon, 12 Aug 2019 19:27:01: 8000000 INFO @ Mon, 12 Aug 2019 19:27:02: 8000000 INFO @ Mon, 12 Aug 2019 19:27:08: 9000000 INFO @ Mon, 12 Aug 2019 19:27:08: 8000000 INFO @ Mon, 12 Aug 2019 19:27:09: 9000000 INFO @ Mon, 12 Aug 2019 19:27:15: 10000000 INFO @ Mon, 12 Aug 2019 19:27:16: 10000000 INFO @ Mon, 12 Aug 2019 19:27:16: 9000000 INFO @ Mon, 12 Aug 2019 19:27:22: 11000000 INFO @ Mon, 12 Aug 2019 19:27:23: 11000000 INFO @ Mon, 12 Aug 2019 19:27:24: 10000000 INFO @ Mon, 12 Aug 2019 19:27:29: 12000000 INFO @ Mon, 12 Aug 2019 19:27:30: 12000000 INFO @ Mon, 12 Aug 2019 19:27:31: 11000000 INFO @ Mon, 12 Aug 2019 19:27:35: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:27:35: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:27:35: #1 total tags in treatment: 12949785 INFO @ Mon, 12 Aug 2019 19:27:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:27:35: #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 19:27:35: #1 tags after filtering in treatment: 12949785 INFO @ Mon, 12 Aug 2019 19:27:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:27:35: #1 finished! INFO @ Mon, 12 Aug 2019 19:27:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:27:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:27:36: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:27:36: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:27:36: #1 total tags in treatment: 12949785 INFO @ Mon, 12 Aug 2019 19:27:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:27:36: #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 19:27:37: #2 number of paired peaks: 276 WARNING @ Mon, 12 Aug 2019 19:27:37: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Mon, 12 Aug 2019 19:27:37: start model_add_line... INFO @ Mon, 12 Aug 2019 19:27:37: #1 tags after filtering in treatment: 12949785 INFO @ Mon, 12 Aug 2019 19:27:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:27:37: #1 finished! INFO @ Mon, 12 Aug 2019 19:27:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:27:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:27:37: start X-correlation... INFO @ Mon, 12 Aug 2019 19:27:37: end of X-cor INFO @ Mon, 12 Aug 2019 19:27:37: #2 finished! INFO @ Mon, 12 Aug 2019 19:27:37: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 19:27:37: #2 alternative fragment length(s) may be 2,45 bps INFO @ Mon, 12 Aug 2019 19:27:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.05_model.r WARNING @ Mon, 12 Aug 2019 19:27:37: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:27:37: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Mon, 12 Aug 2019 19:27:37: #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 19:27:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:27:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:27:38: #2 number of paired peaks: 276 WARNING @ Mon, 12 Aug 2019 19:27:38: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Mon, 12 Aug 2019 19:27:38: start model_add_line... INFO @ Mon, 12 Aug 2019 19:27:38: start X-correlation... INFO @ Mon, 12 Aug 2019 19:27:38: end of X-cor INFO @ Mon, 12 Aug 2019 19:27:38: #2 finished! INFO @ Mon, 12 Aug 2019 19:27:38: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 19:27:38: #2 alternative fragment length(s) may be 2,45 bps INFO @ Mon, 12 Aug 2019 19:27:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.10_model.r WARNING @ Mon, 12 Aug 2019 19:27:38: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:27:38: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Mon, 12 Aug 2019 19:27:38: #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 19:27:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:27:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:27:39: 12000000 INFO @ Mon, 12 Aug 2019 19:27:46: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:27:46: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:27:46: #1 total tags in treatment: 12949785 INFO @ Mon, 12 Aug 2019 19:27:46: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:27:46: #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 19:27:46: #1 tags after filtering in treatment: 12949785 INFO @ Mon, 12 Aug 2019 19:27:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:27:46: #1 finished! INFO @ Mon, 12 Aug 2019 19:27:46: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:27:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:27:47: #2 number of paired peaks: 276 WARNING @ Mon, 12 Aug 2019 19:27:47: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Mon, 12 Aug 2019 19:27:47: start model_add_line... INFO @ Mon, 12 Aug 2019 19:27:47: start X-correlation... INFO @ Mon, 12 Aug 2019 19:27:47: end of X-cor INFO @ Mon, 12 Aug 2019 19:27:47: #2 finished! INFO @ Mon, 12 Aug 2019 19:27:47: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 19:27:47: #2 alternative fragment length(s) may be 2,45 bps INFO @ Mon, 12 Aug 2019 19:27:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.20_model.r WARNING @ Mon, 12 Aug 2019 19:27:47: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:27:47: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Mon, 12 Aug 2019 19:27:47: #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 19:27:47: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:27:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:28:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:28:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:28:19: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:28:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:28:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:28:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.05_summits.bed INFO @ Mon, 12 Aug 2019 19:28:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (615 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:28:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:28:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:28:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.10_summits.bed INFO @ Mon, 12 Aug 2019 19:28:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (372 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:28:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:28:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:28:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494871/SRX494871.20_summits.bed INFO @ Mon, 12 Aug 2019 19:28:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (134 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。