Job ID = 4178395 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,084,797 reads read : 19,084,797 reads written : 19,084,797 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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:04:08 19084797 reads; of these: 19084797 (100.00%) were unpaired; of these: 1324385 (6.94%) aligned 0 times 14837294 (77.74%) aligned exactly 1 time 2923118 (15.32%) aligned >1 times 93.06% overall alignment rate Time searching: 00:04:09 Overall time: 00:04:09 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2399619 / 17760412 = 0.1351 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:34:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.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 @ Thu, 05 Dec 2019 12:34:31: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:34:31: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:34:39: 1000000 INFO @ Thu, 05 Dec 2019 12:34:47: 2000000 INFO @ Thu, 05 Dec 2019 12:34:55: 3000000 INFO @ Thu, 05 Dec 2019 12:35:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.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 @ Thu, 05 Dec 2019 12:35:01: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:35:01: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:35:02: 4000000 INFO @ Thu, 05 Dec 2019 12:35:10: 5000000 INFO @ Thu, 05 Dec 2019 12:35:10: 1000000 INFO @ Thu, 05 Dec 2019 12:35:18: 6000000 INFO @ Thu, 05 Dec 2019 12:35:20: 2000000 INFO @ Thu, 05 Dec 2019 12:35:26: 7000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:35:29: 3000000 INFO @ Thu, 05 Dec 2019 12:35:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.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 @ Thu, 05 Dec 2019 12:35:31: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:35:31: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:35:34: 8000000 INFO @ Thu, 05 Dec 2019 12:35:38: 4000000 INFO @ Thu, 05 Dec 2019 12:35:40: 1000000 INFO @ Thu, 05 Dec 2019 12:35:42: 9000000 INFO @ Thu, 05 Dec 2019 12:35:48: 5000000 INFO @ Thu, 05 Dec 2019 12:35:49: 2000000 INFO @ Thu, 05 Dec 2019 12:35:50: 10000000 INFO @ Thu, 05 Dec 2019 12:35:57: 6000000 INFO @ Thu, 05 Dec 2019 12:35:59: 11000000 INFO @ Thu, 05 Dec 2019 12:35:59: 3000000 INFO @ Thu, 05 Dec 2019 12:36:06: 7000000 INFO @ Thu, 05 Dec 2019 12:36:07: 12000000 INFO @ Thu, 05 Dec 2019 12:36:08: 4000000 INFO @ Thu, 05 Dec 2019 12:36:15: 13000000 INFO @ Thu, 05 Dec 2019 12:36:16: 8000000 INFO @ Thu, 05 Dec 2019 12:36:18: 5000000 INFO @ Thu, 05 Dec 2019 12:36:22: 14000000 INFO @ Thu, 05 Dec 2019 12:36:25: 9000000 INFO @ Thu, 05 Dec 2019 12:36:27: 6000000 INFO @ Thu, 05 Dec 2019 12:36:31: 15000000 INFO @ Thu, 05 Dec 2019 12:36:34: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:36:34: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:36:34: #1 total tags in treatment: 15360793 INFO @ Thu, 05 Dec 2019 12:36:34: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:36:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:36:34: #1 tags after filtering in treatment: 15360793 INFO @ Thu, 05 Dec 2019 12:36:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:36:34: #1 finished! INFO @ Thu, 05 Dec 2019 12:36:34: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:36:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:36:35: 10000000 INFO @ Thu, 05 Dec 2019 12:36:35: #2 number of paired peaks: 292 WARNING @ Thu, 05 Dec 2019 12:36:35: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Thu, 05 Dec 2019 12:36:35: start model_add_line... INFO @ Thu, 05 Dec 2019 12:36:35: start X-correlation... INFO @ Thu, 05 Dec 2019 12:36:35: end of X-cor INFO @ Thu, 05 Dec 2019 12:36:35: #2 finished! INFO @ Thu, 05 Dec 2019 12:36:35: #2 predicted fragment length is 69 bps INFO @ Thu, 05 Dec 2019 12:36:35: #2 alternative fragment length(s) may be 4,69 bps INFO @ Thu, 05 Dec 2019 12:36:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.05_model.r WARNING @ Thu, 05 Dec 2019 12:36:35: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:36:35: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Thu, 05 Dec 2019 12:36:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:36:35: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:36:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:36:36: 7000000 INFO @ Thu, 05 Dec 2019 12:36:44: 11000000 INFO @ Thu, 05 Dec 2019 12:36:45: 8000000 INFO @ Thu, 05 Dec 2019 12:36:53: 12000000 INFO @ Thu, 05 Dec 2019 12:36:55: 9000000 INFO @ Thu, 05 Dec 2019 12:37:02: 13000000 INFO @ Thu, 05 Dec 2019 12:37:04: 10000000 INFO @ Thu, 05 Dec 2019 12:37:10: 14000000 INFO @ Thu, 05 Dec 2019 12:37:13: 11000000 INFO @ Thu, 05 Dec 2019 12:37:15: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:37:19: 15000000 INFO @ Thu, 05 Dec 2019 12:37:22: 12000000 INFO @ Thu, 05 Dec 2019 12:37:22: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:37:22: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:37:22: #1 total tags in treatment: 15360793 INFO @ Thu, 05 Dec 2019 12:37:22: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:37:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:37:23: #1 tags after filtering in treatment: 15360793 INFO @ Thu, 05 Dec 2019 12:37:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:37:23: #1 finished! INFO @ Thu, 05 Dec 2019 12:37:23: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:37:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:37:24: #2 number of paired peaks: 292 WARNING @ Thu, 05 Dec 2019 12:37:24: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Thu, 05 Dec 2019 12:37:24: start model_add_line... INFO @ Thu, 05 Dec 2019 12:37:24: start X-correlation... INFO @ Thu, 05 Dec 2019 12:37:24: end of X-cor INFO @ Thu, 05 Dec 2019 12:37:24: #2 finished! INFO @ Thu, 05 Dec 2019 12:37:24: #2 predicted fragment length is 69 bps INFO @ Thu, 05 Dec 2019 12:37:24: #2 alternative fragment length(s) may be 4,69 bps INFO @ Thu, 05 Dec 2019 12:37:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.10_model.r WARNING @ Thu, 05 Dec 2019 12:37:24: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:37:24: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Thu, 05 Dec 2019 12:37:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:37:24: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:37:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:37:31: 13000000 INFO @ Thu, 05 Dec 2019 12:37:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:37:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:37:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.05_summits.bed INFO @ Thu, 05 Dec 2019 12:37:35: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6967 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:37:40: 14000000 INFO @ Thu, 05 Dec 2019 12:37:49: 15000000 INFO @ Thu, 05 Dec 2019 12:37:52: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:37:52: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:37:52: #1 total tags in treatment: 15360793 INFO @ Thu, 05 Dec 2019 12:37:52: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:37:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:37:52: #1 tags after filtering in treatment: 15360793 INFO @ Thu, 05 Dec 2019 12:37:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:37:52: #1 finished! INFO @ Thu, 05 Dec 2019 12:37:52: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:37:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:37:54: #2 number of paired peaks: 292 WARNING @ Thu, 05 Dec 2019 12:37:54: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Thu, 05 Dec 2019 12:37:54: start model_add_line... INFO @ Thu, 05 Dec 2019 12:37:54: start X-correlation... INFO @ Thu, 05 Dec 2019 12:37:54: end of X-cor INFO @ Thu, 05 Dec 2019 12:37:54: #2 finished! INFO @ Thu, 05 Dec 2019 12:37:54: #2 predicted fragment length is 69 bps INFO @ Thu, 05 Dec 2019 12:37:54: #2 alternative fragment length(s) may be 4,69 bps INFO @ Thu, 05 Dec 2019 12:37:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.20_model.r WARNING @ Thu, 05 Dec 2019 12:37:56: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:37:56: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Thu, 05 Dec 2019 12:37:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:37:56: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:37:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:38:03: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:38:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:38:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:38:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.10_summits.bed INFO @ Thu, 05 Dec 2019 12:38:22: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (3960 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:38:35: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:38:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:38:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:38:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107873/SRX4107873.20_summits.bed INFO @ Thu, 05 Dec 2019 12:38:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1516 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。