Job ID = 2589366 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,998,257 reads read : 24,998,257 reads written : 24,998,257 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: 00:00:00 Multiseed full-index search: 00:06:16 24998257 reads; of these: 24998257 (100.00%) were unpaired; of these: 303349 (1.21%) aligned 0 times 20671683 (82.69%) aligned exactly 1 time 4023225 (16.09%) aligned >1 times 98.79% overall alignment rate Time searching: 00:06:16 Overall time: 00:06:16 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_sort_core] merging from 12 files... [bam_rmdupse_core] 5612596 / 24694908 = 0.2273 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 17:57:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.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 17:57:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:57:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:57:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.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 17:57:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:57:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:57:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.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 17:57:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:57:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:58:04: 1000000 INFO @ Mon, 12 Aug 2019 17:58:04: 1000000 INFO @ Mon, 12 Aug 2019 17:58:05: 1000000 INFO @ Mon, 12 Aug 2019 17:58:11: 2000000 INFO @ Mon, 12 Aug 2019 17:58:11: 2000000 INFO @ Mon, 12 Aug 2019 17:58:11: 2000000 INFO @ Mon, 12 Aug 2019 17:58:18: 3000000 INFO @ Mon, 12 Aug 2019 17:58:18: 3000000 INFO @ Mon, 12 Aug 2019 17:58:19: 3000000 INFO @ Mon, 12 Aug 2019 17:58:25: 4000000 INFO @ Mon, 12 Aug 2019 17:58:26: 4000000 INFO @ Mon, 12 Aug 2019 17:58:26: 4000000 INFO @ Mon, 12 Aug 2019 17:58:31: 5000000 INFO @ Mon, 12 Aug 2019 17:58:33: 5000000 INFO @ Mon, 12 Aug 2019 17:58:33: 5000000 INFO @ Mon, 12 Aug 2019 17:58:38: 6000000 INFO @ Mon, 12 Aug 2019 17:58:40: 6000000 INFO @ Mon, 12 Aug 2019 17:58:41: 6000000 INFO @ Mon, 12 Aug 2019 17:58:44: 7000000 INFO @ Mon, 12 Aug 2019 17:58:47: 7000000 INFO @ Mon, 12 Aug 2019 17:58:48: 7000000 INFO @ Mon, 12 Aug 2019 17:58:51: 8000000 INFO @ Mon, 12 Aug 2019 17:58:53: 8000000 INFO @ Mon, 12 Aug 2019 17:58:55: 8000000 INFO @ Mon, 12 Aug 2019 17:58:57: 9000000 INFO @ Mon, 12 Aug 2019 17:59:00: 9000000 INFO @ Mon, 12 Aug 2019 17:59:02: 9000000 INFO @ Mon, 12 Aug 2019 17:59:03: 10000000 INFO @ Mon, 12 Aug 2019 17:59:07: 10000000 INFO @ Mon, 12 Aug 2019 17:59:09: 10000000 INFO @ Mon, 12 Aug 2019 17:59:10: 11000000 INFO @ Mon, 12 Aug 2019 17:59:14: 11000000 INFO @ Mon, 12 Aug 2019 17:59:16: 12000000 INFO @ Mon, 12 Aug 2019 17:59:16: 11000000 INFO @ Mon, 12 Aug 2019 17:59:21: 12000000 INFO @ Mon, 12 Aug 2019 17:59:23: 13000000 INFO @ Mon, 12 Aug 2019 17:59:24: 12000000 INFO @ Mon, 12 Aug 2019 17:59:28: 13000000 INFO @ Mon, 12 Aug 2019 17:59:29: 14000000 INFO @ Mon, 12 Aug 2019 17:59:31: 13000000 INFO @ Mon, 12 Aug 2019 17:59:35: 14000000 INFO @ Mon, 12 Aug 2019 17:59:36: 15000000 INFO @ Mon, 12 Aug 2019 17:59:38: 14000000 INFO @ Mon, 12 Aug 2019 17:59:42: 15000000 INFO @ Mon, 12 Aug 2019 17:59:42: 16000000 INFO @ Mon, 12 Aug 2019 17:59:45: 15000000 INFO @ Mon, 12 Aug 2019 17:59:48: 16000000 INFO @ Mon, 12 Aug 2019 17:59:49: 17000000 INFO @ Mon, 12 Aug 2019 17:59:52: 16000000 INFO @ Mon, 12 Aug 2019 17:59:55: 18000000 INFO @ Mon, 12 Aug 2019 17:59:55: 17000000 INFO @ Mon, 12 Aug 2019 18:00:00: 17000000 INFO @ Mon, 12 Aug 2019 18:00:02: 19000000 INFO @ Mon, 12 Aug 2019 18:00:02: 18000000 INFO @ Mon, 12 Aug 2019 18:00:02: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:00:02: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:00:02: #1 total tags in treatment: 19082312 INFO @ Mon, 12 Aug 2019 18:00:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:00:02: #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 18:00:03: #1 tags after filtering in treatment: 19082312 INFO @ Mon, 12 Aug 2019 18:00:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:00:03: #1 finished! INFO @ Mon, 12 Aug 2019 18:00:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:00:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:00:04: #2 number of paired peaks: 256 WARNING @ Mon, 12 Aug 2019 18:00:04: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Mon, 12 Aug 2019 18:00:04: start model_add_line... INFO @ Mon, 12 Aug 2019 18:00:04: start X-correlation... INFO @ Mon, 12 Aug 2019 18:00:04: end of X-cor INFO @ Mon, 12 Aug 2019 18:00:04: #2 finished! INFO @ Mon, 12 Aug 2019 18:00:04: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 18:00:04: #2 alternative fragment length(s) may be 1,35,50,555 bps INFO @ Mon, 12 Aug 2019 18:00:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.20_model.r WARNING @ Mon, 12 Aug 2019 18:00:04: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:00:04: #2 You may need to consider one of the other alternative d(s): 1,35,50,555 WARNING @ Mon, 12 Aug 2019 18:00:04: #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 18:00:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:00:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:00:07: 18000000 INFO @ Mon, 12 Aug 2019 18:00:09: 19000000 INFO @ Mon, 12 Aug 2019 18:00:10: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:00:10: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:00:10: #1 total tags in treatment: 19082312 INFO @ Mon, 12 Aug 2019 18:00:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:00:10: #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 18:00:10: #1 tags after filtering in treatment: 19082312 INFO @ Mon, 12 Aug 2019 18:00:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:00:10: #1 finished! INFO @ Mon, 12 Aug 2019 18:00:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:00:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:00:12: #2 number of paired peaks: 256 WARNING @ Mon, 12 Aug 2019 18:00:12: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Mon, 12 Aug 2019 18:00:12: start model_add_line... INFO @ Mon, 12 Aug 2019 18:00:12: start X-correlation... INFO @ Mon, 12 Aug 2019 18:00:12: end of X-cor INFO @ Mon, 12 Aug 2019 18:00:12: #2 finished! INFO @ Mon, 12 Aug 2019 18:00:12: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 18:00:12: #2 alternative fragment length(s) may be 1,35,50,555 bps INFO @ Mon, 12 Aug 2019 18:00:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.10_model.r WARNING @ Mon, 12 Aug 2019 18:00:12: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:00:12: #2 You may need to consider one of the other alternative d(s): 1,35,50,555 WARNING @ Mon, 12 Aug 2019 18:00:12: #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 18:00:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:00:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:00:14: 19000000 INFO @ Mon, 12 Aug 2019 18:00:15: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:00:15: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:00:15: #1 total tags in treatment: 19082312 INFO @ Mon, 12 Aug 2019 18:00:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:00:15: #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 18:00:15: #1 tags after filtering in treatment: 19082312 INFO @ Mon, 12 Aug 2019 18:00:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:00:15: #1 finished! INFO @ Mon, 12 Aug 2019 18:00:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:00:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:00:17: #2 number of paired peaks: 256 WARNING @ Mon, 12 Aug 2019 18:00:17: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Mon, 12 Aug 2019 18:00:17: start model_add_line... INFO @ Mon, 12 Aug 2019 18:00:17: start X-correlation... INFO @ Mon, 12 Aug 2019 18:00:17: end of X-cor INFO @ Mon, 12 Aug 2019 18:00:17: #2 finished! INFO @ Mon, 12 Aug 2019 18:00:17: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 18:00:17: #2 alternative fragment length(s) may be 1,35,50,555 bps INFO @ Mon, 12 Aug 2019 18:00:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.05_model.r WARNING @ Mon, 12 Aug 2019 18:00:17: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:00:17: #2 You may need to consider one of the other alternative d(s): 1,35,50,555 WARNING @ Mon, 12 Aug 2019 18:00:17: #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 18:00:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:00:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:00:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:00:56: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:01:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:01:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:01:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:01:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.20_summits.bed INFO @ Mon, 12 Aug 2019 18:01:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (184 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:01:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:01:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:01:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.10_summits.bed INFO @ Mon, 12 Aug 2019 18:01:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (496 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:01:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:01:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:01:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078718/SRX1078718.05_summits.bed INFO @ Mon, 12 Aug 2019 18:01:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (759 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。