Job ID = 2589377 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,431,794 reads read : 17,431,794 reads written : 17,431,794 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: 00:04:28 17431794 reads; of these: 17431794 (100.00%) were unpaired; of these: 235339 (1.35%) aligned 0 times 14451990 (82.91%) aligned exactly 1 time 2744465 (15.74%) aligned >1 times 98.65% overall alignment rate Time searching: 00:04:28 Overall time: 00:04:28 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] 3133247 / 17196455 = 0.1822 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 17:50:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.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 17:50:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:50:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:50:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.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 17:50:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:50:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:50:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.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 17:50:39: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:50:39: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:50:45: 1000000 INFO @ Mon, 12 Aug 2019 17:50:45: 1000000 INFO @ Mon, 12 Aug 2019 17:50:47: 1000000 INFO @ Mon, 12 Aug 2019 17:50:52: 2000000 INFO @ Mon, 12 Aug 2019 17:50:52: 2000000 INFO @ Mon, 12 Aug 2019 17:50:54: 2000000 INFO @ Mon, 12 Aug 2019 17:50:59: 3000000 INFO @ Mon, 12 Aug 2019 17:51:00: 3000000 INFO @ Mon, 12 Aug 2019 17:51:02: 3000000 INFO @ Mon, 12 Aug 2019 17:51:06: 4000000 INFO @ Mon, 12 Aug 2019 17:51:07: 4000000 INFO @ Mon, 12 Aug 2019 17:51:09: 4000000 INFO @ Mon, 12 Aug 2019 17:51:13: 5000000 INFO @ Mon, 12 Aug 2019 17:51:15: 5000000 INFO @ Mon, 12 Aug 2019 17:51:17: 5000000 INFO @ Mon, 12 Aug 2019 17:51:19: 6000000 INFO @ Mon, 12 Aug 2019 17:51:22: 6000000 INFO @ Mon, 12 Aug 2019 17:51:24: 6000000 INFO @ Mon, 12 Aug 2019 17:51:26: 7000000 INFO @ Mon, 12 Aug 2019 17:51:30: 7000000 INFO @ Mon, 12 Aug 2019 17:51:32: 7000000 INFO @ Mon, 12 Aug 2019 17:51:33: 8000000 INFO @ Mon, 12 Aug 2019 17:51:37: 8000000 INFO @ Mon, 12 Aug 2019 17:51:39: 8000000 INFO @ Mon, 12 Aug 2019 17:51:40: 9000000 INFO @ Mon, 12 Aug 2019 17:51:45: 9000000 INFO @ Mon, 12 Aug 2019 17:51:47: 9000000 INFO @ Mon, 12 Aug 2019 17:51:47: 10000000 INFO @ Mon, 12 Aug 2019 17:51:53: 10000000 INFO @ Mon, 12 Aug 2019 17:51:54: 11000000 INFO @ Mon, 12 Aug 2019 17:51:54: 10000000 INFO @ Mon, 12 Aug 2019 17:52:00: 11000000 INFO @ Mon, 12 Aug 2019 17:52:01: 12000000 INFO @ Mon, 12 Aug 2019 17:52:02: 11000000 INFO @ Mon, 12 Aug 2019 17:52:08: 12000000 INFO @ Mon, 12 Aug 2019 17:52:08: 13000000 INFO @ Mon, 12 Aug 2019 17:52:09: 12000000 INFO @ Mon, 12 Aug 2019 17:52:15: 14000000 INFO @ Mon, 12 Aug 2019 17:52:15: 13000000 INFO @ Mon, 12 Aug 2019 17:52:15: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:52:15: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:52:15: #1 total tags in treatment: 14063208 INFO @ Mon, 12 Aug 2019 17:52:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:52:15: #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 17:52:16: #1 tags after filtering in treatment: 14063208 INFO @ Mon, 12 Aug 2019 17:52:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:52:16: #1 finished! INFO @ Mon, 12 Aug 2019 17:52:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:52:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:52:17: #2 number of paired peaks: 322 WARNING @ Mon, 12 Aug 2019 17:52:17: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Mon, 12 Aug 2019 17:52:17: start model_add_line... INFO @ Mon, 12 Aug 2019 17:52:17: 13000000 INFO @ Mon, 12 Aug 2019 17:52:17: start X-correlation... INFO @ Mon, 12 Aug 2019 17:52:17: end of X-cor INFO @ Mon, 12 Aug 2019 17:52:17: #2 finished! INFO @ Mon, 12 Aug 2019 17:52:17: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 17:52:17: #2 alternative fragment length(s) may be 1,43,560 bps INFO @ Mon, 12 Aug 2019 17:52:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.10_model.r WARNING @ Mon, 12 Aug 2019 17:52:17: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:52:17: #2 You may need to consider one of the other alternative d(s): 1,43,560 WARNING @ Mon, 12 Aug 2019 17:52:17: #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 17:52:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:52:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:52:23: 14000000 INFO @ Mon, 12 Aug 2019 17:52:23: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:52:23: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:52:23: #1 total tags in treatment: 14063208 INFO @ Mon, 12 Aug 2019 17:52:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:52:23: #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 17:52:23: #1 tags after filtering in treatment: 14063208 INFO @ Mon, 12 Aug 2019 17:52:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:52:23: #1 finished! INFO @ Mon, 12 Aug 2019 17:52:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:52:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:52:24: 14000000 INFO @ Mon, 12 Aug 2019 17:52:25: #2 number of paired peaks: 322 WARNING @ Mon, 12 Aug 2019 17:52:25: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Mon, 12 Aug 2019 17:52:25: start model_add_line... INFO @ Mon, 12 Aug 2019 17:52:25: start X-correlation... INFO @ Mon, 12 Aug 2019 17:52:25: end of X-cor INFO @ Mon, 12 Aug 2019 17:52:25: #2 finished! INFO @ Mon, 12 Aug 2019 17:52:25: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 17:52:25: #2 alternative fragment length(s) may be 1,43,560 bps INFO @ Mon, 12 Aug 2019 17:52:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.05_model.r WARNING @ Mon, 12 Aug 2019 17:52:25: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:52:25: #2 You may need to consider one of the other alternative d(s): 1,43,560 WARNING @ Mon, 12 Aug 2019 17:52:25: #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 17:52:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:52:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:52:25: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:52:25: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:52:25: #1 total tags in treatment: 14063208 INFO @ Mon, 12 Aug 2019 17:52:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:52:25: #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 17:52:25: #1 tags after filtering in treatment: 14063208 INFO @ Mon, 12 Aug 2019 17:52:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:52:25: #1 finished! INFO @ Mon, 12 Aug 2019 17:52:25: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:52:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:52:27: #2 number of paired peaks: 322 WARNING @ Mon, 12 Aug 2019 17:52:27: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Mon, 12 Aug 2019 17:52:27: start model_add_line... INFO @ Mon, 12 Aug 2019 17:52:27: start X-correlation... INFO @ Mon, 12 Aug 2019 17:52:27: end of X-cor INFO @ Mon, 12 Aug 2019 17:52:27: #2 finished! INFO @ Mon, 12 Aug 2019 17:52:27: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 17:52:27: #2 alternative fragment length(s) may be 1,43,560 bps INFO @ Mon, 12 Aug 2019 17:52:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.20_model.r WARNING @ Mon, 12 Aug 2019 17:52:27: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:52:27: #2 You may need to consider one of the other alternative d(s): 1,43,560 WARNING @ Mon, 12 Aug 2019 17:52:27: #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 17:52:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:52:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:52:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:53:00: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:53:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:53:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:53:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:53:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.10_summits.bed INFO @ Mon, 12 Aug 2019 17:53:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (478 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:53:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:53:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:53:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.05_summits.bed INFO @ Mon, 12 Aug 2019 17:53:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (729 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:53:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:53:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:53:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078728/SRX1078728.20_summits.bed INFO @ Mon, 12 Aug 2019 17:53:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (159 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。