Job ID = 1291516 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,026,814 reads read : 20,026,814 reads written : 20,026,814 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:03:40 20026814 reads; of these: 20026814 (100.00%) were unpaired; of these: 255928 (1.28%) aligned 0 times 16502508 (82.40%) aligned exactly 1 time 3268378 (16.32%) aligned >1 times 98.72% overall alignment rate Time searching: 00:03:40 Overall time: 00:03:40 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] 2190460 / 19770886 = 0.1108 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 @ Sun, 02 Jun 2019 16:10:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.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 @ Sun, 02 Jun 2019 16:10:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:10:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:10:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.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 @ Sun, 02 Jun 2019 16:10:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:10:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:10:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.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 @ Sun, 02 Jun 2019 16:10:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:10:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:10:53: 1000000 INFO @ Sun, 02 Jun 2019 16:10:54: 1000000 INFO @ Sun, 02 Jun 2019 16:10:56: 1000000 INFO @ Sun, 02 Jun 2019 16:11:00: 2000000 INFO @ Sun, 02 Jun 2019 16:11:02: 2000000 INFO @ Sun, 02 Jun 2019 16:11:05: 2000000 INFO @ Sun, 02 Jun 2019 16:11:08: 3000000 INFO @ Sun, 02 Jun 2019 16:11:10: 3000000 INFO @ Sun, 02 Jun 2019 16:11:15: 3000000 INFO @ Sun, 02 Jun 2019 16:11:15: 4000000 INFO @ Sun, 02 Jun 2019 16:11:18: 4000000 INFO @ Sun, 02 Jun 2019 16:11:22: 5000000 INFO @ Sun, 02 Jun 2019 16:11:25: 4000000 INFO @ Sun, 02 Jun 2019 16:11:26: 5000000 INFO @ Sun, 02 Jun 2019 16:11:29: 6000000 INFO @ Sun, 02 Jun 2019 16:11:33: 6000000 INFO @ Sun, 02 Jun 2019 16:11:34: 5000000 INFO @ Sun, 02 Jun 2019 16:11:36: 7000000 INFO @ Sun, 02 Jun 2019 16:11:41: 7000000 INFO @ Sun, 02 Jun 2019 16:11:43: 8000000 INFO @ Sun, 02 Jun 2019 16:11:43: 6000000 INFO @ Sun, 02 Jun 2019 16:11:49: 8000000 INFO @ Sun, 02 Jun 2019 16:11:50: 9000000 INFO @ Sun, 02 Jun 2019 16:11:52: 7000000 INFO @ Sun, 02 Jun 2019 16:11:56: 9000000 INFO @ Sun, 02 Jun 2019 16:11:57: 10000000 INFO @ Sun, 02 Jun 2019 16:12:01: 8000000 INFO @ Sun, 02 Jun 2019 16:12:03: 11000000 INFO @ Sun, 02 Jun 2019 16:12:04: 10000000 INFO @ Sun, 02 Jun 2019 16:12:10: 12000000 INFO @ Sun, 02 Jun 2019 16:12:10: 9000000 INFO @ Sun, 02 Jun 2019 16:12:12: 11000000 INFO @ Sun, 02 Jun 2019 16:12:17: 13000000 INFO @ Sun, 02 Jun 2019 16:12:19: 12000000 INFO @ Sun, 02 Jun 2019 16:12:19: 10000000 INFO @ Sun, 02 Jun 2019 16:12:24: 14000000 INFO @ Sun, 02 Jun 2019 16:12:27: 13000000 INFO @ Sun, 02 Jun 2019 16:12:28: 11000000 INFO @ Sun, 02 Jun 2019 16:12:31: 15000000 INFO @ Sun, 02 Jun 2019 16:12:34: 14000000 INFO @ Sun, 02 Jun 2019 16:12:37: 12000000 INFO @ Sun, 02 Jun 2019 16:12:38: 16000000 INFO @ Sun, 02 Jun 2019 16:12:42: 15000000 INFO @ Sun, 02 Jun 2019 16:12:45: 17000000 INFO @ Sun, 02 Jun 2019 16:12:46: 13000000 INFO @ Sun, 02 Jun 2019 16:12:49: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:12:49: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:12:49: #1 total tags in treatment: 17580426 INFO @ Sun, 02 Jun 2019 16:12:49: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:12:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:12:49: #1 tags after filtering in treatment: 17580426 INFO @ Sun, 02 Jun 2019 16:12:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:12:49: #1 finished! INFO @ Sun, 02 Jun 2019 16:12:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:12:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:12:50: 16000000 INFO @ Sun, 02 Jun 2019 16:12:51: #2 number of paired peaks: 150 WARNING @ Sun, 02 Jun 2019 16:12:51: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sun, 02 Jun 2019 16:12:51: start model_add_line... INFO @ Sun, 02 Jun 2019 16:12:51: start X-correlation... INFO @ Sun, 02 Jun 2019 16:12:51: end of X-cor INFO @ Sun, 02 Jun 2019 16:12:51: #2 finished! INFO @ Sun, 02 Jun 2019 16:12:51: #2 predicted fragment length is 34 bps INFO @ Sun, 02 Jun 2019 16:12:51: #2 alternative fragment length(s) may be 1,34,543 bps INFO @ Sun, 02 Jun 2019 16:12:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.05_model.r WARNING @ Sun, 02 Jun 2019 16:12:51: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:12:51: #2 You may need to consider one of the other alternative d(s): 1,34,543 WARNING @ Sun, 02 Jun 2019 16:12:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 16:12:51: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:12:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:12:55: 14000000 INFO @ Sun, 02 Jun 2019 16:12:57: 17000000 INFO @ Sun, 02 Jun 2019 16:13:01: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:13:01: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:13:01: #1 total tags in treatment: 17580426 INFO @ Sun, 02 Jun 2019 16:13:01: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:13:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:13:02: #1 tags after filtering in treatment: 17580426 INFO @ Sun, 02 Jun 2019 16:13:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:13:02: #1 finished! INFO @ Sun, 02 Jun 2019 16:13:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:13:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:13:03: #2 number of paired peaks: 150 WARNING @ Sun, 02 Jun 2019 16:13:03: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sun, 02 Jun 2019 16:13:03: start model_add_line... INFO @ Sun, 02 Jun 2019 16:13:03: start X-correlation... INFO @ Sun, 02 Jun 2019 16:13:03: end of X-cor INFO @ Sun, 02 Jun 2019 16:13:03: #2 finished! INFO @ Sun, 02 Jun 2019 16:13:03: #2 predicted fragment length is 34 bps INFO @ Sun, 02 Jun 2019 16:13:03: #2 alternative fragment length(s) may be 1,34,543 bps INFO @ Sun, 02 Jun 2019 16:13:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.10_model.r WARNING @ Sun, 02 Jun 2019 16:13:03: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:13:03: #2 You may need to consider one of the other alternative d(s): 1,34,543 WARNING @ Sun, 02 Jun 2019 16:13:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 16:13:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:13:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:13:04: 15000000 INFO @ Sun, 02 Jun 2019 16:13:12: 16000000 INFO @ Sun, 02 Jun 2019 16:13:21: 17000000 INFO @ Sun, 02 Jun 2019 16:13:26: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:13:26: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:13:26: #1 total tags in treatment: 17580426 INFO @ Sun, 02 Jun 2019 16:13:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:13:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:13:27: #1 tags after filtering in treatment: 17580426 INFO @ Sun, 02 Jun 2019 16:13:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:13:27: #1 finished! INFO @ Sun, 02 Jun 2019 16:13:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:13:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:13:28: #2 number of paired peaks: 150 WARNING @ Sun, 02 Jun 2019 16:13:28: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sun, 02 Jun 2019 16:13:28: start model_add_line... INFO @ Sun, 02 Jun 2019 16:13:28: start X-correlation... INFO @ Sun, 02 Jun 2019 16:13:28: end of X-cor INFO @ Sun, 02 Jun 2019 16:13:28: #2 finished! INFO @ Sun, 02 Jun 2019 16:13:28: #2 predicted fragment length is 34 bps INFO @ Sun, 02 Jun 2019 16:13:28: #2 alternative fragment length(s) may be 1,34,543 bps INFO @ Sun, 02 Jun 2019 16:13:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.20_model.r WARNING @ Sun, 02 Jun 2019 16:13:28: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:13:28: #2 You may need to consider one of the other alternative d(s): 1,34,543 WARNING @ Sun, 02 Jun 2019 16:13:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 16:13:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:13:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:13:32: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:13:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:13:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:13:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:13:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.05_summits.bed INFO @ Sun, 02 Jun 2019 16:13:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (541 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:14:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:14:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:14:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.10_summits.bed INFO @ Sun, 02 Jun 2019 16:14:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (234 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:14:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:14:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:14:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:14:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX105309/SRX105309.20_summits.bed INFO @ Sun, 02 Jun 2019 16:14:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (46 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。