Job ID = 4178408 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,001,637 reads read : 22,003,274 reads written : 11,001,637 reads 0-length : 11,001,637 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: 00:03:21 11001637 reads; of these: 11001637 (100.00%) were unpaired; of these: 1066077 (9.69%) aligned 0 times 8289748 (75.35%) aligned exactly 1 time 1645812 (14.96%) aligned >1 times 90.31% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 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] 789962 / 9935560 = 0.0795 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:28:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.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 12:28:02: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:28:02: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:28:08: 1000000 INFO @ Thu, 05 Dec 2019 12:28:14: 2000000 INFO @ Thu, 05 Dec 2019 12:28:21: 3000000 INFO @ Thu, 05 Dec 2019 12:28:27: 4000000 INFO @ Thu, 05 Dec 2019 12:28:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.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 12:28:32: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:28:32: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:28:33: 5000000 INFO @ Thu, 05 Dec 2019 12:28:38: 1000000 INFO @ Thu, 05 Dec 2019 12:28:40: 6000000 INFO @ Thu, 05 Dec 2019 12:28:45: 2000000 INFO @ Thu, 05 Dec 2019 12:28:46: 7000000 INFO @ Thu, 05 Dec 2019 12:28:52: 3000000 INFO @ Thu, 05 Dec 2019 12:28:53: 8000000 INFO @ Thu, 05 Dec 2019 12:28:58: 4000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:29:00: 9000000 INFO @ Thu, 05 Dec 2019 12:29:01: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:29:01: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:29:01: #1 total tags in treatment: 9145598 INFO @ Thu, 05 Dec 2019 12:29:01: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:29:01: #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 12:29:01: #1 tags after filtering in treatment: 9145598 INFO @ Thu, 05 Dec 2019 12:29:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:29:01: #1 finished! INFO @ Thu, 05 Dec 2019 12:29:01: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:29:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:29:01: #2 number of paired peaks: 330 WARNING @ Thu, 05 Dec 2019 12:29:01: Fewer paired peaks (330) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 330 pairs to build model! INFO @ Thu, 05 Dec 2019 12:29:01: start model_add_line... INFO @ Thu, 05 Dec 2019 12:29:02: start X-correlation... INFO @ Thu, 05 Dec 2019 12:29:02: end of X-cor INFO @ Thu, 05 Dec 2019 12:29:02: #2 finished! INFO @ Thu, 05 Dec 2019 12:29:02: #2 predicted fragment length is 74 bps INFO @ Thu, 05 Dec 2019 12:29:02: #2 alternative fragment length(s) may be 74 bps INFO @ Thu, 05 Dec 2019 12:29:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.05_model.r WARNING @ Thu, 05 Dec 2019 12:29:02: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:29:02: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Thu, 05 Dec 2019 12:29:02: #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 12:29:02: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:29:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.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 12:29:02: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:29:02: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:29:04: 5000000 INFO @ Thu, 05 Dec 2019 12:29:08: 1000000 INFO @ Thu, 05 Dec 2019 12:29:11: 6000000 INFO @ Thu, 05 Dec 2019 12:29:14: 2000000 INFO @ Thu, 05 Dec 2019 12:29:17: 7000000 INFO @ Thu, 05 Dec 2019 12:29:19: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:29:20: 3000000 INFO @ Thu, 05 Dec 2019 12:29:24: 8000000 INFO @ Thu, 05 Dec 2019 12:29:26: 4000000 INFO @ Thu, 05 Dec 2019 12:29:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:29:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:29:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.05_summits.bed INFO @ Thu, 05 Dec 2019 12:29:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (600 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:29:30: 9000000 INFO @ Thu, 05 Dec 2019 12:29:31: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:29:31: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:29:31: #1 total tags in treatment: 9145598 INFO @ Thu, 05 Dec 2019 12:29:31: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:29:31: #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 12:29:31: #1 tags after filtering in treatment: 9145598 INFO @ Thu, 05 Dec 2019 12:29:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:29:31: #1 finished! INFO @ Thu, 05 Dec 2019 12:29:31: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:29:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:29:32: #2 number of paired peaks: 330 WARNING @ Thu, 05 Dec 2019 12:29:32: Fewer paired peaks (330) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 330 pairs to build model! INFO @ Thu, 05 Dec 2019 12:29:32: start model_add_line... INFO @ Thu, 05 Dec 2019 12:29:32: start X-correlation... INFO @ Thu, 05 Dec 2019 12:29:32: end of X-cor INFO @ Thu, 05 Dec 2019 12:29:32: #2 finished! INFO @ Thu, 05 Dec 2019 12:29:32: #2 predicted fragment length is 74 bps INFO @ Thu, 05 Dec 2019 12:29:32: #2 alternative fragment length(s) may be 74 bps INFO @ Thu, 05 Dec 2019 12:29:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.10_model.r WARNING @ Thu, 05 Dec 2019 12:29:32: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:29:32: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Thu, 05 Dec 2019 12:29:32: #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 12:29:32: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:29:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:29:32: 5000000 INFO @ Thu, 05 Dec 2019 12:29:38: 6000000 INFO @ Thu, 05 Dec 2019 12:29:43: 7000000 INFO @ Thu, 05 Dec 2019 12:29:48: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:29:49: 8000000 INFO @ Thu, 05 Dec 2019 12:29:55: 9000000 INFO @ Thu, 05 Dec 2019 12:29:56: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:29:56: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:29:56: #1 total tags in treatment: 9145598 INFO @ Thu, 05 Dec 2019 12:29:56: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:29:56: #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 12:29:56: #1 tags after filtering in treatment: 9145598 INFO @ Thu, 05 Dec 2019 12:29:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:29:56: #1 finished! INFO @ Thu, 05 Dec 2019 12:29:56: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:29:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:29:57: #2 number of paired peaks: 330 WARNING @ Thu, 05 Dec 2019 12:29:57: Fewer paired peaks (330) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 330 pairs to build model! INFO @ Thu, 05 Dec 2019 12:29:57: start model_add_line... INFO @ Thu, 05 Dec 2019 12:29:57: start X-correlation... INFO @ Thu, 05 Dec 2019 12:29:57: end of X-cor INFO @ Thu, 05 Dec 2019 12:29:57: #2 finished! INFO @ Thu, 05 Dec 2019 12:29:57: #2 predicted fragment length is 74 bps INFO @ Thu, 05 Dec 2019 12:29:57: #2 alternative fragment length(s) may be 74 bps INFO @ Thu, 05 Dec 2019 12:29:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.20_model.r WARNING @ Thu, 05 Dec 2019 12:29:57: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:29:57: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Thu, 05 Dec 2019 12:29:57: #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 12:29:57: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:29:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:29:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:29:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:29:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.10_summits.bed INFO @ Thu, 05 Dec 2019 12:29:58: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (374 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:30:13: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:30:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:30:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:30:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5729151/SRX5729151.20_summits.bed INFO @ Thu, 05 Dec 2019 12:30:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (214 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。