Job ID = 4303032 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,187,826 reads read : 7,187,826 reads written : 7,187,826 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947508.sra.cache’: 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: 00:01:17 7187826 reads; of these: 7187826 (100.00%) were unpaired; of these: 287944 (4.01%) aligned 0 times 5911550 (82.24%) aligned exactly 1 time 988332 (13.75%) aligned >1 times 95.99% overall alignment rate Time searching: 00:01:17 Overall time: 00:01:17 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_rmdupse_core] 912562 / 6899882 = 0.1323 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:35:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.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, 12 Dec 2019 00:35:02: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:35:02: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:35:09: 1000000 INFO @ Thu, 12 Dec 2019 00:35:16: 2000000 INFO @ Thu, 12 Dec 2019 00:35:24: 3000000 INFO @ Thu, 12 Dec 2019 00:35:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.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, 12 Dec 2019 00:35:30: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:35:30: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:35:31: 4000000 INFO @ Thu, 12 Dec 2019 00:35:37: 1000000 INFO @ Thu, 12 Dec 2019 00:35:38: 5000000 INFO @ Thu, 12 Dec 2019 00:35:44: 2000000 INFO @ Thu, 12 Dec 2019 00:35:45: #1 tag size is determined as 32 bps INFO @ Thu, 12 Dec 2019 00:35:45: #1 tag size = 32 INFO @ Thu, 12 Dec 2019 00:35:45: #1 total tags in treatment: 5987320 INFO @ Thu, 12 Dec 2019 00:35:45: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:35:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:35:45: #1 tags after filtering in treatment: 5987320 INFO @ Thu, 12 Dec 2019 00:35:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:35:45: #1 finished! INFO @ Thu, 12 Dec 2019 00:35:45: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:35:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:35:46: #2 number of paired peaks: 383 WARNING @ Thu, 12 Dec 2019 00:35:46: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Thu, 12 Dec 2019 00:35:46: start model_add_line... INFO @ Thu, 12 Dec 2019 00:35:46: start X-correlation... INFO @ Thu, 12 Dec 2019 00:35:46: end of X-cor INFO @ Thu, 12 Dec 2019 00:35:46: #2 finished! INFO @ Thu, 12 Dec 2019 00:35:46: #2 predicted fragment length is 29 bps INFO @ Thu, 12 Dec 2019 00:35:46: #2 alternative fragment length(s) may be 3,29 bps INFO @ Thu, 12 Dec 2019 00:35:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.05_model.r WARNING @ Thu, 12 Dec 2019 00:35:49: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:35:49: #2 You may need to consider one of the other alternative d(s): 3,29 WARNING @ Thu, 12 Dec 2019 00:35:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:35:49: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:35:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:35:50: 3000000 INFO @ Thu, 12 Dec 2019 00:35:57: 4000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:36:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.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, 12 Dec 2019 00:36:00: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:36:00: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:36:03: 5000000 INFO @ Thu, 12 Dec 2019 00:36:06: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:36:09: 1000000 INFO @ Thu, 12 Dec 2019 00:36:10: #1 tag size is determined as 32 bps INFO @ Thu, 12 Dec 2019 00:36:10: #1 tag size = 32 INFO @ Thu, 12 Dec 2019 00:36:10: #1 total tags in treatment: 5987320 INFO @ Thu, 12 Dec 2019 00:36:10: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:36:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:36:10: #1 tags after filtering in treatment: 5987320 INFO @ Thu, 12 Dec 2019 00:36:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:36:10: #1 finished! INFO @ Thu, 12 Dec 2019 00:36:10: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:36:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:36:10: #2 number of paired peaks: 383 WARNING @ Thu, 12 Dec 2019 00:36:10: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Thu, 12 Dec 2019 00:36:10: start model_add_line... INFO @ Thu, 12 Dec 2019 00:36:10: start X-correlation... INFO @ Thu, 12 Dec 2019 00:36:10: end of X-cor INFO @ Thu, 12 Dec 2019 00:36:10: #2 finished! INFO @ Thu, 12 Dec 2019 00:36:10: #2 predicted fragment length is 29 bps INFO @ Thu, 12 Dec 2019 00:36:10: #2 alternative fragment length(s) may be 3,29 bps INFO @ Thu, 12 Dec 2019 00:36:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.10_model.r WARNING @ Thu, 12 Dec 2019 00:36:10: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:36:10: #2 You may need to consider one of the other alternative d(s): 3,29 WARNING @ Thu, 12 Dec 2019 00:36:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:36:10: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:36:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:36:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:36:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:36:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.05_summits.bed INFO @ Thu, 12 Dec 2019 00:36:14: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (463 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:36:17: 2000000 INFO @ Thu, 12 Dec 2019 00:36:25: 3000000 INFO @ Thu, 12 Dec 2019 00:36:28: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:36:33: 4000000 INFO @ Thu, 12 Dec 2019 00:36:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:36:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:36:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.10_summits.bed INFO @ Thu, 12 Dec 2019 00:36:36: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (205 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:36:41: 5000000 INFO @ Thu, 12 Dec 2019 00:36:48: #1 tag size is determined as 32 bps INFO @ Thu, 12 Dec 2019 00:36:48: #1 tag size = 32 INFO @ Thu, 12 Dec 2019 00:36:48: #1 total tags in treatment: 5987320 INFO @ Thu, 12 Dec 2019 00:36:48: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:36:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:36:48: #1 tags after filtering in treatment: 5987320 INFO @ Thu, 12 Dec 2019 00:36:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:36:48: #1 finished! INFO @ Thu, 12 Dec 2019 00:36:48: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:36:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:36:49: #2 number of paired peaks: 383 WARNING @ Thu, 12 Dec 2019 00:36:49: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Thu, 12 Dec 2019 00:36:49: start model_add_line... INFO @ Thu, 12 Dec 2019 00:36:49: start X-correlation... INFO @ Thu, 12 Dec 2019 00:36:49: end of X-cor INFO @ Thu, 12 Dec 2019 00:36:49: #2 finished! INFO @ Thu, 12 Dec 2019 00:36:49: #2 predicted fragment length is 29 bps INFO @ Thu, 12 Dec 2019 00:36:49: #2 alternative fragment length(s) may be 3,29 bps INFO @ Thu, 12 Dec 2019 00:36:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.20_model.r WARNING @ Thu, 12 Dec 2019 00:36:49: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:36:49: #2 You may need to consider one of the other alternative d(s): 3,29 WARNING @ Thu, 12 Dec 2019 00:36:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:36:49: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:36:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:37:06: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:37:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:37:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:37:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331273/SRX331273.20_summits.bed INFO @ Thu, 12 Dec 2019 00:37:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (54 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。