Job ID = 2589946 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,595,479 reads read : 5,595,479 reads written : 5,595,479 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: 00:01:37 5595479 reads; of these: 5595479 (100.00%) were unpaired; of these: 127650 (2.28%) aligned 0 times 4499804 (80.42%) aligned exactly 1 time 968025 (17.30%) aligned >1 times 97.72% overall alignment rate Time searching: 00:01:37 Overall time: 00:01:37 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] 319506 / 5467829 = 0.0584 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 18:54:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.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 18:54:46: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:54:46: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:54:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.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 18:54:47: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:54:47: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:54:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.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 18:54:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:54:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:54:55: 1000000 INFO @ Mon, 12 Aug 2019 18:54:55: 1000000 INFO @ Mon, 12 Aug 2019 18:54:57: 1000000 INFO @ Mon, 12 Aug 2019 18:55:01: 2000000 INFO @ Mon, 12 Aug 2019 18:55:04: 2000000 INFO @ Mon, 12 Aug 2019 18:55:05: 2000000 INFO @ Mon, 12 Aug 2019 18:55:08: 3000000 INFO @ Mon, 12 Aug 2019 18:55:12: 3000000 INFO @ Mon, 12 Aug 2019 18:55:13: 3000000 INFO @ Mon, 12 Aug 2019 18:55:15: 4000000 INFO @ Mon, 12 Aug 2019 18:55:20: 4000000 INFO @ Mon, 12 Aug 2019 18:55:21: 4000000 INFO @ Mon, 12 Aug 2019 18:55:21: 5000000 INFO @ Mon, 12 Aug 2019 18:55:22: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 18:55:22: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 18:55:22: #1 total tags in treatment: 5148323 INFO @ Mon, 12 Aug 2019 18:55:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:55:22: #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 18:55:22: #1 tags after filtering in treatment: 5148323 INFO @ Mon, 12 Aug 2019 18:55:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:55:22: #1 finished! INFO @ Mon, 12 Aug 2019 18:55:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:55:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:55:23: #2 number of paired peaks: 438 WARNING @ Mon, 12 Aug 2019 18:55:23: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Mon, 12 Aug 2019 18:55:23: start model_add_line... INFO @ Mon, 12 Aug 2019 18:55:23: start X-correlation... INFO @ Mon, 12 Aug 2019 18:55:23: end of X-cor INFO @ Mon, 12 Aug 2019 18:55:23: #2 finished! INFO @ Mon, 12 Aug 2019 18:55:23: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 18:55:23: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 12 Aug 2019 18:55:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.10_model.r WARNING @ Mon, 12 Aug 2019 18:55:23: #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 18:55:23: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 12 Aug 2019 18:55:23: #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 18:55:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:55:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:55:28: 5000000 INFO @ Mon, 12 Aug 2019 18:55:29: 5000000 INFO @ Mon, 12 Aug 2019 18:55:30: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 18:55:30: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 18:55:30: #1 total tags in treatment: 5148323 INFO @ Mon, 12 Aug 2019 18:55:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:55:30: #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 18:55:30: #1 tags after filtering in treatment: 5148323 INFO @ Mon, 12 Aug 2019 18:55:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:55:30: #1 finished! INFO @ Mon, 12 Aug 2019 18:55:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:55:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:55:30: #2 number of paired peaks: 438 WARNING @ Mon, 12 Aug 2019 18:55:30: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Mon, 12 Aug 2019 18:55:30: start model_add_line... INFO @ Mon, 12 Aug 2019 18:55:30: start X-correlation... INFO @ Mon, 12 Aug 2019 18:55:30: end of X-cor INFO @ Mon, 12 Aug 2019 18:55:30: #2 finished! INFO @ Mon, 12 Aug 2019 18:55:30: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 18:55:30: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 12 Aug 2019 18:55:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.05_model.r WARNING @ Mon, 12 Aug 2019 18:55:30: #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 18:55:30: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 12 Aug 2019 18:55:30: #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 18:55:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:55:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:55:30: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 18:55:30: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 18:55:30: #1 total tags in treatment: 5148323 INFO @ Mon, 12 Aug 2019 18:55:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:55:30: #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 18:55:31: #1 tags after filtering in treatment: 5148323 INFO @ Mon, 12 Aug 2019 18:55:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:55:31: #1 finished! INFO @ Mon, 12 Aug 2019 18:55:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:55:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:55:31: #2 number of paired peaks: 438 WARNING @ Mon, 12 Aug 2019 18:55:31: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Mon, 12 Aug 2019 18:55:31: start model_add_line... INFO @ Mon, 12 Aug 2019 18:55:31: start X-correlation... INFO @ Mon, 12 Aug 2019 18:55:31: end of X-cor INFO @ Mon, 12 Aug 2019 18:55:31: #2 finished! INFO @ Mon, 12 Aug 2019 18:55:31: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 18:55:31: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 12 Aug 2019 18:55:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.20_model.r WARNING @ Mon, 12 Aug 2019 18:55:31: #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 18:55:31: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 12 Aug 2019 18:55:31: #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 18:55:31: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:55:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:55:38: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:55:45: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:55:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:55:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:55:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.10_summits.bed INFO @ Mon, 12 Aug 2019 18:55:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (345 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:55:46: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:55:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:55:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:55:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.05_summits.bed INFO @ Mon, 12 Aug 2019 18:55:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (559 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:55:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:55:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:55:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466455/SRX466455.20_summits.bed INFO @ Mon, 12 Aug 2019 18:55:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (141 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。