Job ID = 2590036 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,666,423 reads read : 22,666,423 reads written : 22,666,423 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: 00:05:47 22666423 reads; of these: 22666423 (100.00%) were unpaired; of these: 1047686 (4.62%) aligned 0 times 18456426 (81.43%) aligned exactly 1 time 3162311 (13.95%) aligned >1 times 95.38% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 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 12 files... [bam_rmdupse_core] 12022264 / 21618737 = 0.5561 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 19:31:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.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 19:31:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:31:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:31:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.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 19:31:26: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:31:26: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:31:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.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 19:31:27: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:31:27: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:31:34: 1000000 INFO @ Mon, 12 Aug 2019 19:31:34: 1000000 INFO @ Mon, 12 Aug 2019 19:31:35: 1000000 INFO @ Mon, 12 Aug 2019 19:31:42: 2000000 INFO @ Mon, 12 Aug 2019 19:31:43: 2000000 INFO @ Mon, 12 Aug 2019 19:31:44: 2000000 INFO @ Mon, 12 Aug 2019 19:31:50: 3000000 INFO @ Mon, 12 Aug 2019 19:31:52: 3000000 INFO @ Mon, 12 Aug 2019 19:31:53: 3000000 INFO @ Mon, 12 Aug 2019 19:31:58: 4000000 INFO @ Mon, 12 Aug 2019 19:32:01: 4000000 INFO @ Mon, 12 Aug 2019 19:32:02: 4000000 INFO @ Mon, 12 Aug 2019 19:32:06: 5000000 INFO @ Mon, 12 Aug 2019 19:32:10: 5000000 INFO @ Mon, 12 Aug 2019 19:32:10: 5000000 INFO @ Mon, 12 Aug 2019 19:32:13: 6000000 INFO @ Mon, 12 Aug 2019 19:32:18: 6000000 INFO @ Mon, 12 Aug 2019 19:32:19: 6000000 INFO @ Mon, 12 Aug 2019 19:32:21: 7000000 INFO @ Mon, 12 Aug 2019 19:32:27: 7000000 INFO @ Mon, 12 Aug 2019 19:32:27: 7000000 INFO @ Mon, 12 Aug 2019 19:32:29: 8000000 INFO @ Mon, 12 Aug 2019 19:32:35: 8000000 INFO @ Mon, 12 Aug 2019 19:32:36: 8000000 INFO @ Mon, 12 Aug 2019 19:32:37: 9000000 INFO @ Mon, 12 Aug 2019 19:32:41: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:32:41: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:32:41: #1 total tags in treatment: 9596473 INFO @ Mon, 12 Aug 2019 19:32:41: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:32:41: #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 19:32:41: #1 tags after filtering in treatment: 9596473 INFO @ Mon, 12 Aug 2019 19:32:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:32:41: #1 finished! INFO @ Mon, 12 Aug 2019 19:32:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:32:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:32:42: #2 number of paired peaks: 700 WARNING @ Mon, 12 Aug 2019 19:32:42: Fewer paired peaks (700) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 700 pairs to build model! INFO @ Mon, 12 Aug 2019 19:32:42: start model_add_line... INFO @ Mon, 12 Aug 2019 19:32:42: start X-correlation... INFO @ Mon, 12 Aug 2019 19:32:42: end of X-cor INFO @ Mon, 12 Aug 2019 19:32:42: #2 finished! INFO @ Mon, 12 Aug 2019 19:32:42: #2 predicted fragment length is 61 bps INFO @ Mon, 12 Aug 2019 19:32:42: #2 alternative fragment length(s) may be 4,61 bps INFO @ Mon, 12 Aug 2019 19:32:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.10_model.r WARNING @ Mon, 12 Aug 2019 19:32:42: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:32:42: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Mon, 12 Aug 2019 19:32:42: #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 19:32:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:32:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:32:44: 9000000 INFO @ Mon, 12 Aug 2019 19:32:44: 9000000 INFO @ Mon, 12 Aug 2019 19:32:49: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:32:49: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:32:49: #1 total tags in treatment: 9596473 INFO @ Mon, 12 Aug 2019 19:32:49: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:32:49: #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 19:32:49: #1 tags after filtering in treatment: 9596473 INFO @ Mon, 12 Aug 2019 19:32:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:32:49: #1 finished! INFO @ Mon, 12 Aug 2019 19:32:49: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:32:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:32:49: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:32:49: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:32:49: #1 total tags in treatment: 9596473 INFO @ Mon, 12 Aug 2019 19:32:49: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:32:49: #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 19:32:50: #1 tags after filtering in treatment: 9596473 INFO @ Mon, 12 Aug 2019 19:32:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:32:50: #1 finished! INFO @ Mon, 12 Aug 2019 19:32:50: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:32:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:32:50: #2 number of paired peaks: 700 WARNING @ Mon, 12 Aug 2019 19:32:50: Fewer paired peaks (700) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 700 pairs to build model! INFO @ Mon, 12 Aug 2019 19:32:50: start model_add_line... INFO @ Mon, 12 Aug 2019 19:32:50: start X-correlation... INFO @ Mon, 12 Aug 2019 19:32:50: end of X-cor INFO @ Mon, 12 Aug 2019 19:32:50: #2 finished! INFO @ Mon, 12 Aug 2019 19:32:50: #2 predicted fragment length is 61 bps INFO @ Mon, 12 Aug 2019 19:32:50: #2 alternative fragment length(s) may be 4,61 bps INFO @ Mon, 12 Aug 2019 19:32:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.05_model.r WARNING @ Mon, 12 Aug 2019 19:32:50: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:32:50: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Mon, 12 Aug 2019 19:32:50: #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 19:32:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:32:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:32:51: #2 number of paired peaks: 700 WARNING @ Mon, 12 Aug 2019 19:32:51: Fewer paired peaks (700) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 700 pairs to build model! INFO @ Mon, 12 Aug 2019 19:32:51: start model_add_line... INFO @ Mon, 12 Aug 2019 19:32:51: start X-correlation... INFO @ Mon, 12 Aug 2019 19:32:51: end of X-cor INFO @ Mon, 12 Aug 2019 19:32:51: #2 finished! INFO @ Mon, 12 Aug 2019 19:32:51: #2 predicted fragment length is 61 bps INFO @ Mon, 12 Aug 2019 19:32:51: #2 alternative fragment length(s) may be 4,61 bps INFO @ Mon, 12 Aug 2019 19:32:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.20_model.r WARNING @ Mon, 12 Aug 2019 19:32:51: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:32:51: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Mon, 12 Aug 2019 19:32:51: #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 19:32:51: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:32:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:33:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:33:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:33:17: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:33:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:33:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:33:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.10_summits.bed INFO @ Mon, 12 Aug 2019 19:33:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (895 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:33:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:33:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:33:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.05_summits.bed INFO @ Mon, 12 Aug 2019 19:33:29: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2241 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:33:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:33:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:33:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494880/SRX494880.20_summits.bed INFO @ Mon, 12 Aug 2019 19:33:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (317 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。