Job ID = 2589927 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,388,946 reads read : 18,388,946 reads written : 18,388,946 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: 00:04:33 18388946 reads; of these: 18388946 (100.00%) were unpaired; of these: 4337561 (23.59%) aligned 0 times 11667752 (63.45%) aligned exactly 1 time 2383633 (12.96%) aligned >1 times 76.41% overall alignment rate Time searching: 00:04:33 Overall time: 00:04:33 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] 1117650 / 14051385 = 0.0795 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 19:05:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.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 19:05:27: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:05:27: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:05:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.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 19:05:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:05:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:05:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.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 19:05:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:05:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:05:35: 1000000 INFO @ Mon, 12 Aug 2019 19:05:35: 1000000 INFO @ Mon, 12 Aug 2019 19:05:37: 1000000 INFO @ Mon, 12 Aug 2019 19:05:42: 2000000 INFO @ Mon, 12 Aug 2019 19:05:43: 2000000 INFO @ Mon, 12 Aug 2019 19:05:43: 2000000 INFO @ Mon, 12 Aug 2019 19:05:49: 3000000 INFO @ Mon, 12 Aug 2019 19:05:50: 3000000 INFO @ Mon, 12 Aug 2019 19:05:50: 3000000 INFO @ Mon, 12 Aug 2019 19:05:56: 4000000 INFO @ Mon, 12 Aug 2019 19:05:57: 4000000 INFO @ Mon, 12 Aug 2019 19:05:57: 4000000 INFO @ Mon, 12 Aug 2019 19:06:02: 5000000 INFO @ Mon, 12 Aug 2019 19:06:03: 5000000 INFO @ Mon, 12 Aug 2019 19:06:05: 5000000 INFO @ Mon, 12 Aug 2019 19:06:09: 6000000 INFO @ Mon, 12 Aug 2019 19:06:10: 6000000 INFO @ Mon, 12 Aug 2019 19:06:13: 6000000 INFO @ Mon, 12 Aug 2019 19:06:16: 7000000 INFO @ Mon, 12 Aug 2019 19:06:17: 7000000 INFO @ Mon, 12 Aug 2019 19:06:20: 7000000 INFO @ Mon, 12 Aug 2019 19:06:23: 8000000 INFO @ Mon, 12 Aug 2019 19:06:23: 8000000 INFO @ Mon, 12 Aug 2019 19:06:27: 8000000 INFO @ Mon, 12 Aug 2019 19:06:29: 9000000 INFO @ Mon, 12 Aug 2019 19:06:30: 9000000 INFO @ Mon, 12 Aug 2019 19:06:35: 9000000 INFO @ Mon, 12 Aug 2019 19:06:36: 10000000 INFO @ Mon, 12 Aug 2019 19:06:37: 10000000 INFO @ Mon, 12 Aug 2019 19:06:42: 10000000 INFO @ Mon, 12 Aug 2019 19:06:43: 11000000 INFO @ Mon, 12 Aug 2019 19:06:44: 11000000 INFO @ Mon, 12 Aug 2019 19:06:49: 11000000 INFO @ Mon, 12 Aug 2019 19:06:50: 12000000 INFO @ Mon, 12 Aug 2019 19:06:50: 12000000 INFO @ Mon, 12 Aug 2019 19:06:56: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:06:56: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:06:56: #1 total tags in treatment: 12933735 INFO @ Mon, 12 Aug 2019 19:06:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:06:56: #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 19:06:56: 12000000 INFO @ Mon, 12 Aug 2019 19:06:56: #1 tags after filtering in treatment: 12933735 INFO @ Mon, 12 Aug 2019 19:06:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:06:56: #1 finished! INFO @ Mon, 12 Aug 2019 19:06:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:06:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:06:57: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:06:57: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:06:57: #1 total tags in treatment: 12933735 INFO @ Mon, 12 Aug 2019 19:06:57: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:06:57: #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 19:06:57: #1 tags after filtering in treatment: 12933735 INFO @ Mon, 12 Aug 2019 19:06:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:06:57: #1 finished! INFO @ Mon, 12 Aug 2019 19:06:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:06:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:06:58: #2 number of paired peaks: 334 WARNING @ Mon, 12 Aug 2019 19:06:58: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Mon, 12 Aug 2019 19:06:58: start model_add_line... INFO @ Mon, 12 Aug 2019 19:06:58: start X-correlation... INFO @ Mon, 12 Aug 2019 19:06:58: end of X-cor INFO @ Mon, 12 Aug 2019 19:06:58: #2 finished! INFO @ Mon, 12 Aug 2019 19:06:58: #2 predicted fragment length is 42 bps INFO @ Mon, 12 Aug 2019 19:06:58: #2 alternative fragment length(s) may be 2,42,584 bps INFO @ Mon, 12 Aug 2019 19:06:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.10_model.r WARNING @ Mon, 12 Aug 2019 19:06:58: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:06:58: #2 You may need to consider one of the other alternative d(s): 2,42,584 WARNING @ Mon, 12 Aug 2019 19:06:58: #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 19:06:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:06:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:06:58: #2 number of paired peaks: 334 WARNING @ Mon, 12 Aug 2019 19:06:58: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Mon, 12 Aug 2019 19:06:58: start model_add_line... INFO @ Mon, 12 Aug 2019 19:06:58: start X-correlation... INFO @ Mon, 12 Aug 2019 19:06:58: end of X-cor INFO @ Mon, 12 Aug 2019 19:06:58: #2 finished! INFO @ Mon, 12 Aug 2019 19:06:58: #2 predicted fragment length is 42 bps INFO @ Mon, 12 Aug 2019 19:06:58: #2 alternative fragment length(s) may be 2,42,584 bps INFO @ Mon, 12 Aug 2019 19:06:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.20_model.r WARNING @ Mon, 12 Aug 2019 19:06:58: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:06:58: #2 You may need to consider one of the other alternative d(s): 2,42,584 WARNING @ Mon, 12 Aug 2019 19:06:58: #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 19:06:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:06:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:07:03: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:07:03: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:07:03: #1 total tags in treatment: 12933735 INFO @ Mon, 12 Aug 2019 19:07:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:07:03: #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 19:07:03: #1 tags after filtering in treatment: 12933735 INFO @ Mon, 12 Aug 2019 19:07:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:07:03: #1 finished! INFO @ Mon, 12 Aug 2019 19:07:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:07:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:07:05: #2 number of paired peaks: 334 WARNING @ Mon, 12 Aug 2019 19:07:05: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Mon, 12 Aug 2019 19:07:05: start model_add_line... INFO @ Mon, 12 Aug 2019 19:07:05: start X-correlation... INFO @ Mon, 12 Aug 2019 19:07:05: end of X-cor INFO @ Mon, 12 Aug 2019 19:07:05: #2 finished! INFO @ Mon, 12 Aug 2019 19:07:05: #2 predicted fragment length is 42 bps INFO @ Mon, 12 Aug 2019 19:07:05: #2 alternative fragment length(s) may be 2,42,584 bps INFO @ Mon, 12 Aug 2019 19:07:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.05_model.r WARNING @ Mon, 12 Aug 2019 19:07:05: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:07:05: #2 You may need to consider one of the other alternative d(s): 2,42,584 WARNING @ Mon, 12 Aug 2019 19:07:05: #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 19:07:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:07:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:07:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:07:31: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:07:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:07:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:07:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:07:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.10_summits.bed INFO @ Mon, 12 Aug 2019 19:07:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (444 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:07:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:07:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:07:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.20_summits.bed INFO @ Mon, 12 Aug 2019 19:07:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (173 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:07:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:07:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:07:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331338/SRX331338.05_summits.bed INFO @ Mon, 12 Aug 2019 19:07:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (679 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。