Job ID = 2589640 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,279,156 reads read : 7,279,156 reads written : 7,279,156 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: 00:01:10 7279156 reads; of these: 7279156 (100.00%) were unpaired; of these: 1217554 (16.73%) aligned 0 times 5132308 (70.51%) aligned exactly 1 time 929294 (12.77%) aligned >1 times 83.27% overall alignment rate Time searching: 00:01:10 Overall time: 00:01:10 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] 438147 / 6061602 = 0.0723 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 18:12:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.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 18:12:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:12:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:12:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.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 18:12:23: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:12:23: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:12:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.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 18:12:24: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:12:24: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:12:28: 1000000 INFO @ Mon, 12 Aug 2019 18:12:29: 1000000 INFO @ Mon, 12 Aug 2019 18:12:32: 1000000 INFO @ Mon, 12 Aug 2019 18:12:34: 2000000 INFO @ Mon, 12 Aug 2019 18:12:36: 2000000 INFO @ Mon, 12 Aug 2019 18:12:40: 3000000 INFO @ Mon, 12 Aug 2019 18:12:40: 2000000 INFO @ Mon, 12 Aug 2019 18:12:42: 3000000 INFO @ Mon, 12 Aug 2019 18:12:46: 4000000 INFO @ Mon, 12 Aug 2019 18:12:48: 3000000 INFO @ Mon, 12 Aug 2019 18:12:49: 4000000 INFO @ Mon, 12 Aug 2019 18:12:52: 5000000 INFO @ Mon, 12 Aug 2019 18:12:56: 5000000 INFO @ Mon, 12 Aug 2019 18:12:56: 4000000 INFO @ Mon, 12 Aug 2019 18:12:56: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:12:56: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:12:56: #1 total tags in treatment: 5623455 INFO @ Mon, 12 Aug 2019 18:12:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:12:56: #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 18:12:56: #1 tags after filtering in treatment: 5623455 INFO @ Mon, 12 Aug 2019 18:12:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:12:56: #1 finished! INFO @ Mon, 12 Aug 2019 18:12:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:12:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:12:57: #2 number of paired peaks: 650 WARNING @ Mon, 12 Aug 2019 18:12:57: Fewer paired peaks (650) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 650 pairs to build model! INFO @ Mon, 12 Aug 2019 18:12:57: start model_add_line... INFO @ Mon, 12 Aug 2019 18:12:57: start X-correlation... INFO @ Mon, 12 Aug 2019 18:12:57: end of X-cor INFO @ Mon, 12 Aug 2019 18:12:57: #2 finished! INFO @ Mon, 12 Aug 2019 18:12:57: #2 predicted fragment length is 129 bps INFO @ Mon, 12 Aug 2019 18:12:57: #2 alternative fragment length(s) may be 129 bps INFO @ Mon, 12 Aug 2019 18:12:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.05_model.r INFO @ Mon, 12 Aug 2019 18:12:57: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:12:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:13:00: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:13:00: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:13:00: #1 total tags in treatment: 5623455 INFO @ Mon, 12 Aug 2019 18:13:00: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:13:00: #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 18:13:00: #1 tags after filtering in treatment: 5623455 INFO @ Mon, 12 Aug 2019 18:13:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:13:00: #1 finished! INFO @ Mon, 12 Aug 2019 18:13:00: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:13:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:13:00: #2 number of paired peaks: 650 WARNING @ Mon, 12 Aug 2019 18:13:00: Fewer paired peaks (650) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 650 pairs to build model! INFO @ Mon, 12 Aug 2019 18:13:00: start model_add_line... INFO @ Mon, 12 Aug 2019 18:13:00: start X-correlation... INFO @ Mon, 12 Aug 2019 18:13:00: end of X-cor INFO @ Mon, 12 Aug 2019 18:13:00: #2 finished! INFO @ Mon, 12 Aug 2019 18:13:00: #2 predicted fragment length is 129 bps INFO @ Mon, 12 Aug 2019 18:13:00: #2 alternative fragment length(s) may be 129 bps INFO @ Mon, 12 Aug 2019 18:13:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.10_model.r INFO @ Mon, 12 Aug 2019 18:13:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:13:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:13:04: 5000000 INFO @ Mon, 12 Aug 2019 18:13:08: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:13:08: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:13:08: #1 total tags in treatment: 5623455 INFO @ Mon, 12 Aug 2019 18:13:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:13:08: #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 18:13:08: #1 tags after filtering in treatment: 5623455 INFO @ Mon, 12 Aug 2019 18:13:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:13:08: #1 finished! INFO @ Mon, 12 Aug 2019 18:13:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:13:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:13:09: #2 number of paired peaks: 650 WARNING @ Mon, 12 Aug 2019 18:13:09: Fewer paired peaks (650) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 650 pairs to build model! INFO @ Mon, 12 Aug 2019 18:13:09: start model_add_line... INFO @ Mon, 12 Aug 2019 18:13:09: start X-correlation... INFO @ Mon, 12 Aug 2019 18:13:09: end of X-cor INFO @ Mon, 12 Aug 2019 18:13:09: #2 finished! INFO @ Mon, 12 Aug 2019 18:13:09: #2 predicted fragment length is 129 bps INFO @ Mon, 12 Aug 2019 18:13:09: #2 alternative fragment length(s) may be 129 bps INFO @ Mon, 12 Aug 2019 18:13:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.20_model.r INFO @ Mon, 12 Aug 2019 18:13:09: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:13:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:13:13: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:13:17: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:13:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:13:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:13:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.05_summits.bed INFO @ Mon, 12 Aug 2019 18:13:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1583 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:13:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:13:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:13:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.10_summits.bed INFO @ Mon, 12 Aug 2019 18:13:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (872 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:13:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:13:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:13:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:13:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277079/SRX277079.20_summits.bed INFO @ Mon, 12 Aug 2019 18:13:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (428 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。