Job ID = 2589656 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,680,929 reads read : 7,680,929 reads written : 7,680,929 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: 00:01:23 7680929 reads; of these: 7680929 (100.00%) were unpaired; of these: 505498 (6.58%) aligned 0 times 6147307 (80.03%) aligned exactly 1 time 1028124 (13.39%) aligned >1 times 93.42% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 863834 / 7175431 = 0.1204 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 18:15:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.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 18:15:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:15:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:15:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.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 18:15:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:15:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:15:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.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 18:15:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:15:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:15:25: 1000000 INFO @ Mon, 12 Aug 2019 18:15:26: 1000000 INFO @ Mon, 12 Aug 2019 18:15:28: 1000000 INFO @ Mon, 12 Aug 2019 18:15:32: 2000000 INFO @ Mon, 12 Aug 2019 18:15:34: 2000000 INFO @ Mon, 12 Aug 2019 18:15:36: 2000000 INFO @ Mon, 12 Aug 2019 18:15:40: 3000000 INFO @ Mon, 12 Aug 2019 18:15:41: 3000000 INFO @ Mon, 12 Aug 2019 18:15:45: 3000000 INFO @ Mon, 12 Aug 2019 18:15:47: 4000000 INFO @ Mon, 12 Aug 2019 18:15:47: 4000000 INFO @ Mon, 12 Aug 2019 18:15:53: 4000000 INFO @ Mon, 12 Aug 2019 18:15:54: 5000000 INFO @ Mon, 12 Aug 2019 18:15:54: 5000000 INFO @ Mon, 12 Aug 2019 18:16:01: 6000000 INFO @ Mon, 12 Aug 2019 18:16:01: 6000000 INFO @ Mon, 12 Aug 2019 18:16:02: 5000000 INFO @ Mon, 12 Aug 2019 18:16:03: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:16:03: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:16:03: #1 total tags in treatment: 6311597 INFO @ Mon, 12 Aug 2019 18:16:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:16:03: #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 18:16:03: #1 tags after filtering in treatment: 6311597 INFO @ Mon, 12 Aug 2019 18:16:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:16:03: #1 finished! INFO @ Mon, 12 Aug 2019 18:16:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:16:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:16:04: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:16:04: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:16:04: #1 total tags in treatment: 6311597 INFO @ Mon, 12 Aug 2019 18:16:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:16:04: #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 18:16:04: #2 number of paired peaks: 495 WARNING @ Mon, 12 Aug 2019 18:16:04: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Mon, 12 Aug 2019 18:16:04: start model_add_line... INFO @ Mon, 12 Aug 2019 18:16:04: #1 tags after filtering in treatment: 6311597 INFO @ Mon, 12 Aug 2019 18:16:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:16:04: #1 finished! INFO @ Mon, 12 Aug 2019 18:16:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:16:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:16:04: start X-correlation... INFO @ Mon, 12 Aug 2019 18:16:04: end of X-cor INFO @ Mon, 12 Aug 2019 18:16:04: #2 finished! INFO @ Mon, 12 Aug 2019 18:16:04: #2 predicted fragment length is 66 bps INFO @ Mon, 12 Aug 2019 18:16:04: #2 alternative fragment length(s) may be 4,66,586 bps INFO @ Mon, 12 Aug 2019 18:16:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.10_model.r INFO @ Mon, 12 Aug 2019 18:16:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:16:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:16:04: #2 number of paired peaks: 495 WARNING @ Mon, 12 Aug 2019 18:16:04: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Mon, 12 Aug 2019 18:16:04: start model_add_line... INFO @ Mon, 12 Aug 2019 18:16:04: start X-correlation... INFO @ Mon, 12 Aug 2019 18:16:04: end of X-cor INFO @ Mon, 12 Aug 2019 18:16:04: #2 finished! INFO @ Mon, 12 Aug 2019 18:16:04: #2 predicted fragment length is 66 bps INFO @ Mon, 12 Aug 2019 18:16:04: #2 alternative fragment length(s) may be 4,66,586 bps INFO @ Mon, 12 Aug 2019 18:16:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.05_model.r INFO @ Mon, 12 Aug 2019 18:16:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:16:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:16:09: 6000000 INFO @ Mon, 12 Aug 2019 18:16:11: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:16:11: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:16:11: #1 total tags in treatment: 6311597 INFO @ Mon, 12 Aug 2019 18:16:11: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:16:11: #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 18:16:11: #1 tags after filtering in treatment: 6311597 INFO @ Mon, 12 Aug 2019 18:16:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:16:11: #1 finished! INFO @ Mon, 12 Aug 2019 18:16:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:16:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:16:12: #2 number of paired peaks: 495 WARNING @ Mon, 12 Aug 2019 18:16:12: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Mon, 12 Aug 2019 18:16:12: start model_add_line... INFO @ Mon, 12 Aug 2019 18:16:12: start X-correlation... INFO @ Mon, 12 Aug 2019 18:16:12: end of X-cor INFO @ Mon, 12 Aug 2019 18:16:12: #2 finished! INFO @ Mon, 12 Aug 2019 18:16:12: #2 predicted fragment length is 66 bps INFO @ Mon, 12 Aug 2019 18:16:12: #2 alternative fragment length(s) may be 4,66,586 bps INFO @ Mon, 12 Aug 2019 18:16:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.20_model.r INFO @ Mon, 12 Aug 2019 18:16:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:16:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:16:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:16:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:16:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:16:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:16:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.10_summits.bed INFO @ Mon, 12 Aug 2019 18:16:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (480 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:16:31: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:16:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:16:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:16:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.05_summits.bed INFO @ Mon, 12 Aug 2019 18:16:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1230 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:16:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:16:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:16:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277100/SRX277100.20_summits.bed INFO @ Mon, 12 Aug 2019 18:16:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (145 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。