Job ID = 2590151 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,778,723 reads read : 15,778,723 reads written : 15,778,723 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: 00:03:01 15778723 reads; of these: 15778723 (100.00%) were unpaired; of these: 2297487 (14.56%) aligned 0 times 10953727 (69.42%) aligned exactly 1 time 2527509 (16.02%) aligned >1 times 85.44% overall alignment rate Time searching: 00:03:01 Overall time: 00:03:01 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] 7350685 / 13481236 = 0.5453 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 19:53:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.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 19:53:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:53:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:53:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.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 19:53:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:53:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:53:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.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 19:53:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:53:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:53:07: 1000000 INFO @ Mon, 12 Aug 2019 19:53:10: 1000000 INFO @ Mon, 12 Aug 2019 19:53:11: 1000000 INFO @ Mon, 12 Aug 2019 19:53:13: 2000000 INFO @ Mon, 12 Aug 2019 19:53:17: 2000000 INFO @ Mon, 12 Aug 2019 19:53:20: 2000000 INFO @ Mon, 12 Aug 2019 19:53:20: 3000000 INFO @ Mon, 12 Aug 2019 19:53:25: 3000000 INFO @ Mon, 12 Aug 2019 19:53:27: 4000000 INFO @ Mon, 12 Aug 2019 19:53:29: 3000000 INFO @ Mon, 12 Aug 2019 19:53:33: 4000000 INFO @ Mon, 12 Aug 2019 19:53:34: 5000000 INFO @ Mon, 12 Aug 2019 19:53:39: 4000000 INFO @ Mon, 12 Aug 2019 19:53:41: 6000000 INFO @ Mon, 12 Aug 2019 19:53:41: 5000000 INFO @ Mon, 12 Aug 2019 19:53:42: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:53:42: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:53:42: #1 total tags in treatment: 6130551 INFO @ Mon, 12 Aug 2019 19:53:42: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:53:42: #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 19:53:42: #1 tags after filtering in treatment: 6130551 INFO @ Mon, 12 Aug 2019 19:53:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:53:42: #1 finished! INFO @ Mon, 12 Aug 2019 19:53:42: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:53:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:53:43: #2 number of paired peaks: 996 WARNING @ Mon, 12 Aug 2019 19:53:43: Fewer paired peaks (996) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 996 pairs to build model! INFO @ Mon, 12 Aug 2019 19:53:43: start model_add_line... INFO @ Mon, 12 Aug 2019 19:53:43: start X-correlation... INFO @ Mon, 12 Aug 2019 19:53:43: end of X-cor INFO @ Mon, 12 Aug 2019 19:53:43: #2 finished! INFO @ Mon, 12 Aug 2019 19:53:43: #2 predicted fragment length is 207 bps INFO @ Mon, 12 Aug 2019 19:53:43: #2 alternative fragment length(s) may be 207 bps INFO @ Mon, 12 Aug 2019 19:53:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.05_model.r INFO @ Mon, 12 Aug 2019 19:53:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:53:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:53:49: 5000000 INFO @ Mon, 12 Aug 2019 19:53:49: 6000000 INFO @ Mon, 12 Aug 2019 19:53:50: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:53:50: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:53:50: #1 total tags in treatment: 6130551 INFO @ Mon, 12 Aug 2019 19:53:50: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:53:50: #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 19:53:50: #1 tags after filtering in treatment: 6130551 INFO @ Mon, 12 Aug 2019 19:53:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:53:50: #1 finished! INFO @ Mon, 12 Aug 2019 19:53:50: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:53:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:53:51: #2 number of paired peaks: 996 WARNING @ Mon, 12 Aug 2019 19:53:51: Fewer paired peaks (996) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 996 pairs to build model! INFO @ Mon, 12 Aug 2019 19:53:51: start model_add_line... INFO @ Mon, 12 Aug 2019 19:53:51: start X-correlation... INFO @ Mon, 12 Aug 2019 19:53:51: end of X-cor INFO @ Mon, 12 Aug 2019 19:53:51: #2 finished! INFO @ Mon, 12 Aug 2019 19:53:51: #2 predicted fragment length is 207 bps INFO @ Mon, 12 Aug 2019 19:53:51: #2 alternative fragment length(s) may be 207 bps INFO @ Mon, 12 Aug 2019 19:53:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.20_model.r INFO @ Mon, 12 Aug 2019 19:53:51: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:53:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:53:58: 6000000 INFO @ Mon, 12 Aug 2019 19:53:59: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:53:59: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:53:59: #1 total tags in treatment: 6130551 INFO @ Mon, 12 Aug 2019 19:53:59: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:53:59: #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 19:53:59: #1 tags after filtering in treatment: 6130551 INFO @ Mon, 12 Aug 2019 19:53:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:53:59: #1 finished! INFO @ Mon, 12 Aug 2019 19:53:59: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:53:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:54:00: #2 number of paired peaks: 996 WARNING @ Mon, 12 Aug 2019 19:54:00: Fewer paired peaks (996) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 996 pairs to build model! INFO @ Mon, 12 Aug 2019 19:54:00: start model_add_line... INFO @ Mon, 12 Aug 2019 19:54:00: start X-correlation... INFO @ Mon, 12 Aug 2019 19:54:00: end of X-cor INFO @ Mon, 12 Aug 2019 19:54:00: #2 finished! INFO @ Mon, 12 Aug 2019 19:54:00: #2 predicted fragment length is 207 bps INFO @ Mon, 12 Aug 2019 19:54:00: #2 alternative fragment length(s) may be 207 bps INFO @ Mon, 12 Aug 2019 19:54:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.10_model.r INFO @ Mon, 12 Aug 2019 19:54:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:54:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:54:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:54:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:54:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:54:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:54:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.05_summits.bed INFO @ Mon, 12 Aug 2019 19:54:12: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1738 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:54:21: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:54:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:54:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:54:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.20_summits.bed INFO @ Mon, 12 Aug 2019 19:54:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (818 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:54:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:54:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:54:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494999/SRX494999.10_summits.bed INFO @ Mon, 12 Aug 2019 19:54:30: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1173 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。