Job ID = 2590107 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,778,538 reads read : 17,778,538 reads written : 17,778,538 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: 00:03:12 17778538 reads; of these: 17778538 (100.00%) were unpaired; of these: 749042 (4.21%) aligned 0 times 13795201 (77.59%) aligned exactly 1 time 3234295 (18.19%) aligned >1 times 95.79% overall alignment rate Time searching: 00:03:12 Overall time: 00:03:12 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] 2484542 / 17029496 = 0.1459 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 19:47:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.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 19:47:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:47:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:47:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.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 19:47:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:47:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:47:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.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 19:47:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:47:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:47:43: 1000000 INFO @ Mon, 12 Aug 2019 19:47:44: 1000000 INFO @ Mon, 12 Aug 2019 19:47:45: 1000000 INFO @ Mon, 12 Aug 2019 19:47:50: 2000000 INFO @ Mon, 12 Aug 2019 19:47:51: 2000000 INFO @ Mon, 12 Aug 2019 19:47:52: 2000000 INFO @ Mon, 12 Aug 2019 19:47:57: 3000000 INFO @ Mon, 12 Aug 2019 19:47:58: 3000000 INFO @ Mon, 12 Aug 2019 19:47:59: 3000000 INFO @ Mon, 12 Aug 2019 19:48:05: 4000000 INFO @ Mon, 12 Aug 2019 19:48:06: 4000000 INFO @ Mon, 12 Aug 2019 19:48:07: 4000000 INFO @ Mon, 12 Aug 2019 19:48:12: 5000000 INFO @ Mon, 12 Aug 2019 19:48:13: 5000000 INFO @ Mon, 12 Aug 2019 19:48:14: 5000000 INFO @ Mon, 12 Aug 2019 19:48:19: 6000000 INFO @ Mon, 12 Aug 2019 19:48:20: 6000000 INFO @ Mon, 12 Aug 2019 19:48:21: 6000000 INFO @ Mon, 12 Aug 2019 19:48:27: 7000000 INFO @ Mon, 12 Aug 2019 19:48:28: 7000000 INFO @ Mon, 12 Aug 2019 19:48:29: 7000000 INFO @ Mon, 12 Aug 2019 19:48:34: 8000000 INFO @ Mon, 12 Aug 2019 19:48:35: 8000000 INFO @ Mon, 12 Aug 2019 19:48:36: 8000000 INFO @ Mon, 12 Aug 2019 19:48:41: 9000000 INFO @ Mon, 12 Aug 2019 19:48:42: 9000000 INFO @ Mon, 12 Aug 2019 19:48:43: 9000000 INFO @ Mon, 12 Aug 2019 19:48:48: 10000000 INFO @ Mon, 12 Aug 2019 19:48:50: 10000000 INFO @ Mon, 12 Aug 2019 19:48:51: 10000000 INFO @ Mon, 12 Aug 2019 19:48:56: 11000000 INFO @ Mon, 12 Aug 2019 19:48:57: 11000000 INFO @ Mon, 12 Aug 2019 19:48:58: 11000000 INFO @ Mon, 12 Aug 2019 19:49:03: 12000000 INFO @ Mon, 12 Aug 2019 19:49:04: 12000000 INFO @ Mon, 12 Aug 2019 19:49:05: 12000000 INFO @ Mon, 12 Aug 2019 19:49:10: 13000000 INFO @ Mon, 12 Aug 2019 19:49:12: 13000000 INFO @ Mon, 12 Aug 2019 19:49:12: 13000000 INFO @ Mon, 12 Aug 2019 19:49:18: 14000000 INFO @ Mon, 12 Aug 2019 19:49:19: 14000000 INFO @ Mon, 12 Aug 2019 19:49:20: 14000000 INFO @ Mon, 12 Aug 2019 19:49:22: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 19:49:22: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 19:49:22: #1 total tags in treatment: 14544954 INFO @ Mon, 12 Aug 2019 19:49:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:49:22: #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 19:49:22: #1 tags after filtering in treatment: 14544954 INFO @ Mon, 12 Aug 2019 19:49:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:49:22: #1 finished! INFO @ Mon, 12 Aug 2019 19:49:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:49:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:49:23: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 19:49:23: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 19:49:23: #1 total tags in treatment: 14544954 INFO @ Mon, 12 Aug 2019 19:49:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:49:23: #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 19:49:23: #1 tags after filtering in treatment: 14544954 INFO @ Mon, 12 Aug 2019 19:49:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:49:23: #1 finished! INFO @ Mon, 12 Aug 2019 19:49:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:49:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:49:23: #2 number of paired peaks: 427 WARNING @ Mon, 12 Aug 2019 19:49:23: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Mon, 12 Aug 2019 19:49:23: start model_add_line... INFO @ Mon, 12 Aug 2019 19:49:23: start X-correlation... INFO @ Mon, 12 Aug 2019 19:49:23: end of X-cor INFO @ Mon, 12 Aug 2019 19:49:23: #2 finished! INFO @ Mon, 12 Aug 2019 19:49:23: #2 predicted fragment length is 75 bps INFO @ Mon, 12 Aug 2019 19:49:23: #2 alternative fragment length(s) may be 3,75 bps INFO @ Mon, 12 Aug 2019 19:49:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.05_model.r INFO @ Mon, 12 Aug 2019 19:49:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:49:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:49:24: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 19:49:24: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 19:49:24: #1 total tags in treatment: 14544954 INFO @ Mon, 12 Aug 2019 19:49:24: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:49:24: #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 19:49:24: #1 tags after filtering in treatment: 14544954 INFO @ Mon, 12 Aug 2019 19:49:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:49:24: #1 finished! INFO @ Mon, 12 Aug 2019 19:49:24: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:49:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:49:24: #2 number of paired peaks: 427 WARNING @ Mon, 12 Aug 2019 19:49:24: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Mon, 12 Aug 2019 19:49:24: start model_add_line... INFO @ Mon, 12 Aug 2019 19:49:25: start X-correlation... INFO @ Mon, 12 Aug 2019 19:49:25: end of X-cor INFO @ Mon, 12 Aug 2019 19:49:25: #2 finished! INFO @ Mon, 12 Aug 2019 19:49:25: #2 predicted fragment length is 75 bps INFO @ Mon, 12 Aug 2019 19:49:25: #2 alternative fragment length(s) may be 3,75 bps INFO @ Mon, 12 Aug 2019 19:49:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.10_model.r INFO @ Mon, 12 Aug 2019 19:49:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:49:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:49:25: #2 number of paired peaks: 427 WARNING @ Mon, 12 Aug 2019 19:49:25: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Mon, 12 Aug 2019 19:49:25: start model_add_line... INFO @ Mon, 12 Aug 2019 19:49:25: start X-correlation... INFO @ Mon, 12 Aug 2019 19:49:25: end of X-cor INFO @ Mon, 12 Aug 2019 19:49:25: #2 finished! INFO @ Mon, 12 Aug 2019 19:49:25: #2 predicted fragment length is 75 bps INFO @ Mon, 12 Aug 2019 19:49:25: #2 alternative fragment length(s) may be 3,75 bps INFO @ Mon, 12 Aug 2019 19:49:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.20_model.r INFO @ Mon, 12 Aug 2019 19:49:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:49:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:50:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:50:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:50:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:50:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:50:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:50:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.05_summits.bed INFO @ Mon, 12 Aug 2019 19:50:20: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (9183 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:50:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:50:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:50:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.10_summits.bed INFO @ Mon, 12 Aug 2019 19:50:21: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4726 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:50:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:50:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:50:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494957/SRX494957.20_summits.bed INFO @ Mon, 12 Aug 2019 19:50:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1722 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。