Job ID = 2589985 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,677,270 reads read : 23,677,270 reads written : 23,677,270 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163637.sra.cache’: 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: 00:05:29 23677270 reads; of these: 23677270 (100.00%) were unpaired; of these: 1784309 (7.54%) aligned 0 times 19271743 (81.39%) aligned exactly 1 time 2621218 (11.07%) aligned >1 times 92.46% overall alignment rate Time searching: 00:05:29 Overall time: 00:05:29 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 12 files... [bam_rmdupse_core] 7418385 / 21892961 = 0.3388 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 19:08:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.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 19:08:09: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:08:09: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:08:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.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 19:08:10: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:08:10: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:08:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.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 19:08:11: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:08:11: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:08:19: 1000000 INFO @ Mon, 12 Aug 2019 19:08:20: 1000000 INFO @ Mon, 12 Aug 2019 19:08:22: 1000000 INFO @ Mon, 12 Aug 2019 19:08:28: 2000000 INFO @ Mon, 12 Aug 2019 19:08:29: 2000000 INFO @ Mon, 12 Aug 2019 19:08:33: 2000000 INFO @ Mon, 12 Aug 2019 19:08:38: 3000000 INFO @ Mon, 12 Aug 2019 19:08:39: 3000000 INFO @ Mon, 12 Aug 2019 19:08:44: 3000000 INFO @ Mon, 12 Aug 2019 19:08:48: 4000000 INFO @ Mon, 12 Aug 2019 19:08:49: 4000000 INFO @ Mon, 12 Aug 2019 19:08:56: 4000000 INFO @ Mon, 12 Aug 2019 19:08:57: 5000000 INFO @ Mon, 12 Aug 2019 19:08:58: 5000000 INFO @ Mon, 12 Aug 2019 19:09:07: 5000000 INFO @ Mon, 12 Aug 2019 19:09:07: 6000000 INFO @ Mon, 12 Aug 2019 19:09:08: 6000000 INFO @ Mon, 12 Aug 2019 19:09:16: 7000000 INFO @ Mon, 12 Aug 2019 19:09:17: 7000000 INFO @ Mon, 12 Aug 2019 19:09:17: 6000000 INFO @ Mon, 12 Aug 2019 19:09:26: 8000000 INFO @ Mon, 12 Aug 2019 19:09:27: 8000000 INFO @ Mon, 12 Aug 2019 19:09:28: 7000000 INFO @ Mon, 12 Aug 2019 19:09:35: 9000000 INFO @ Mon, 12 Aug 2019 19:09:36: 9000000 INFO @ Mon, 12 Aug 2019 19:09:39: 8000000 INFO @ Mon, 12 Aug 2019 19:09:45: 10000000 INFO @ Mon, 12 Aug 2019 19:09:46: 10000000 INFO @ Mon, 12 Aug 2019 19:09:50: 9000000 INFO @ Mon, 12 Aug 2019 19:09:54: 11000000 INFO @ Mon, 12 Aug 2019 19:09:55: 11000000 INFO @ Mon, 12 Aug 2019 19:10:01: 10000000 INFO @ Mon, 12 Aug 2019 19:10:04: 12000000 INFO @ Mon, 12 Aug 2019 19:10:05: 12000000 INFO @ Mon, 12 Aug 2019 19:10:12: 11000000 INFO @ Mon, 12 Aug 2019 19:10:13: 13000000 INFO @ Mon, 12 Aug 2019 19:10:14: 13000000 INFO @ Mon, 12 Aug 2019 19:10:23: 14000000 INFO @ Mon, 12 Aug 2019 19:10:23: 12000000 INFO @ Mon, 12 Aug 2019 19:10:24: 14000000 INFO @ Mon, 12 Aug 2019 19:10:27: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:10:27: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:10:27: #1 total tags in treatment: 14474576 INFO @ Mon, 12 Aug 2019 19:10:27: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:10:27: #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 19:10:27: #1 tags after filtering in treatment: 14474576 INFO @ Mon, 12 Aug 2019 19:10:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:10:27: #1 finished! INFO @ Mon, 12 Aug 2019 19:10:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:10:28: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:10:28: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:10:28: #1 total tags in treatment: 14474576 INFO @ Mon, 12 Aug 2019 19:10:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:10:28: #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 19:10:28: #1 tags after filtering in treatment: 14474576 INFO @ Mon, 12 Aug 2019 19:10:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:10:28: #1 finished! INFO @ Mon, 12 Aug 2019 19:10:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:10:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:10:29: #2 number of paired peaks: 1046 INFO @ Mon, 12 Aug 2019 19:10:29: start model_add_line... INFO @ Mon, 12 Aug 2019 19:10:29: start X-correlation... INFO @ Mon, 12 Aug 2019 19:10:29: end of X-cor INFO @ Mon, 12 Aug 2019 19:10:29: #2 finished! INFO @ Mon, 12 Aug 2019 19:10:29: #2 predicted fragment length is 113 bps INFO @ Mon, 12 Aug 2019 19:10:29: #2 alternative fragment length(s) may be 4,113 bps INFO @ Mon, 12 Aug 2019 19:10:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.05_model.r INFO @ Mon, 12 Aug 2019 19:10:29: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:10:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:10:30: #2 number of paired peaks: 1046 INFO @ Mon, 12 Aug 2019 19:10:30: start model_add_line... INFO @ Mon, 12 Aug 2019 19:10:30: start X-correlation... INFO @ Mon, 12 Aug 2019 19:10:30: end of X-cor INFO @ Mon, 12 Aug 2019 19:10:30: #2 finished! INFO @ Mon, 12 Aug 2019 19:10:30: #2 predicted fragment length is 113 bps INFO @ Mon, 12 Aug 2019 19:10:30: #2 alternative fragment length(s) may be 4,113 bps INFO @ Mon, 12 Aug 2019 19:10:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.10_model.r INFO @ Mon, 12 Aug 2019 19:10:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:10:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:10:33: 13000000 INFO @ Mon, 12 Aug 2019 19:10:43: 14000000 INFO @ Mon, 12 Aug 2019 19:10:48: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:10:48: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:10:48: #1 total tags in treatment: 14474576 INFO @ Mon, 12 Aug 2019 19:10:48: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:10:48: #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 19:10:48: #1 tags after filtering in treatment: 14474576 INFO @ Mon, 12 Aug 2019 19:10:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:10:48: #1 finished! INFO @ Mon, 12 Aug 2019 19:10:48: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:10:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:10:50: #2 number of paired peaks: 1046 INFO @ Mon, 12 Aug 2019 19:10:50: start model_add_line... INFO @ Mon, 12 Aug 2019 19:10:50: start X-correlation... INFO @ Mon, 12 Aug 2019 19:10:50: end of X-cor INFO @ Mon, 12 Aug 2019 19:10:50: #2 finished! INFO @ Mon, 12 Aug 2019 19:10:50: #2 predicted fragment length is 113 bps INFO @ Mon, 12 Aug 2019 19:10:50: #2 alternative fragment length(s) may be 4,113 bps INFO @ Mon, 12 Aug 2019 19:10:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.20_model.r INFO @ Mon, 12 Aug 2019 19:10:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:10:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:11:08: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:11:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:11:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:11:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:11:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.05_summits.bed INFO @ Mon, 12 Aug 2019 19:11:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4613 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:11:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:11:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:11:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.10_summits.bed INFO @ Mon, 12 Aug 2019 19:11:27: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2293 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:11:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:11:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:11:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:11:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466571/SRX466571.20_summits.bed INFO @ Mon, 12 Aug 2019 19:11:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (693 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。