Job ID = 2009992 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,039,150 reads read : 12,078,300 reads written : 12,078,300 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: 00:05:12 6039150 reads; of these: 6039150 (100.00%) were paired; of these: 937988 (15.53%) aligned concordantly 0 times 2921840 (48.38%) aligned concordantly exactly 1 time 2179322 (36.09%) aligned concordantly >1 times ---- 937988 pairs aligned concordantly 0 times; of these: 29410 (3.14%) aligned discordantly 1 time ---- 908578 pairs aligned 0 times concordantly or discordantly; of these: 1817156 mates make up the pairs; of these: 1556962 (85.68%) aligned 0 times 125277 (6.89%) aligned exactly 1 time 134917 (7.42%) aligned >1 times 87.11% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 1156550 / 5122539 = 0.2258 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 @ Fri, 05 Jul 2019 20:59:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 20:59:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:59:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:59:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 20:59:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:59:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:59:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 20:59:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:59:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:59:09: 1000000 INFO @ Fri, 05 Jul 2019 20:59:09: 1000000 INFO @ Fri, 05 Jul 2019 20:59:10: 1000000 INFO @ Fri, 05 Jul 2019 20:59:17: 2000000 INFO @ Fri, 05 Jul 2019 20:59:18: 2000000 INFO @ Fri, 05 Jul 2019 20:59:19: 2000000 INFO @ Fri, 05 Jul 2019 20:59:24: 3000000 INFO @ Fri, 05 Jul 2019 20:59:27: 3000000 INFO @ Fri, 05 Jul 2019 20:59:28: 3000000 INFO @ Fri, 05 Jul 2019 20:59:32: 4000000 INFO @ Fri, 05 Jul 2019 20:59:36: 4000000 INFO @ Fri, 05 Jul 2019 20:59:37: 4000000 INFO @ Fri, 05 Jul 2019 20:59:39: 5000000 INFO @ Fri, 05 Jul 2019 20:59:45: 5000000 INFO @ Fri, 05 Jul 2019 20:59:46: 5000000 INFO @ Fri, 05 Jul 2019 20:59:46: 6000000 INFO @ Fri, 05 Jul 2019 20:59:53: 6000000 INFO @ Fri, 05 Jul 2019 20:59:54: 7000000 INFO @ Fri, 05 Jul 2019 20:59:54: 6000000 INFO @ Fri, 05 Jul 2019 21:00:01: 8000000 INFO @ Fri, 05 Jul 2019 21:00:02: 7000000 INFO @ Fri, 05 Jul 2019 21:00:03: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:00:03: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:00:03: #1 total tags in treatment: 3945334 INFO @ Fri, 05 Jul 2019 21:00:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:00:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:00:03: #1 tags after filtering in treatment: 1678580 INFO @ Fri, 05 Jul 2019 21:00:03: #1 Redundant rate of treatment: 0.57 INFO @ Fri, 05 Jul 2019 21:00:03: #1 finished! INFO @ Fri, 05 Jul 2019 21:00:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:00:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:00:03: 7000000 INFO @ Fri, 05 Jul 2019 21:00:03: #2 number of paired peaks: 1316 INFO @ Fri, 05 Jul 2019 21:00:03: start model_add_line... INFO @ Fri, 05 Jul 2019 21:00:03: start X-correlation... INFO @ Fri, 05 Jul 2019 21:00:03: end of X-cor INFO @ Fri, 05 Jul 2019 21:00:03: #2 finished! INFO @ Fri, 05 Jul 2019 21:00:03: #2 predicted fragment length is 165 bps INFO @ Fri, 05 Jul 2019 21:00:03: #2 alternative fragment length(s) may be 0,76,96,165,195,244,298 bps INFO @ Fri, 05 Jul 2019 21:00:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.20_model.r INFO @ Fri, 05 Jul 2019 21:00:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:00:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:00:10: 8000000 INFO @ Fri, 05 Jul 2019 21:00:12: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:00:12: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:00:12: #1 total tags in treatment: 3945334 INFO @ Fri, 05 Jul 2019 21:00:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:00:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:00:12: #1 tags after filtering in treatment: 1678580 INFO @ Fri, 05 Jul 2019 21:00:12: #1 Redundant rate of treatment: 0.57 INFO @ Fri, 05 Jul 2019 21:00:12: #1 finished! INFO @ Fri, 05 Jul 2019 21:00:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:00:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:00:12: 8000000 INFO @ Fri, 05 Jul 2019 21:00:12: #2 number of paired peaks: 1316 INFO @ Fri, 05 Jul 2019 21:00:12: start model_add_line... INFO @ Fri, 05 Jul 2019 21:00:12: start X-correlation... INFO @ Fri, 05 Jul 2019 21:00:12: end of X-cor INFO @ Fri, 05 Jul 2019 21:00:12: #2 finished! INFO @ Fri, 05 Jul 2019 21:00:12: #2 predicted fragment length is 165 bps INFO @ Fri, 05 Jul 2019 21:00:12: #2 alternative fragment length(s) may be 0,76,96,165,195,244,298 bps INFO @ Fri, 05 Jul 2019 21:00:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.05_model.r INFO @ Fri, 05 Jul 2019 21:00:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:00:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:00:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:00:14: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:00:14: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:00:14: #1 total tags in treatment: 3945334 INFO @ Fri, 05 Jul 2019 21:00:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:00:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:00:14: #1 tags after filtering in treatment: 1678580 INFO @ Fri, 05 Jul 2019 21:00:14: #1 Redundant rate of treatment: 0.57 INFO @ Fri, 05 Jul 2019 21:00:14: #1 finished! INFO @ Fri, 05 Jul 2019 21:00:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:00:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:00:14: #2 number of paired peaks: 1316 INFO @ Fri, 05 Jul 2019 21:00:14: start model_add_line... INFO @ Fri, 05 Jul 2019 21:00:14: start X-correlation... INFO @ Fri, 05 Jul 2019 21:00:14: end of X-cor INFO @ Fri, 05 Jul 2019 21:00:14: #2 finished! INFO @ Fri, 05 Jul 2019 21:00:14: #2 predicted fragment length is 165 bps INFO @ Fri, 05 Jul 2019 21:00:14: #2 alternative fragment length(s) may be 0,76,96,165,195,244,298 bps INFO @ Fri, 05 Jul 2019 21:00:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.10_model.r INFO @ Fri, 05 Jul 2019 21:00:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:00:14: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 21:00:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.20_peaks.xls INFO @ Fri, 05 Jul 2019 21:00:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:00:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.20_summits.bed INFO @ Fri, 05 Jul 2019 21:00:15: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (348 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:00:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 21:00:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.05_peaks.xls INFO @ Fri, 05 Jul 2019 21:00:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:00:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.05_summits.bed INFO @ Fri, 05 Jul 2019 21:00:24: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (657 records, 4 fields): 5 millis INFO @ Fri, 05 Jul 2019 21:00:24: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:00:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.10_peaks.xls INFO @ Fri, 05 Jul 2019 21:00:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:00:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339857/SRX2339857.10_summits.bed INFO @ Fri, 05 Jul 2019 21:00:26: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (554 records, 4 fields): 5 millis CompletedMACS2peakCalling