Job ID = 2010541 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,591,417 reads read : 25,182,834 reads written : 25,182,834 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: 00:05:35 12591417 reads; of these: 12591417 (100.00%) were paired; of these: 9078098 (72.10%) aligned concordantly 0 times 2536834 (20.15%) aligned concordantly exactly 1 time 976485 (7.76%) aligned concordantly >1 times ---- 9078098 pairs aligned concordantly 0 times; of these: 93935 (1.03%) aligned discordantly 1 time ---- 8984163 pairs aligned 0 times concordantly or discordantly; of these: 17968326 mates make up the pairs; of these: 17728542 (98.67%) aligned 0 times 79052 (0.44%) aligned exactly 1 time 160732 (0.89%) aligned >1 times 29.60% overall alignment rate Time searching: 00:05:35 Overall time: 00:05:35 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_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] 580671 / 3599662 = 0.1613 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 23:12:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.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 23:12:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:12:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:12:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.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 23:12:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:12:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:12:10: 1000000 INFO @ Fri, 05 Jul 2019 23:12:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.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 23:12:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:12:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:12:11: 1000000 INFO @ Fri, 05 Jul 2019 23:12:18: 2000000 INFO @ Fri, 05 Jul 2019 23:12:19: 1000000 INFO @ Fri, 05 Jul 2019 23:12:19: 2000000 INFO @ Fri, 05 Jul 2019 23:12:25: 3000000 INFO @ Fri, 05 Jul 2019 23:12:27: 3000000 INFO @ Fri, 05 Jul 2019 23:12:27: 2000000 INFO @ Fri, 05 Jul 2019 23:12:33: 4000000 INFO @ Fri, 05 Jul 2019 23:12:34: 4000000 INFO @ Fri, 05 Jul 2019 23:12:35: 3000000 INFO @ Fri, 05 Jul 2019 23:12:40: 5000000 INFO @ Fri, 05 Jul 2019 23:12:42: 5000000 INFO @ Fri, 05 Jul 2019 23:12:43: 4000000 INFO @ Fri, 05 Jul 2019 23:12:47: 6000000 INFO @ Fri, 05 Jul 2019 23:12:49: 6000000 INFO @ Fri, 05 Jul 2019 23:12:49: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:12:49: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:12:49: #1 total tags in treatment: 2946051 INFO @ Fri, 05 Jul 2019 23:12:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:12:49: #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 23:12:50: #1 tags after filtering in treatment: 1590048 INFO @ Fri, 05 Jul 2019 23:12:50: #1 Redundant rate of treatment: 0.46 INFO @ Fri, 05 Jul 2019 23:12:50: #1 finished! INFO @ Fri, 05 Jul 2019 23:12:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:12:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:12:50: #2 number of paired peaks: 1040 INFO @ Fri, 05 Jul 2019 23:12:50: start model_add_line... INFO @ Fri, 05 Jul 2019 23:12:50: start X-correlation... INFO @ Fri, 05 Jul 2019 23:12:50: end of X-cor INFO @ Fri, 05 Jul 2019 23:12:50: #2 finished! INFO @ Fri, 05 Jul 2019 23:12:50: #2 predicted fragment length is 266 bps INFO @ Fri, 05 Jul 2019 23:12:50: #2 alternative fragment length(s) may be 2,175,226,235,260,266,315,524 bps INFO @ Fri, 05 Jul 2019 23:12:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.05_model.r INFO @ Fri, 05 Jul 2019 23:12:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:12:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:12:51: 5000000 INFO @ Fri, 05 Jul 2019 23:12:51: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:12:51: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:12:51: #1 total tags in treatment: 2946051 INFO @ Fri, 05 Jul 2019 23:12:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:12:51: #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 23:12:52: #1 tags after filtering in treatment: 1590048 INFO @ Fri, 05 Jul 2019 23:12:52: #1 Redundant rate of treatment: 0.46 INFO @ Fri, 05 Jul 2019 23:12:52: #1 finished! INFO @ Fri, 05 Jul 2019 23:12:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:12:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:12:52: #2 number of paired peaks: 1040 INFO @ Fri, 05 Jul 2019 23:12:52: start model_add_line... INFO @ Fri, 05 Jul 2019 23:12:52: start X-correlation... INFO @ Fri, 05 Jul 2019 23:12:52: end of X-cor INFO @ Fri, 05 Jul 2019 23:12:52: #2 finished! INFO @ Fri, 05 Jul 2019 23:12:52: #2 predicted fragment length is 266 bps INFO @ Fri, 05 Jul 2019 23:12:52: #2 alternative fragment length(s) may be 2,175,226,235,260,266,315,524 bps INFO @ Fri, 05 Jul 2019 23:12:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.10_model.r INFO @ Fri, 05 Jul 2019 23:12:59: 6000000 BedGraph に変換しました。 INFO @ Fri, 05 Jul 2019 23:13:01: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:13:01: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:13:01: #1 total tags in treatment: 2946051 INFO @ Fri, 05 Jul 2019 23:13:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:13:01: #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 23:13:01: #1 tags after filtering in treatment: 1590048 INFO @ Fri, 05 Jul 2019 23:13:01: #1 Redundant rate of treatment: 0.46 INFO @ Fri, 05 Jul 2019 23:13:01: #1 finished! INFO @ Fri, 05 Jul 2019 23:13:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:13:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:13:02: #2 number of paired peaks: 1040 INFO @ Fri, 05 Jul 2019 23:13:02: start model_add_line... INFO @ Fri, 05 Jul 2019 23:13:02: start X-correlation... INFO @ Fri, 05 Jul 2019 23:13:02: end of X-cor INFO @ Fri, 05 Jul 2019 23:13:02: #2 finished! INFO @ Fri, 05 Jul 2019 23:13:02: #2 predicted fragment length is 266 bps INFO @ Fri, 05 Jul 2019 23:13:02: #2 alternative fragment length(s) may be 2,175,226,235,260,266,315,524 bps INFO @ Fri, 05 Jul 2019 23:13:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.20_model.r INFO @ Fri, 05 Jul 2019 23:13:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:13:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.05_peaks.xls BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:13:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:13:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:13:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:13:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:13:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:13:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.05_summits.bed INFO @ Fri, 05 Jul 2019 23:13:28: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (397 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:13:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:13:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:13:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:13:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:13:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:13:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.20_summits.bed INFO @ Fri, 05 Jul 2019 23:13:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:13:43: Done! INFO @ Fri, 05 Jul 2019 23:13:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381243/SRX381243.10_summits.bed INFO @ Fri, 05 Jul 2019 23:13:43: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (337 records, 4 fields): 2 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (245 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling