Job ID = 2011906 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,286,934 reads read : 8,573,868 reads written : 8,573,868 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: 00:02:59 4286934 reads; of these: 4286934 (100.00%) were paired; of these: 603129 (14.07%) aligned concordantly 0 times 3269587 (76.27%) aligned concordantly exactly 1 time 414218 (9.66%) aligned concordantly >1 times ---- 603129 pairs aligned concordantly 0 times; of these: 375266 (62.22%) aligned discordantly 1 time ---- 227863 pairs aligned 0 times concordantly or discordantly; of these: 455726 mates make up the pairs; of these: 244807 (53.72%) aligned 0 times 99206 (21.77%) aligned exactly 1 time 111713 (24.51%) aligned >1 times 97.14% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 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] 115215 / 4057513 = 0.0284 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 @ Sat, 06 Jul 2019 03:16:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.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 @ Sat, 06 Jul 2019 03:16:49: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:16:49: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:16:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.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 @ Sat, 06 Jul 2019 03:16:50: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:16:50: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:16:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.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 @ Sat, 06 Jul 2019 03:16:51: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:16:51: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:16:57: 1000000 INFO @ Sat, 06 Jul 2019 03:16:58: 1000000 INFO @ Sat, 06 Jul 2019 03:16:59: 1000000 INFO @ Sat, 06 Jul 2019 03:17:04: 2000000 INFO @ Sat, 06 Jul 2019 03:17:06: 2000000 INFO @ Sat, 06 Jul 2019 03:17:07: 2000000 INFO @ Sat, 06 Jul 2019 03:17:11: 3000000 INFO @ Sat, 06 Jul 2019 03:17:14: 3000000 INFO @ Sat, 06 Jul 2019 03:17:14: 3000000 INFO @ Sat, 06 Jul 2019 03:17:17: 4000000 INFO @ Sat, 06 Jul 2019 03:17:22: 4000000 INFO @ Sat, 06 Jul 2019 03:17:24: 4000000 INFO @ Sat, 06 Jul 2019 03:17:24: 5000000 INFO @ Sat, 06 Jul 2019 03:17:30: 5000000 INFO @ Sat, 06 Jul 2019 03:17:30: 6000000 INFO @ Sat, 06 Jul 2019 03:17:33: 5000000 INFO @ Sat, 06 Jul 2019 03:17:37: 7000000 INFO @ Sat, 06 Jul 2019 03:17:37: 6000000 INFO @ Sat, 06 Jul 2019 03:17:42: 6000000 INFO @ Sat, 06 Jul 2019 03:17:43: 8000000 INFO @ Sat, 06 Jul 2019 03:17:44: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:17:44: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:17:44: #1 total tags in treatment: 3576128 INFO @ Sat, 06 Jul 2019 03:17:44: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:17:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:17:44: #1 tags after filtering in treatment: 3004984 INFO @ Sat, 06 Jul 2019 03:17:44: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 06 Jul 2019 03:17:44: #1 finished! INFO @ Sat, 06 Jul 2019 03:17:44: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:17:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:17:44: #2 number of paired peaks: 173 WARNING @ Sat, 06 Jul 2019 03:17:44: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 06 Jul 2019 03:17:44: start model_add_line... INFO @ Sat, 06 Jul 2019 03:17:44: start X-correlation... INFO @ Sat, 06 Jul 2019 03:17:44: end of X-cor INFO @ Sat, 06 Jul 2019 03:17:44: #2 finished! INFO @ Sat, 06 Jul 2019 03:17:44: #2 predicted fragment length is 339 bps INFO @ Sat, 06 Jul 2019 03:17:44: #2 alternative fragment length(s) may be 0,16,65,101,105,127,143,207,225,244,272,294,303,305,307,339,362,397,481,526,540,562,597 bps INFO @ Sat, 06 Jul 2019 03:17:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.05_model.r INFO @ Sat, 06 Jul 2019 03:17:44: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:17:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:17:45: 7000000 INFO @ Sat, 06 Jul 2019 03:17:52: 7000000 INFO @ Sat, 06 Jul 2019 03:17:52: 8000000 INFO @ Sat, 06 Jul 2019 03:17:53: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:17:53: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:17:53: #1 total tags in treatment: 3576128 INFO @ Sat, 06 Jul 2019 03:17:53: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:17:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:17:53: #1 tags after filtering in treatment: 3004984 INFO @ Sat, 06 Jul 2019 03:17:53: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 06 Jul 2019 03:17:53: #1 finished! INFO @ Sat, 06 Jul 2019 03:17:53: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:17:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:17:53: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:17:53: #2 number of paired peaks: 173 WARNING @ Sat, 06 Jul 2019 03:17:53: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 06 Jul 2019 03:17:53: start model_add_line... INFO @ Sat, 06 Jul 2019 03:17:53: start X-correlation... INFO @ Sat, 06 Jul 2019 03:17:53: end of X-cor INFO @ Sat, 06 Jul 2019 03:17:53: #2 finished! INFO @ Sat, 06 Jul 2019 03:17:53: #2 predicted fragment length is 339 bps INFO @ Sat, 06 Jul 2019 03:17:53: #2 alternative fragment length(s) may be 0,16,65,101,105,127,143,207,225,244,272,294,303,305,307,339,362,397,481,526,540,562,597 bps INFO @ Sat, 06 Jul 2019 03:17:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.20_model.r INFO @ Sat, 06 Jul 2019 03:17:53: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:17:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:17:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:17:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:17:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.05_summits.bed INFO @ Sat, 06 Jul 2019 03:17:56: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (185 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:18:01: 8000000 INFO @ Sat, 06 Jul 2019 03:18:01: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:18:01: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:18:01: #1 total tags in treatment: 3576128 INFO @ Sat, 06 Jul 2019 03:18:01: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:18:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:18:02: #1 tags after filtering in treatment: 3004984 INFO @ Sat, 06 Jul 2019 03:18:02: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 06 Jul 2019 03:18:02: #1 finished! INFO @ Sat, 06 Jul 2019 03:18:02: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:18:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:18:02: #2 number of paired peaks: 173 WARNING @ Sat, 06 Jul 2019 03:18:02: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 06 Jul 2019 03:18:02: start model_add_line... INFO @ Sat, 06 Jul 2019 03:18:02: start X-correlation... INFO @ Sat, 06 Jul 2019 03:18:02: end of X-cor INFO @ Sat, 06 Jul 2019 03:18:02: #2 finished! INFO @ Sat, 06 Jul 2019 03:18:02: #2 predicted fragment length is 339 bps INFO @ Sat, 06 Jul 2019 03:18:02: #2 alternative fragment length(s) may be 0,16,65,101,105,127,143,207,225,244,272,294,303,305,307,339,362,397,481,526,540,562,597 bps INFO @ Sat, 06 Jul 2019 03:18:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.10_model.r INFO @ Sat, 06 Jul 2019 03:18:02: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:18:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.20_peaks.xls BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:18:33: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:18:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:18:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:18:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.20_summits.bed INFO @ Sat, 06 Jul 2019 03:18:33: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:18:42: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:18:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:18:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:18:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383679/SRX5383679.10_summits.bed INFO @ Sat, 06 Jul 2019 03:18:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。