Job ID = 2011908 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,524,539 reads read : 9,049,078 reads written : 9,049,078 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: 00:03:10 4524539 reads; of these: 4524539 (100.00%) were paired; of these: 523093 (11.56%) aligned concordantly 0 times 3487741 (77.09%) aligned concordantly exactly 1 time 513705 (11.35%) aligned concordantly >1 times ---- 523093 pairs aligned concordantly 0 times; of these: 317852 (60.76%) aligned discordantly 1 time ---- 205241 pairs aligned 0 times concordantly or discordantly; of these: 410482 mates make up the pairs; of these: 219958 (53.59%) aligned 0 times 84161 (20.50%) aligned exactly 1 time 106363 (25.91%) aligned >1 times 97.57% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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] 133563 / 4315995 = 0.0309 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 03:18:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.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 03:18:11: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:18:11: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:18:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.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 03:18:12: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:18:12: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:18:17: 1000000 INFO @ Sat, 06 Jul 2019 03:18:18: 1000000 INFO @ Sat, 06 Jul 2019 03:18:23: 2000000 INFO @ Sat, 06 Jul 2019 03:18:24: 2000000 INFO @ Sat, 06 Jul 2019 03:18:30: 3000000 INFO @ Sat, 06 Jul 2019 03:18:31: 3000000 INFO @ Sat, 06 Jul 2019 03:18:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.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 03:18:36: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:18:36: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:18:36: 4000000 INFO @ Sat, 06 Jul 2019 03:18:37: 4000000 INFO @ Sat, 06 Jul 2019 03:18:41: 1000000 INFO @ Sat, 06 Jul 2019 03:18:42: 5000000 INFO @ Sat, 06 Jul 2019 03:18:43: 5000000 INFO @ Sat, 06 Jul 2019 03:18:47: 2000000 INFO @ Sat, 06 Jul 2019 03:18:48: 6000000 INFO @ Sat, 06 Jul 2019 03:18:49: 6000000 INFO @ Sat, 06 Jul 2019 03:18:53: 3000000 INFO @ Sat, 06 Jul 2019 03:18:55: 7000000 INFO @ Sat, 06 Jul 2019 03:18:56: 7000000 INFO @ Sat, 06 Jul 2019 03:18:58: 4000000 INFO @ Sat, 06 Jul 2019 03:19:01: 8000000 INFO @ Sat, 06 Jul 2019 03:19:02: 8000000 INFO @ Sat, 06 Jul 2019 03:19:04: 5000000 INFO @ Sat, 06 Jul 2019 03:19:04: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:19:04: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:19:04: #1 total tags in treatment: 3874204 INFO @ Sat, 06 Jul 2019 03:19:04: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:19:04: #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 03:19:05: #1 tags after filtering in treatment: 3230857 INFO @ Sat, 06 Jul 2019 03:19:05: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 06 Jul 2019 03:19:05: #1 finished! INFO @ Sat, 06 Jul 2019 03:19:05: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:19:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:19:05: #2 number of paired peaks: 158 WARNING @ Sat, 06 Jul 2019 03:19:05: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 06 Jul 2019 03:19:05: start model_add_line... INFO @ Sat, 06 Jul 2019 03:19:05: start X-correlation... INFO @ Sat, 06 Jul 2019 03:19:05: end of X-cor INFO @ Sat, 06 Jul 2019 03:19:05: #2 finished! INFO @ Sat, 06 Jul 2019 03:19:05: #2 predicted fragment length is 241 bps INFO @ Sat, 06 Jul 2019 03:19:05: #2 alternative fragment length(s) may be 0,17,78,96,114,139,161,189,200,216,241,270,283,306,338,379,428,457,463,513,548,593,597 bps INFO @ Sat, 06 Jul 2019 03:19:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.05_model.r INFO @ Sat, 06 Jul 2019 03:19:05: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:19:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:19:05: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:19:05: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:19:05: #1 total tags in treatment: 3874204 INFO @ Sat, 06 Jul 2019 03:19:05: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:19:05: #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 03:19:06: #1 tags after filtering in treatment: 3230857 INFO @ Sat, 06 Jul 2019 03:19:06: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 06 Jul 2019 03:19:06: #1 finished! INFO @ Sat, 06 Jul 2019 03:19:06: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:19:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:19:06: #2 number of paired peaks: 158 WARNING @ Sat, 06 Jul 2019 03:19:06: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 06 Jul 2019 03:19:06: start model_add_line... INFO @ Sat, 06 Jul 2019 03:19:06: start X-correlation... INFO @ Sat, 06 Jul 2019 03:19:06: end of X-cor INFO @ Sat, 06 Jul 2019 03:19:06: #2 finished! INFO @ Sat, 06 Jul 2019 03:19:06: #2 predicted fragment length is 241 bps INFO @ Sat, 06 Jul 2019 03:19:06: #2 alternative fragment length(s) may be 0,17,78,96,114,139,161,189,200,216,241,270,283,306,338,379,428,457,463,513,548,593,597 bps INFO @ Sat, 06 Jul 2019 03:19:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.10_model.r INFO @ Sat, 06 Jul 2019 03:19:06: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:19:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:19:09: 6000000 INFO @ Sat, 06 Jul 2019 03:19:13: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:19:14: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:19:15: 7000000 INFO @ Sat, 06 Jul 2019 03:19:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:19:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:19:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.05_summits.bed INFO @ Sat, 06 Jul 2019 03:19:16: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (21 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:19:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:19:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:19:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.10_summits.bed INFO @ Sat, 06 Jul 2019 03:19:17: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:19:20: 8000000 INFO @ Sat, 06 Jul 2019 03:19:23: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:19:23: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:19:23: #1 total tags in treatment: 3874204 INFO @ Sat, 06 Jul 2019 03:19:23: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:19:23: #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 03:19:24: #1 tags after filtering in treatment: 3230857 INFO @ Sat, 06 Jul 2019 03:19:24: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 06 Jul 2019 03:19:24: #1 finished! INFO @ Sat, 06 Jul 2019 03:19:24: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:19:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:19:24: #2 number of paired peaks: 158 WARNING @ Sat, 06 Jul 2019 03:19:24: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 06 Jul 2019 03:19:24: start model_add_line... INFO @ Sat, 06 Jul 2019 03:19:24: start X-correlation... INFO @ Sat, 06 Jul 2019 03:19:24: end of X-cor INFO @ Sat, 06 Jul 2019 03:19:24: #2 finished! INFO @ Sat, 06 Jul 2019 03:19:24: #2 predicted fragment length is 241 bps INFO @ Sat, 06 Jul 2019 03:19:24: #2 alternative fragment length(s) may be 0,17,78,96,114,139,161,189,200,216,241,270,283,306,338,379,428,457,463,513,548,593,597 bps INFO @ Sat, 06 Jul 2019 03:19:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.20_model.r INFO @ Sat, 06 Jul 2019 03:19:24: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:19:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:19:32: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:19:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.20_peaks.xls INFO @ Sat, 06 Jul 2019 03:19:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:19:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383681/SRX5383681.20_summits.bed INFO @ Sat, 06 Jul 2019 03:19:35: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (8 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。