Job ID = 2011890 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,588,971 reads read : 9,177,942 reads written : 9,177,942 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 4588971 reads; of these: 4588971 (100.00%) were paired; of these: 367443 (8.01%) aligned concordantly 0 times 3266029 (71.17%) aligned concordantly exactly 1 time 955499 (20.82%) aligned concordantly >1 times ---- 367443 pairs aligned concordantly 0 times; of these: 178686 (48.63%) aligned discordantly 1 time ---- 188757 pairs aligned 0 times concordantly or discordantly; of these: 377514 mates make up the pairs; of these: 202577 (53.66%) aligned 0 times 59147 (15.67%) aligned exactly 1 time 115790 (30.67%) aligned >1 times 97.79% 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] 222448 / 4397870 = 0.0506 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 03:08:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.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 03:08:45: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:08:45: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:08:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.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 03:08:46: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:08:46: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:08:51: 1000000 INFO @ Sat, 06 Jul 2019 03:08:54: 1000000 INFO @ Sat, 06 Jul 2019 03:08:58: 2000000 INFO @ Sat, 06 Jul 2019 03:09:02: 2000000 INFO @ Sat, 06 Jul 2019 03:09:04: 3000000 INFO @ Sat, 06 Jul 2019 03:09:10: 3000000 INFO @ Sat, 06 Jul 2019 03:09:11: 4000000 INFO @ Sat, 06 Jul 2019 03:09:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.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 03:09:16: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:09:16: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:09:18: 5000000 INFO @ Sat, 06 Jul 2019 03:09:19: 4000000 INFO @ Sat, 06 Jul 2019 03:09:24: 1000000 INFO @ Sat, 06 Jul 2019 03:09:24: 6000000 INFO @ Sat, 06 Jul 2019 03:09:27: 5000000 INFO @ Sat, 06 Jul 2019 03:09:31: 7000000 INFO @ Sat, 06 Jul 2019 03:09:32: 2000000 INFO @ Sat, 06 Jul 2019 03:09:35: 6000000 INFO @ Sat, 06 Jul 2019 03:09:37: 8000000 INFO @ Sat, 06 Jul 2019 03:09:39: 3000000 INFO @ Sat, 06 Jul 2019 03:09:41: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:09:41: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:09:41: #1 total tags in treatment: 4003342 INFO @ Sat, 06 Jul 2019 03:09:41: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:09:41: #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 03:09:41: #1 tags after filtering in treatment: 2972814 INFO @ Sat, 06 Jul 2019 03:09:41: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 03:09:41: #1 finished! INFO @ Sat, 06 Jul 2019 03:09:41: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:09:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:09:41: #2 number of paired peaks: 101 WARNING @ Sat, 06 Jul 2019 03:09:41: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sat, 06 Jul 2019 03:09:41: start model_add_line... INFO @ Sat, 06 Jul 2019 03:09:41: start X-correlation... INFO @ Sat, 06 Jul 2019 03:09:41: end of X-cor INFO @ Sat, 06 Jul 2019 03:09:41: #2 finished! INFO @ Sat, 06 Jul 2019 03:09:41: #2 predicted fragment length is 259 bps INFO @ Sat, 06 Jul 2019 03:09:41: #2 alternative fragment length(s) may be 2,229,259 bps INFO @ Sat, 06 Jul 2019 03:09:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.05_model.r INFO @ Sat, 06 Jul 2019 03:09:41: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:09:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:09:43: 7000000 INFO @ Sat, 06 Jul 2019 03:09:47: 4000000 INFO @ Sat, 06 Jul 2019 03:09:50: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:09:51: 8000000 INFO @ Sat, 06 Jul 2019 03:09:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:09:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:09:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.05_summits.bed INFO @ Sat, 06 Jul 2019 03:09:53: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (139 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:09:55: 5000000 INFO @ Sat, 06 Jul 2019 03:09:55: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:09:55: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:09:55: #1 total tags in treatment: 4003342 INFO @ Sat, 06 Jul 2019 03:09:55: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:09:55: #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 03:09:55: #1 tags after filtering in treatment: 2972814 INFO @ Sat, 06 Jul 2019 03:09:55: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 03:09:55: #1 finished! INFO @ Sat, 06 Jul 2019 03:09:55: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:09:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:09:56: #2 number of paired peaks: 101 WARNING @ Sat, 06 Jul 2019 03:09:56: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sat, 06 Jul 2019 03:09:56: start model_add_line... INFO @ Sat, 06 Jul 2019 03:09:56: start X-correlation... INFO @ Sat, 06 Jul 2019 03:09:56: end of X-cor INFO @ Sat, 06 Jul 2019 03:09:56: #2 finished! INFO @ Sat, 06 Jul 2019 03:09:56: #2 predicted fragment length is 259 bps INFO @ Sat, 06 Jul 2019 03:09:56: #2 alternative fragment length(s) may be 2,229,259 bps INFO @ Sat, 06 Jul 2019 03:09:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.10_model.r INFO @ Sat, 06 Jul 2019 03:09:56: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:09:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:10:02: 6000000 INFO @ Sat, 06 Jul 2019 03:10:04: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:10:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:10:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:10:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.10_summits.bed INFO @ Sat, 06 Jul 2019 03:10:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (94 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:10:09: 7000000 INFO @ Sat, 06 Jul 2019 03:10:16: 8000000 INFO @ Sat, 06 Jul 2019 03:10:20: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:10:20: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:10:20: #1 total tags in treatment: 4003342 INFO @ Sat, 06 Jul 2019 03:10:20: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:10:20: #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 03:10:20: #1 tags after filtering in treatment: 2972814 INFO @ Sat, 06 Jul 2019 03:10:20: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 03:10:20: #1 finished! INFO @ Sat, 06 Jul 2019 03:10:20: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:10:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:10:20: #2 number of paired peaks: 101 WARNING @ Sat, 06 Jul 2019 03:10:20: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sat, 06 Jul 2019 03:10:20: start model_add_line... INFO @ Sat, 06 Jul 2019 03:10:20: start X-correlation... INFO @ Sat, 06 Jul 2019 03:10:20: end of X-cor INFO @ Sat, 06 Jul 2019 03:10:20: #2 finished! INFO @ Sat, 06 Jul 2019 03:10:20: #2 predicted fragment length is 259 bps INFO @ Sat, 06 Jul 2019 03:10:20: #2 alternative fragment length(s) may be 2,229,259 bps INFO @ Sat, 06 Jul 2019 03:10:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.20_model.r INFO @ Sat, 06 Jul 2019 03:10:23: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:10:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:10:32: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:10:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.20_peaks.xls INFO @ Sat, 06 Jul 2019 03:10:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:10:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383666/SRX5383666.20_summits.bed INFO @ Sat, 06 Jul 2019 03:10:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (62 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。