Job ID = 11632752 sra ファイルのダウンロード中... Completed: 295138K bytes transferred in 14 seconds (165413K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Read 2905454 spots for /home/okishinya/chipatlas/results/sacCer3/DRX123822/DRR131084.sra Written 2905454 spots for /home/okishinya/chipatlas/results/sacCer3/DRX123822/DRR131084.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:03:05 2905454 reads; of these: 2905454 (100.00%) were paired; of these: 268693 (9.25%) aligned concordantly 0 times 2409041 (82.91%) aligned concordantly exactly 1 time 227720 (7.84%) aligned concordantly >1 times ---- 268693 pairs aligned concordantly 0 times; of these: 133696 (49.76%) aligned discordantly 1 time ---- 134997 pairs aligned 0 times concordantly or discordantly; of these: 269994 mates make up the pairs; of these: 207695 (76.93%) aligned 0 times 30438 (11.27%) aligned exactly 1 time 31861 (11.80%) aligned >1 times 96.43% overall alignment rate Time searching: 00:03:05 Overall time: 00:03:05 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] 5786 / 2763401 = 0.0021 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, 15 Feb 2019 07:16:24: # Command line: callpeak -t DRX123822.bam -f BAM -g 12100000 -n DRX123822.20 -q 1e-20 # ARGUMENTS LIST: # name = DRX123822.20 # format = BAM # ChIP-seq file = ['DRX123822.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, 15 Feb 2019 07:16:24: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:16:24: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:16:24: # Command line: callpeak -t DRX123822.bam -f BAM -g 12100000 -n DRX123822.05 -q 1e-05 # ARGUMENTS LIST: # name = DRX123822.05 # format = BAM # ChIP-seq file = ['DRX123822.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, 15 Feb 2019 07:16:24: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:16:24: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:16:24: # Command line: callpeak -t DRX123822.bam -f BAM -g 12100000 -n DRX123822.10 -q 1e-10 # ARGUMENTS LIST: # name = DRX123822.10 # format = BAM # ChIP-seq file = ['DRX123822.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, 15 Feb 2019 07:16:24: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:16:24: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:16:31: 1000000 INFO @ Fri, 15 Feb 2019 07:16:31: 1000000 INFO @ Fri, 15 Feb 2019 07:16:31: 1000000 INFO @ Fri, 15 Feb 2019 07:16:38: 2000000 INFO @ Fri, 15 Feb 2019 07:16:38: 2000000 INFO @ Fri, 15 Feb 2019 07:16:39: 2000000 INFO @ Fri, 15 Feb 2019 07:16:45: 3000000 INFO @ Fri, 15 Feb 2019 07:16:45: 3000000 INFO @ Fri, 15 Feb 2019 07:16:45: 3000000 INFO @ Fri, 15 Feb 2019 07:16:52: 4000000 INFO @ Fri, 15 Feb 2019 07:16:52: 4000000 INFO @ Fri, 15 Feb 2019 07:16:52: 4000000 INFO @ Fri, 15 Feb 2019 07:16:59: 5000000 INFO @ Fri, 15 Feb 2019 07:16:59: 5000000 INFO @ Fri, 15 Feb 2019 07:16:59: 5000000 INFO @ Fri, 15 Feb 2019 07:17:03: #1 tag size is determined as 74 bps INFO @ Fri, 15 Feb 2019 07:17:03: #1 tag size = 74 INFO @ Fri, 15 Feb 2019 07:17:03: #1 total tags in treatment: 2631094 INFO @ Fri, 15 Feb 2019 07:17:03: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:17:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:17:03: #1 tag size is determined as 74 bps INFO @ Fri, 15 Feb 2019 07:17:03: #1 tag size = 74 INFO @ Fri, 15 Feb 2019 07:17:03: #1 total tags in treatment: 2631094 INFO @ Fri, 15 Feb 2019 07:17:03: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:17:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:17:03: #1 tags after filtering in treatment: 2325937 INFO @ Fri, 15 Feb 2019 07:17:03: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 15 Feb 2019 07:17:03: #1 finished! INFO @ Fri, 15 Feb 2019 07:17:03: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:17:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:17:03: #1 tags after filtering in treatment: 2325937 INFO @ Fri, 15 Feb 2019 07:17:03: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 15 Feb 2019 07:17:03: #1 finished! INFO @ Fri, 15 Feb 2019 07:17:03: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:17:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:17:03: #2 number of paired peaks: 187 WARNING @ Fri, 15 Feb 2019 07:17:03: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Fri, 15 Feb 2019 07:17:03: start model_add_line... INFO @ Fri, 15 Feb 2019 07:17:03: #2 number of paired peaks: 187 WARNING @ Fri, 15 Feb 2019 07:17:03: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Fri, 15 Feb 2019 07:17:03: start model_add_line... INFO @ Fri, 15 Feb 2019 07:17:03: start X-correlation... INFO @ Fri, 15 Feb 2019 07:17:03: start X-correlation... INFO @ Fri, 15 Feb 2019 07:17:03: end of X-cor INFO @ Fri, 15 Feb 2019 07:17:03: end of X-cor INFO @ Fri, 15 Feb 2019 07:17:03: #2 finished! INFO @ Fri, 15 Feb 2019 07:17:03: #2 finished! INFO @ Fri, 15 Feb 2019 07:17:03: #2 predicted fragment length is 180 bps INFO @ Fri, 15 Feb 2019 07:17:03: #2 predicted fragment length is 180 bps INFO @ Fri, 15 Feb 2019 07:17:03: #2 alternative fragment length(s) may be 0,77,107,125,156,171,180,210,235,267,317,352,391,457,481,501,527,567,589 bps INFO @ Fri, 15 Feb 2019 07:17:03: #2 alternative fragment length(s) may be 0,77,107,125,156,171,180,210,235,267,317,352,391,457,481,501,527,567,589 bps INFO @ Fri, 15 Feb 2019 07:17:03: #2.2 Generate R script for model : DRX123822.05_model.r INFO @ Fri, 15 Feb 2019 07:17:03: #2.2 Generate R script for model : DRX123822.10_model.r INFO @ Fri, 15 Feb 2019 07:17:03: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:17:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:17:03: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:17:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:17:03: #1 tag size is determined as 74 bps INFO @ Fri, 15 Feb 2019 07:17:03: #1 tag size = 74 INFO @ Fri, 15 Feb 2019 07:17:03: #1 total tags in treatment: 2631094 INFO @ Fri, 15 Feb 2019 07:17:03: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:17:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:17:03: #1 tags after filtering in treatment: 2325937 INFO @ Fri, 15 Feb 2019 07:17:03: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 15 Feb 2019 07:17:03: #1 finished! INFO @ Fri, 15 Feb 2019 07:17:03: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:17:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:17:03: #2 number of paired peaks: 187 WARNING @ Fri, 15 Feb 2019 07:17:03: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Fri, 15 Feb 2019 07:17:03: start model_add_line... INFO @ Fri, 15 Feb 2019 07:17:03: start X-correlation... INFO @ Fri, 15 Feb 2019 07:17:03: end of X-cor INFO @ Fri, 15 Feb 2019 07:17:03: #2 finished! INFO @ Fri, 15 Feb 2019 07:17:03: #2 predicted fragment length is 180 bps INFO @ Fri, 15 Feb 2019 07:17:03: #2 alternative fragment length(s) may be 0,77,107,125,156,171,180,210,235,267,317,352,391,457,481,501,527,567,589 bps INFO @ Fri, 15 Feb 2019 07:17:03: #2.2 Generate R script for model : DRX123822.20_model.r INFO @ Fri, 15 Feb 2019 07:17:03: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:17:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:17:09: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:17:09: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:17:09: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:17:11: #4 Write output xls file... DRX123822.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:17:11: #4 Write peak in narrowPeak format file... DRX123822.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:17:11: #4 Write summits bed file... DRX123822.10_summits.bed INFO @ Fri, 15 Feb 2019 07:17:11: Done! pass1 - making usageList (4 chroms): 2 millis pass2 - checking and writing primary data (12 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:17:11: #4 Write output xls file... DRX123822.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:17:11: #4 Write peak in narrowPeak format file... DRX123822.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:17:11: #4 Write summits bed file... DRX123822.05_summits.bed INFO @ Fri, 15 Feb 2019 07:17:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (17 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:17:11: #4 Write output xls file... DRX123822.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:17:11: #4 Write peak in narrowPeak format file... DRX123822.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:17:11: #4 Write summits bed file... DRX123822.20_summits.bed INFO @ Fri, 15 Feb 2019 07:17:11: Done! pass1 - making usageList (3 chroms): 2 millis pass2 - checking and writing primary data (6 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。