Job ID = 11632744 sra ファイルのダウンロード中... Completed: 140107K bytes transferred in 4 seconds (259490K 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 1371681 spots for /home/okishinya/chipatlas/results/sacCer3/DRX123814/DRR131076.sra Written 1371681 spots for /home/okishinya/chipatlas/results/sacCer3/DRX123814/DRR131076.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: 00:01:25 1371681 reads; of these: 1371681 (100.00%) were paired; of these: 154156 (11.24%) aligned concordantly 0 times 1139257 (83.06%) aligned concordantly exactly 1 time 78268 (5.71%) aligned concordantly >1 times ---- 154156 pairs aligned concordantly 0 times; of these: 64386 (41.77%) aligned discordantly 1 time ---- 89770 pairs aligned 0 times concordantly or discordantly; of these: 179540 mates make up the pairs; of these: 152161 (84.75%) aligned 0 times 15868 (8.84%) aligned exactly 1 time 11511 (6.41%) aligned >1 times 94.45% overall alignment rate Time searching: 00:01:25 Overall time: 00:01:25 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] 1496 / 1277860 = 0.0012 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 07:03:39: # Command line: callpeak -t DRX123814.bam -f BAM -g 12100000 -n DRX123814.20 -q 1e-20 # ARGUMENTS LIST: # name = DRX123814.20 # format = BAM # ChIP-seq file = ['DRX123814.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 07:03:39: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:03:39: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:03:39: # Command line: callpeak -t DRX123814.bam -f BAM -g 12100000 -n DRX123814.10 -q 1e-10 # ARGUMENTS LIST: # name = DRX123814.10 # format = BAM # ChIP-seq file = ['DRX123814.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 07:03:39: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:03:39: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:03:39: # Command line: callpeak -t DRX123814.bam -f BAM -g 12100000 -n DRX123814.05 -q 1e-05 # ARGUMENTS LIST: # name = DRX123814.05 # format = BAM # ChIP-seq file = ['DRX123814.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 07:03:39: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:03:39: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:03:46: 1000000 INFO @ Fri, 15 Feb 2019 07:03:46: 1000000 INFO @ Fri, 15 Feb 2019 07:03:47: 1000000 INFO @ Fri, 15 Feb 2019 07:03:54: 2000000 INFO @ Fri, 15 Feb 2019 07:03:54: 2000000 INFO @ Fri, 15 Feb 2019 07:03:54: 2000000 INFO @ Fri, 15 Feb 2019 07:03:58: #1 tag size is determined as 74 bps INFO @ Fri, 15 Feb 2019 07:03:58: #1 tag size = 74 INFO @ Fri, 15 Feb 2019 07:03:58: #1 total tags in treatment: 1216073 INFO @ Fri, 15 Feb 2019 07:03:58: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:03:58: #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 07:03:58: #1 tags after filtering in treatment: 1157498 INFO @ Fri, 15 Feb 2019 07:03:58: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 15 Feb 2019 07:03:58: #1 finished! INFO @ Fri, 15 Feb 2019 07:03:58: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:03:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:03:58: #2 number of paired peaks: 159 WARNING @ Fri, 15 Feb 2019 07:03:58: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Fri, 15 Feb 2019 07:03:58: start model_add_line... INFO @ Fri, 15 Feb 2019 07:03:58: start X-correlation... INFO @ Fri, 15 Feb 2019 07:03:58: end of X-cor INFO @ Fri, 15 Feb 2019 07:03:58: #2 finished! INFO @ Fri, 15 Feb 2019 07:03:58: #2 predicted fragment length is 161 bps INFO @ Fri, 15 Feb 2019 07:03:58: #2 alternative fragment length(s) may be 1,45,72,100,129,161,192,214,236,254,257,290,320,384,434,486,509,554,589 bps INFO @ Fri, 15 Feb 2019 07:03:58: #2.2 Generate R script for model : DRX123814.20_model.r INFO @ Fri, 15 Feb 2019 07:03:58: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:03:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:03:58: #1 tag size is determined as 74 bps INFO @ Fri, 15 Feb 2019 07:03:58: #1 tag size = 74 INFO @ Fri, 15 Feb 2019 07:03:58: #1 total tags in treatment: 1216073 INFO @ Fri, 15 Feb 2019 07:03:58: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:03:58: #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 07:03:58: #1 tags after filtering in treatment: 1157498 INFO @ Fri, 15 Feb 2019 07:03:58: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 15 Feb 2019 07:03:58: #1 finished! INFO @ Fri, 15 Feb 2019 07:03:58: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:03:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:03:59: #2 number of paired peaks: 159 WARNING @ Fri, 15 Feb 2019 07:03:59: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Fri, 15 Feb 2019 07:03:59: start model_add_line... INFO @ Fri, 15 Feb 2019 07:03:59: start X-correlation... INFO @ Fri, 15 Feb 2019 07:03:59: end of X-cor INFO @ Fri, 15 Feb 2019 07:03:59: #2 finished! INFO @ Fri, 15 Feb 2019 07:03:59: #2 predicted fragment length is 161 bps INFO @ Fri, 15 Feb 2019 07:03:59: #2 alternative fragment length(s) may be 1,45,72,100,129,161,192,214,236,254,257,290,320,384,434,486,509,554,589 bps INFO @ Fri, 15 Feb 2019 07:03:59: #2.2 Generate R script for model : DRX123814.05_model.r INFO @ Fri, 15 Feb 2019 07:03:59: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:03:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:03:59: #1 tag size is determined as 74 bps INFO @ Fri, 15 Feb 2019 07:03:59: #1 tag size = 74 INFO @ Fri, 15 Feb 2019 07:03:59: #1 total tags in treatment: 1216073 INFO @ Fri, 15 Feb 2019 07:03:59: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:03:59: #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 07:03:59: #1 tags after filtering in treatment: 1157498 INFO @ Fri, 15 Feb 2019 07:03:59: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 15 Feb 2019 07:03:59: #1 finished! INFO @ Fri, 15 Feb 2019 07:03:59: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:03:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:03:59: #2 number of paired peaks: 159 WARNING @ Fri, 15 Feb 2019 07:03:59: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Fri, 15 Feb 2019 07:03:59: start model_add_line... INFO @ Fri, 15 Feb 2019 07:03:59: start X-correlation... INFO @ Fri, 15 Feb 2019 07:03:59: end of X-cor INFO @ Fri, 15 Feb 2019 07:03:59: #2 finished! INFO @ Fri, 15 Feb 2019 07:03:59: #2 predicted fragment length is 161 bps INFO @ Fri, 15 Feb 2019 07:03:59: #2 alternative fragment length(s) may be 1,45,72,100,129,161,192,214,236,254,257,290,320,384,434,486,509,554,589 bps INFO @ Fri, 15 Feb 2019 07:03:59: #2.2 Generate R script for model : DRX123814.10_model.r INFO @ Fri, 15 Feb 2019 07:03:59: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:03:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:04:01: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:04:01: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:04:02: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:04:02: #4 Write output xls file... DRX123814.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:04:02: #4 Write peak in narrowPeak format file... DRX123814.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:04:02: #4 Write summits bed file... DRX123814.20_summits.bed INFO @ Fri, 15 Feb 2019 07:04:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:04:03: #4 Write output xls file... DRX123814.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:04:03: #4 Write peak in narrowPeak format file... DRX123814.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:04:03: #4 Write summits bed file... DRX123814.05_summits.bed INFO @ Fri, 15 Feb 2019 07:04:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (13 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:04:03: #4 Write output xls file... DRX123814.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:04:03: #4 Write peak in narrowPeak format file... DRX123814.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:04:03: #4 Write summits bed file... DRX123814.10_summits.bed INFO @ Fri, 15 Feb 2019 07:04:03: Done! pass1 - making usageList (4 chroms): 2 millis pass2 - checking and writing primary data (6 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。