Job ID = 11632740 sra ファイルのダウンロード中... Completed: 189412K bytes transferred in 5 seconds (286281K 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 1864950 spots for /home/okishinya/chipatlas/results/sacCer3/DRX123810/DRR131072.sra Written 1864950 spots for /home/okishinya/chipatlas/results/sacCer3/DRX123810/DRR131072.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: 00:01:58 1864950 reads; of these: 1864950 (100.00%) were paired; of these: 196230 (10.52%) aligned concordantly 0 times 1538156 (82.48%) aligned concordantly exactly 1 time 130564 (7.00%) aligned concordantly >1 times ---- 196230 pairs aligned concordantly 0 times; of these: 95426 (48.63%) aligned discordantly 1 time ---- 100804 pairs aligned 0 times concordantly or discordantly; of these: 201608 mates make up the pairs; of these: 161730 (80.22%) aligned 0 times 20731 (10.28%) aligned exactly 1 time 19147 (9.50%) aligned >1 times 95.66% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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] 2420 / 1759983 = 0.0014 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 07:00:38: # Command line: callpeak -t DRX123810.bam -f BAM -g 12100000 -n DRX123810.10 -q 1e-10 # ARGUMENTS LIST: # name = DRX123810.10 # format = BAM # ChIP-seq file = ['DRX123810.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 07:00:38: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:00:38: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:00:39: # Command line: callpeak -t DRX123810.bam -f BAM -g 12100000 -n DRX123810.20 -q 1e-20 # ARGUMENTS LIST: # name = DRX123810.20 # format = BAM # ChIP-seq file = ['DRX123810.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 07:00:39: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:00:39: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:00:39: # Command line: callpeak -t DRX123810.bam -f BAM -g 12100000 -n DRX123810.05 -q 1e-05 # ARGUMENTS LIST: # name = DRX123810.05 # format = BAM # ChIP-seq file = ['DRX123810.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 07:00:39: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:00:39: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:00:45: 1000000 INFO @ Fri, 15 Feb 2019 07:00:45: 1000000 INFO @ Fri, 15 Feb 2019 07:00:46: 1000000 INFO @ Fri, 15 Feb 2019 07:00:52: 2000000 INFO @ Fri, 15 Feb 2019 07:00:52: 2000000 INFO @ Fri, 15 Feb 2019 07:00:53: 2000000 INFO @ Fri, 15 Feb 2019 07:00:59: 3000000 INFO @ Fri, 15 Feb 2019 07:01:00: 3000000 INFO @ Fri, 15 Feb 2019 07:01:00: 3000000 INFO @ Fri, 15 Feb 2019 07:01:03: #1 tag size is determined as 75 bps INFO @ Fri, 15 Feb 2019 07:01:03: #1 tag size = 75 INFO @ Fri, 15 Feb 2019 07:01:03: #1 total tags in treatment: 1666380 INFO @ Fri, 15 Feb 2019 07:01:03: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:01:03: #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 07:01:03: #1 tags after filtering in treatment: 1549743 INFO @ Fri, 15 Feb 2019 07:01:03: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 15 Feb 2019 07:01:03: #1 finished! INFO @ Fri, 15 Feb 2019 07:01:03: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:01:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:01:03: #2 number of paired peaks: 185 WARNING @ Fri, 15 Feb 2019 07:01:03: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Fri, 15 Feb 2019 07:01:03: start model_add_line... INFO @ Fri, 15 Feb 2019 07:01:03: start X-correlation... INFO @ Fri, 15 Feb 2019 07:01:03: end of X-cor INFO @ Fri, 15 Feb 2019 07:01:03: #2 finished! INFO @ Fri, 15 Feb 2019 07:01:03: #2 predicted fragment length is 184 bps INFO @ Fri, 15 Feb 2019 07:01:03: #2 alternative fragment length(s) may be 1,19,52,88,156,184,202,207,237,251,294,321,347,355,412,487,518,550,579 bps INFO @ Fri, 15 Feb 2019 07:01:03: #2.2 Generate R script for model : DRX123810.10_model.r INFO @ Fri, 15 Feb 2019 07:01:03: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:01:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:01:04: #1 tag size is determined as 75 bps INFO @ Fri, 15 Feb 2019 07:01:04: #1 tag size = 75 INFO @ Fri, 15 Feb 2019 07:01:04: #1 total tags in treatment: 1666380 INFO @ Fri, 15 Feb 2019 07:01:04: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:01:04: #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 07:01:04: #1 tags after filtering in treatment: 1549743 INFO @ Fri, 15 Feb 2019 07:01:04: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 15 Feb 2019 07:01:04: #1 finished! INFO @ Fri, 15 Feb 2019 07:01:04: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:01:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:01:04: #2 number of paired peaks: 185 WARNING @ Fri, 15 Feb 2019 07:01:04: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Fri, 15 Feb 2019 07:01:04: start model_add_line... INFO @ Fri, 15 Feb 2019 07:01:04: start X-correlation... INFO @ Fri, 15 Feb 2019 07:01:04: end of X-cor INFO @ Fri, 15 Feb 2019 07:01:04: #2 finished! INFO @ Fri, 15 Feb 2019 07:01:04: #2 predicted fragment length is 184 bps INFO @ Fri, 15 Feb 2019 07:01:04: #2 alternative fragment length(s) may be 1,19,52,88,156,184,202,207,237,251,294,321,347,355,412,487,518,550,579 bps INFO @ Fri, 15 Feb 2019 07:01:04: #2.2 Generate R script for model : DRX123810.05_model.r INFO @ Fri, 15 Feb 2019 07:01:04: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:01:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:01:04: #1 tag size is determined as 75 bps INFO @ Fri, 15 Feb 2019 07:01:04: #1 tag size = 75 INFO @ Fri, 15 Feb 2019 07:01:04: #1 total tags in treatment: 1666380 INFO @ Fri, 15 Feb 2019 07:01:04: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:01:04: #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 07:01:04: #1 tags after filtering in treatment: 1549743 INFO @ Fri, 15 Feb 2019 07:01:04: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 15 Feb 2019 07:01:04: #1 finished! INFO @ Fri, 15 Feb 2019 07:01:04: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:01:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:01:04: #2 number of paired peaks: 185 WARNING @ Fri, 15 Feb 2019 07:01:04: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Fri, 15 Feb 2019 07:01:04: start model_add_line... INFO @ Fri, 15 Feb 2019 07:01:04: start X-correlation... INFO @ Fri, 15 Feb 2019 07:01:04: end of X-cor INFO @ Fri, 15 Feb 2019 07:01:04: #2 finished! INFO @ Fri, 15 Feb 2019 07:01:04: #2 predicted fragment length is 184 bps INFO @ Fri, 15 Feb 2019 07:01:04: #2 alternative fragment length(s) may be 1,19,52,88,156,184,202,207,237,251,294,321,347,355,412,487,518,550,579 bps INFO @ Fri, 15 Feb 2019 07:01:04: #2.2 Generate R script for model : DRX123810.20_model.r INFO @ Fri, 15 Feb 2019 07:01:04: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:01:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:01:07: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:01:08: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:01:08: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:01:08: #4 Write output xls file... DRX123810.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:01:08: #4 Write peak in narrowPeak format file... DRX123810.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:01:08: #4 Write summits bed file... DRX123810.10_summits.bed INFO @ Fri, 15 Feb 2019 07:01:08: Done! pass1 - making usageList (4 chroms): 4 millis pass2 - checking and writing primary data (13 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:01:09: #4 Write output xls file... DRX123810.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:01:09: #4 Write peak in narrowPeak format file... DRX123810.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:01:09: #4 Write summits bed file... DRX123810.05_summits.bed INFO @ Fri, 15 Feb 2019 07:01:09: Done! pass1 - making usageList (5 chroms): 3 millis pass2 - checking and writing primary data (15 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:01:10: #4 Write output xls file... DRX123810.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:01:10: #4 Write peak in narrowPeak format file... DRX123810.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:01:10: #4 Write summits bed file... DRX123810.20_summits.bed INFO @ Fri, 15 Feb 2019 07:01:10: Done! pass1 - making usageList (1 chroms): 4 millis pass2 - checking and writing primary data (2 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。