Job ID = 11192910 sra ファイルのダウンロード中... Completed: 842081K bytes transferred in 10 seconds (642332K 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 21250696 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242025/SRR6129637.sra Written 21250696 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242025/SRR6129637.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: 00:15:09 21250696 reads; of these: 21250696 (100.00%) were paired; of these: 17250997 (81.18%) aligned concordantly 0 times 2566393 (12.08%) aligned concordantly exactly 1 time 1433306 (6.74%) aligned concordantly >1 times ---- 17250997 pairs aligned concordantly 0 times; of these: 2180208 (12.64%) aligned discordantly 1 time ---- 15070789 pairs aligned 0 times concordantly or discordantly; of these: 30141578 mates make up the pairs; of these: 18961903 (62.91%) aligned 0 times 9419563 (31.25%) aligned exactly 1 time 1760112 (5.84%) aligned >1 times 55.39% overall alignment rate Time searching: 00:15:09 Overall time: 00:15:09 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_sort_core] merging from 12 files... [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] 1724105 / 5507313 = 0.3131 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, 15 Sep 2018 10:45:42: # Command line: callpeak -t SRX3242025.bam -f BAM -g 12100000 -n SRX3242025.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3242025.05 # format = BAM # ChIP-seq file = ['SRX3242025.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, 15 Sep 2018 10:45:42: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:45:42: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:45:42: # Command line: callpeak -t SRX3242025.bam -f BAM -g 12100000 -n SRX3242025.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3242025.20 # format = BAM # ChIP-seq file = ['SRX3242025.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, 15 Sep 2018 10:45:42: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:45:42: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:45:42: # Command line: callpeak -t SRX3242025.bam -f BAM -g 12100000 -n SRX3242025.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3242025.10 # format = BAM # ChIP-seq file = ['SRX3242025.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, 15 Sep 2018 10:45:42: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:45:42: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:45:47: 1000000 INFO @ Sat, 15 Sep 2018 10:45:47: 1000000 INFO @ Sat, 15 Sep 2018 10:45:47: 1000000 INFO @ Sat, 15 Sep 2018 10:45:52: 2000000 INFO @ Sat, 15 Sep 2018 10:45:53: 2000000 INFO @ Sat, 15 Sep 2018 10:45:53: 2000000 INFO @ Sat, 15 Sep 2018 10:45:58: 3000000 INFO @ Sat, 15 Sep 2018 10:45:58: 3000000 INFO @ Sat, 15 Sep 2018 10:45:58: 3000000 INFO @ Sat, 15 Sep 2018 10:46:03: 4000000 INFO @ Sat, 15 Sep 2018 10:46:03: 4000000 INFO @ Sat, 15 Sep 2018 10:46:04: 4000000 INFO @ Sat, 15 Sep 2018 10:46:08: 5000000 INFO @ Sat, 15 Sep 2018 10:46:09: 5000000 INFO @ Sat, 15 Sep 2018 10:46:09: 5000000 INFO @ Sat, 15 Sep 2018 10:46:13: 6000000 INFO @ Sat, 15 Sep 2018 10:46:14: 6000000 INFO @ Sat, 15 Sep 2018 10:46:15: 6000000 INFO @ Sat, 15 Sep 2018 10:46:17: 7000000 INFO @ Sat, 15 Sep 2018 10:46:19: 7000000 INFO @ Sat, 15 Sep 2018 10:46:20: 7000000 INFO @ Sat, 15 Sep 2018 10:46:22: 8000000 INFO @ Sat, 15 Sep 2018 10:46:24: 8000000 INFO @ Sat, 15 Sep 2018 10:46:25: 8000000 INFO @ Sat, 15 Sep 2018 10:46:27: 9000000 INFO @ Sat, 15 Sep 2018 10:46:30: 9000000 INFO @ Sat, 15 Sep 2018 10:46:31: 9000000 INFO @ Sat, 15 Sep 2018 10:46:32: 10000000 INFO @ Sat, 15 Sep 2018 10:46:35: 10000000 INFO @ Sat, 15 Sep 2018 10:46:37: 10000000 INFO @ Sat, 15 Sep 2018 10:46:38: 11000000 INFO @ Sat, 15 Sep 2018 10:46:41: 11000000 INFO @ Sat, 15 Sep 2018 10:46:43: 11000000 INFO @ Sat, 15 Sep 2018 10:46:43: 12000000 INFO @ Sat, 15 Sep 2018 10:46:46: 12000000 INFO @ Sat, 15 Sep 2018 10:46:48: 13000000 INFO @ Sat, 15 Sep 2018 10:46:48: 12000000 INFO @ Sat, 15 Sep 2018 10:46:52: 13000000 INFO @ Sat, 15 Sep 2018 10:46:53: 14000000 INFO @ Sat, 15 Sep 2018 10:46:54: 13000000 INFO @ Sat, 15 Sep 2018 10:46:58: 14000000 INFO @ Sat, 15 Sep 2018 10:46:58: 15000000 INFO @ Sat, 15 Sep 2018 10:47:00: 14000000 INFO @ Sat, 15 Sep 2018 10:47:03: 15000000 INFO @ Sat, 15 Sep 2018 10:47:04: 16000000 INFO @ Sat, 15 Sep 2018 10:47:06: 15000000 INFO @ Sat, 15 Sep 2018 10:47:09: 17000000 INFO @ Sat, 15 Sep 2018 10:47:09: 16000000 INFO @ Sat, 15 Sep 2018 10:47:11: 16000000 INFO @ Sat, 15 Sep 2018 10:47:14: 18000000 INFO @ Sat, 15 Sep 2018 10:47:14: 17000000 INFO @ Sat, 15 Sep 2018 10:47:17: 17000000 INFO @ Sat, 15 Sep 2018 10:47:19: 19000000 INFO @ Sat, 15 Sep 2018 10:47:20: 18000000 INFO @ Sat, 15 Sep 2018 10:47:23: 18000000 INFO @ Sat, 15 Sep 2018 10:47:24: 20000000 INFO @ Sat, 15 Sep 2018 10:47:25: #1 tag size is determined as 39 bps INFO @ Sat, 15 Sep 2018 10:47:25: #1 tag size = 39 INFO @ Sat, 15 Sep 2018 10:47:25: #1 total tags in treatment: 3286573 INFO @ Sat, 15 Sep 2018 10:47:25: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:47:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:47:25: #1 tags after filtering in treatment: 1974528 INFO @ Sat, 15 Sep 2018 10:47:25: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 15 Sep 2018 10:47:25: #1 finished! INFO @ Sat, 15 Sep 2018 10:47:25: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:47:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:47:25: #2 number of paired peaks: 640 WARNING @ Sat, 15 Sep 2018 10:47:25: Fewer paired peaks (640) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 640 pairs to build model! INFO @ Sat, 15 Sep 2018 10:47:25: start model_add_line... INFO @ Sat, 15 Sep 2018 10:47:25: start X-correlation... INFO @ Sat, 15 Sep 2018 10:47:25: end of X-cor INFO @ Sat, 15 Sep 2018 10:47:25: #2 finished! INFO @ Sat, 15 Sep 2018 10:47:25: #2 predicted fragment length is 188 bps INFO @ Sat, 15 Sep 2018 10:47:25: #2 alternative fragment length(s) may be 4,182,188 bps INFO @ Sat, 15 Sep 2018 10:47:25: #2.2 Generate R script for model : SRX3242025.10_model.r INFO @ Sat, 15 Sep 2018 10:47:25: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:47:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:47:25: 19000000 INFO @ Sat, 15 Sep 2018 10:47:28: 19000000 INFO @ Sat, 15 Sep 2018 10:47:31: 20000000 INFO @ Sat, 15 Sep 2018 10:47:31: #1 tag size is determined as 39 bps INFO @ Sat, 15 Sep 2018 10:47:31: #1 tag size = 39 INFO @ Sat, 15 Sep 2018 10:47:31: #1 total tags in treatment: 3286573 INFO @ Sat, 15 Sep 2018 10:47:31: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:47:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:47:32: #1 tags after filtering in treatment: 1974528 INFO @ Sat, 15 Sep 2018 10:47:32: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 15 Sep 2018 10:47:32: #1 finished! INFO @ Sat, 15 Sep 2018 10:47:32: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:47:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:47:32: #2 number of paired peaks: 640 WARNING @ Sat, 15 Sep 2018 10:47:32: Fewer paired peaks (640) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 640 pairs to build model! INFO @ Sat, 15 Sep 2018 10:47:32: start model_add_line... INFO @ Sat, 15 Sep 2018 10:47:32: start X-correlation... INFO @ Sat, 15 Sep 2018 10:47:32: end of X-cor INFO @ Sat, 15 Sep 2018 10:47:32: #2 finished! INFO @ Sat, 15 Sep 2018 10:47:32: #2 predicted fragment length is 188 bps INFO @ Sat, 15 Sep 2018 10:47:32: #2 alternative fragment length(s) may be 4,182,188 bps INFO @ Sat, 15 Sep 2018 10:47:32: #2.2 Generate R script for model : SRX3242025.05_model.r INFO @ Sat, 15 Sep 2018 10:47:32: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:47:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:47:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:47:34: 20000000 INFO @ Sat, 15 Sep 2018 10:47:34: #1 tag size is determined as 39 bps INFO @ Sat, 15 Sep 2018 10:47:34: #1 tag size = 39 INFO @ Sat, 15 Sep 2018 10:47:34: #1 total tags in treatment: 3286573 INFO @ Sat, 15 Sep 2018 10:47:34: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:47:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:47:34: #1 tags after filtering in treatment: 1974528 INFO @ Sat, 15 Sep 2018 10:47:34: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 15 Sep 2018 10:47:34: #1 finished! INFO @ Sat, 15 Sep 2018 10:47:34: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:47:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:47:35: #2 number of paired peaks: 640 WARNING @ Sat, 15 Sep 2018 10:47:35: Fewer paired peaks (640) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 640 pairs to build model! INFO @ Sat, 15 Sep 2018 10:47:35: start model_add_line... INFO @ Sat, 15 Sep 2018 10:47:35: start X-correlation... INFO @ Sat, 15 Sep 2018 10:47:35: end of X-cor INFO @ Sat, 15 Sep 2018 10:47:35: #2 finished! INFO @ Sat, 15 Sep 2018 10:47:35: #2 predicted fragment length is 188 bps INFO @ Sat, 15 Sep 2018 10:47:35: #2 alternative fragment length(s) may be 4,182,188 bps INFO @ Sat, 15 Sep 2018 10:47:35: #2.2 Generate R script for model : SRX3242025.20_model.r INFO @ Sat, 15 Sep 2018 10:47:35: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:47:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:47:36: #4 Write output xls file... SRX3242025.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:47:36: #4 Write peak in narrowPeak format file... SRX3242025.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:47:36: #4 Write summits bed file... SRX3242025.10_summits.bed INFO @ Sat, 15 Sep 2018 10:47:36: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (369 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:47:41: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:47:43: #4 Write output xls file... SRX3242025.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:47:43: #4 Write peak in narrowPeak format file... SRX3242025.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:47:43: #4 Write summits bed file... SRX3242025.05_summits.bed INFO @ Sat, 15 Sep 2018 10:47:43: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (424 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:47:44: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:47:46: #4 Write output xls file... SRX3242025.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:47:46: #4 Write peak in narrowPeak format file... SRX3242025.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:47:46: #4 Write summits bed file... SRX3242025.20_summits.bed INFO @ Sat, 15 Sep 2018 10:47:46: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。