Job ID = 11632706 sra ファイルのダウンロード中... Completed: 1768335K bytes transferred in 21 seconds (687974K 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: SINGLE fastq に変換中... Read 67846359 spots for /home/okishinya/chipatlas/results/rn6/SRX3782465/SRR6826283.sra Written 67846359 spots for /home/okishinya/chipatlas/results/rn6/SRX3782465/SRR6826283.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:29:04 67846359 reads; of these: 67846359 (100.00%) were unpaired; of these: 5437034 (8.01%) aligned 0 times 48608358 (71.64%) aligned exactly 1 time 13800967 (20.34%) aligned >1 times 91.99% overall alignment rate Time searching: 00:29:06 Overall time: 00:29:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 48728233 / 62409325 = 0.7808 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 07:11:42: # Command line: callpeak -t SRX3782465.bam -f BAM -g 2.15e9 -n SRX3782465.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782465.05 # format = BAM # ChIP-seq file = ['SRX3782465.bam'] # control file = None # effective genome size = 2.15e+09 # 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 07:11:42: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:11:42: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:11:42: # Command line: callpeak -t SRX3782465.bam -f BAM -g 2.15e9 -n SRX3782465.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782465.20 # format = BAM # ChIP-seq file = ['SRX3782465.bam'] # control file = None # effective genome size = 2.15e+09 # 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 07:11:42: # Command line: callpeak -t SRX3782465.bam -f BAM -g 2.15e9 -n SRX3782465.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782465.10 # format = BAM # ChIP-seq file = ['SRX3782465.bam'] # control file = None # effective genome size = 2.15e+09 # 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 07:11:42: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:11:42: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:11:42: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:11:42: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:11:49: 1000000 INFO @ Fri, 15 Feb 2019 07:11:49: 1000000 INFO @ Fri, 15 Feb 2019 07:11:49: 1000000 INFO @ Fri, 15 Feb 2019 07:11:56: 2000000 INFO @ Fri, 15 Feb 2019 07:11:56: 2000000 INFO @ Fri, 15 Feb 2019 07:11:56: 2000000 INFO @ Fri, 15 Feb 2019 07:12:03: 3000000 INFO @ Fri, 15 Feb 2019 07:12:04: 3000000 INFO @ Fri, 15 Feb 2019 07:12:04: 3000000 INFO @ Fri, 15 Feb 2019 07:12:10: 4000000 INFO @ Fri, 15 Feb 2019 07:12:11: 4000000 INFO @ Fri, 15 Feb 2019 07:12:11: 4000000 INFO @ Fri, 15 Feb 2019 07:12:18: 5000000 INFO @ Fri, 15 Feb 2019 07:12:18: 5000000 INFO @ Fri, 15 Feb 2019 07:12:18: 5000000 INFO @ Fri, 15 Feb 2019 07:12:25: 6000000 INFO @ Fri, 15 Feb 2019 07:12:25: 6000000 INFO @ Fri, 15 Feb 2019 07:12:25: 6000000 INFO @ Fri, 15 Feb 2019 07:12:32: 7000000 INFO @ Fri, 15 Feb 2019 07:12:33: 7000000 INFO @ Fri, 15 Feb 2019 07:12:33: 7000000 INFO @ Fri, 15 Feb 2019 07:12:39: 8000000 INFO @ Fri, 15 Feb 2019 07:12:40: 8000000 INFO @ Fri, 15 Feb 2019 07:12:40: 8000000 INFO @ Fri, 15 Feb 2019 07:12:46: 9000000 INFO @ Fri, 15 Feb 2019 07:12:47: 9000000 INFO @ Fri, 15 Feb 2019 07:12:47: 9000000 INFO @ Fri, 15 Feb 2019 07:12:54: 10000000 INFO @ Fri, 15 Feb 2019 07:12:55: 10000000 INFO @ Fri, 15 Feb 2019 07:12:55: 10000000 INFO @ Fri, 15 Feb 2019 07:13:01: 11000000 INFO @ Fri, 15 Feb 2019 07:13:02: 11000000 INFO @ Fri, 15 Feb 2019 07:13:02: 11000000 INFO @ Fri, 15 Feb 2019 07:13:08: 12000000 INFO @ Fri, 15 Feb 2019 07:13:09: 12000000 INFO @ Fri, 15 Feb 2019 07:13:10: 12000000 INFO @ Fri, 15 Feb 2019 07:13:15: 13000000 INFO @ Fri, 15 Feb 2019 07:13:17: 13000000 INFO @ Fri, 15 Feb 2019 07:13:17: 13000000 INFO @ Fri, 15 Feb 2019 07:13:20: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:13:20: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:13:20: #1 total tags in treatment: 13681092 INFO @ Fri, 15 Feb 2019 07:13:20: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:13:20: #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 07:13:21: #1 tags after filtering in treatment: 13680939 INFO @ Fri, 15 Feb 2019 07:13:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:13:21: #1 finished! INFO @ Fri, 15 Feb 2019 07:13:21: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:13:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:13:22: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:13:22: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:13:22: #1 total tags in treatment: 13681092 INFO @ Fri, 15 Feb 2019 07:13:22: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:13:22: #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 07:13:22: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:13:22: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:13:22: #1 total tags in treatment: 13681092 INFO @ Fri, 15 Feb 2019 07:13:22: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:13:22: #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 07:13:23: #1 tags after filtering in treatment: 13680939 INFO @ Fri, 15 Feb 2019 07:13:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:13:23: #1 finished! INFO @ Fri, 15 Feb 2019 07:13:23: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:13:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:13:23: #1 tags after filtering in treatment: 13680939 INFO @ Fri, 15 Feb 2019 07:13:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:13:23: #1 finished! INFO @ Fri, 15 Feb 2019 07:13:23: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:13:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:13:23: #2 number of paired peaks: 29657 INFO @ Fri, 15 Feb 2019 07:13:23: start model_add_line... INFO @ Fri, 15 Feb 2019 07:13:24: start X-correlation... INFO @ Fri, 15 Feb 2019 07:13:24: end of X-cor INFO @ Fri, 15 Feb 2019 07:13:24: #2 finished! INFO @ Fri, 15 Feb 2019 07:13:24: #2 predicted fragment length is 242 bps INFO @ Fri, 15 Feb 2019 07:13:24: #2 alternative fragment length(s) may be 44,242 bps INFO @ Fri, 15 Feb 2019 07:13:24: #2.2 Generate R script for model : SRX3782465.10_model.r INFO @ Fri, 15 Feb 2019 07:13:24: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:13:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:13:25: #2 number of paired peaks: 29657 INFO @ Fri, 15 Feb 2019 07:13:25: start model_add_line... INFO @ Fri, 15 Feb 2019 07:13:25: start X-correlation... INFO @ Fri, 15 Feb 2019 07:13:25: end of X-cor INFO @ Fri, 15 Feb 2019 07:13:25: #2 finished! INFO @ Fri, 15 Feb 2019 07:13:25: #2 predicted fragment length is 242 bps INFO @ Fri, 15 Feb 2019 07:13:25: #2 alternative fragment length(s) may be 44,242 bps INFO @ Fri, 15 Feb 2019 07:13:25: #2.2 Generate R script for model : SRX3782465.05_model.r INFO @ Fri, 15 Feb 2019 07:13:25: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:13:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:13:26: #2 number of paired peaks: 29657 INFO @ Fri, 15 Feb 2019 07:13:26: start model_add_line... INFO @ Fri, 15 Feb 2019 07:13:26: start X-correlation... INFO @ Fri, 15 Feb 2019 07:13:26: end of X-cor INFO @ Fri, 15 Feb 2019 07:13:26: #2 finished! INFO @ Fri, 15 Feb 2019 07:13:26: #2 predicted fragment length is 242 bps INFO @ Fri, 15 Feb 2019 07:13:26: #2 alternative fragment length(s) may be 44,242 bps INFO @ Fri, 15 Feb 2019 07:13:26: #2.2 Generate R script for model : SRX3782465.20_model.r INFO @ Fri, 15 Feb 2019 07:13:26: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:13:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:14:02: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:14:02: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:14:03: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:14:21: #4 Write output xls file... SRX3782465.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:14:21: #4 Write peak in narrowPeak format file... SRX3782465.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:14:21: #4 Write summits bed file... SRX3782465.20_summits.bed INFO @ Fri, 15 Feb 2019 07:14:21: Done! pass1 - making usageList (34 chroms): 3 millis pass2 - checking and writing primary data (360 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:14:23: #4 Write output xls file... SRX3782465.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:14:23: #4 Write peak in narrowPeak format file... SRX3782465.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:14:23: #4 Write summits bed file... SRX3782465.10_summits.bed INFO @ Fri, 15 Feb 2019 07:14:23: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (869 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:14:23: #4 Write output xls file... SRX3782465.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:14:23: #4 Write peak in narrowPeak format file... SRX3782465.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:14:23: #4 Write summits bed file... SRX3782465.05_summits.bed INFO @ Fri, 15 Feb 2019 07:14:23: Done! pass1 - making usageList (41 chroms): 3 millis pass2 - checking and writing primary data (1893 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。