Job ID = 11632683 sra ファイルのダウンロード中... Completed: 1308179K bytes transferred in 15 seconds (701955K 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 51366873 spots for /home/okishinya/chipatlas/results/rn6/SRX3782443/SRR6826261.sra Written 51366873 spots for /home/okishinya/chipatlas/results/rn6/SRX3782443/SRR6826261.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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:22:06 51366873 reads; of these: 51366873 (100.00%) were unpaired; of these: 8716433 (16.97%) aligned 0 times 36729097 (71.50%) aligned exactly 1 time 5921343 (11.53%) aligned >1 times 83.03% overall alignment rate Time searching: 00:22:10 Overall time: 00:22:10 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] 34559315 / 42650440 = 0.8103 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 06:16:26: # Command line: callpeak -t SRX3782443.bam -f BAM -g 2.15e9 -n SRX3782443.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782443.05 # format = BAM # ChIP-seq file = ['SRX3782443.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 06:16:26: # Command line: callpeak -t SRX3782443.bam -f BAM -g 2.15e9 -n SRX3782443.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782443.20 # format = BAM # ChIP-seq file = ['SRX3782443.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 06:16:26: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:16:26: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:16:26: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:16:26: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:16:26: # Command line: callpeak -t SRX3782443.bam -f BAM -g 2.15e9 -n SRX3782443.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782443.10 # format = BAM # ChIP-seq file = ['SRX3782443.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 06:16:26: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:16:26: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:16:33: 1000000 INFO @ Fri, 15 Feb 2019 06:16:33: 1000000 INFO @ Fri, 15 Feb 2019 06:16:33: 1000000 INFO @ Fri, 15 Feb 2019 06:16:39: 2000000 INFO @ Fri, 15 Feb 2019 06:16:39: 2000000 INFO @ Fri, 15 Feb 2019 06:16:41: 2000000 INFO @ Fri, 15 Feb 2019 06:16:45: 3000000 INFO @ Fri, 15 Feb 2019 06:16:46: 3000000 INFO @ Fri, 15 Feb 2019 06:16:48: 3000000 INFO @ Fri, 15 Feb 2019 06:16:52: 4000000 INFO @ Fri, 15 Feb 2019 06:16:53: 4000000 INFO @ Fri, 15 Feb 2019 06:16:56: 4000000 INFO @ Fri, 15 Feb 2019 06:16:59: 5000000 INFO @ Fri, 15 Feb 2019 06:16:59: 5000000 INFO @ Fri, 15 Feb 2019 06:17:04: 5000000 INFO @ Fri, 15 Feb 2019 06:17:05: 6000000 INFO @ Fri, 15 Feb 2019 06:17:06: 6000000 INFO @ Fri, 15 Feb 2019 06:17:11: 6000000 INFO @ Fri, 15 Feb 2019 06:17:12: 7000000 INFO @ Fri, 15 Feb 2019 06:17:13: 7000000 INFO @ Fri, 15 Feb 2019 06:17:17: 7000000 INFO @ Fri, 15 Feb 2019 06:17:19: 8000000 INFO @ Fri, 15 Feb 2019 06:17:20: #1 tag size is determined as 43 bps INFO @ Fri, 15 Feb 2019 06:17:20: #1 tag size = 43 INFO @ Fri, 15 Feb 2019 06:17:20: #1 total tags in treatment: 8091125 INFO @ Fri, 15 Feb 2019 06:17:20: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:17:20: #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 06:17:20: 8000000 INFO @ Fri, 15 Feb 2019 06:17:20: #1 tags after filtering in treatment: 8090903 INFO @ Fri, 15 Feb 2019 06:17:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:17:20: #1 finished! INFO @ Fri, 15 Feb 2019 06:17:20: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:17:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:17:21: #1 tag size is determined as 43 bps INFO @ Fri, 15 Feb 2019 06:17:21: #1 tag size = 43 INFO @ Fri, 15 Feb 2019 06:17:21: #1 total tags in treatment: 8091125 INFO @ Fri, 15 Feb 2019 06:17:21: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:17:21: #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 06:17:21: #1 tags after filtering in treatment: 8090903 INFO @ Fri, 15 Feb 2019 06:17:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:17:21: #1 finished! INFO @ Fri, 15 Feb 2019 06:17:21: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:17:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:17:24: #2 number of paired peaks: 91506 INFO @ Fri, 15 Feb 2019 06:17:24: start model_add_line... INFO @ Fri, 15 Feb 2019 06:17:24: start X-correlation... INFO @ Fri, 15 Feb 2019 06:17:24: end of X-cor INFO @ Fri, 15 Feb 2019 06:17:24: #2 finished! INFO @ Fri, 15 Feb 2019 06:17:24: #2 predicted fragment length is 163 bps INFO @ Fri, 15 Feb 2019 06:17:24: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 15 Feb 2019 06:17:24: #2.2 Generate R script for model : SRX3782443.10_model.r INFO @ Fri, 15 Feb 2019 06:17:24: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:17:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:17:24: 8000000 INFO @ Fri, 15 Feb 2019 06:17:24: #2 number of paired peaks: 91506 INFO @ Fri, 15 Feb 2019 06:17:24: start model_add_line... INFO @ Fri, 15 Feb 2019 06:17:25: start X-correlation... INFO @ Fri, 15 Feb 2019 06:17:25: end of X-cor INFO @ Fri, 15 Feb 2019 06:17:25: #2 finished! INFO @ Fri, 15 Feb 2019 06:17:25: #2 predicted fragment length is 163 bps INFO @ Fri, 15 Feb 2019 06:17:25: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 15 Feb 2019 06:17:25: #2.2 Generate R script for model : SRX3782443.20_model.r INFO @ Fri, 15 Feb 2019 06:17:25: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:17:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:17:25: #1 tag size is determined as 43 bps INFO @ Fri, 15 Feb 2019 06:17:25: #1 tag size = 43 INFO @ Fri, 15 Feb 2019 06:17:25: #1 total tags in treatment: 8091125 INFO @ Fri, 15 Feb 2019 06:17:25: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:17:25: #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 06:17:25: #1 tags after filtering in treatment: 8090903 INFO @ Fri, 15 Feb 2019 06:17:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:17:25: #1 finished! INFO @ Fri, 15 Feb 2019 06:17:25: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:17:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:17:29: #2 number of paired peaks: 91506 INFO @ Fri, 15 Feb 2019 06:17:29: start model_add_line... INFO @ Fri, 15 Feb 2019 06:17:29: start X-correlation... INFO @ Fri, 15 Feb 2019 06:17:29: end of X-cor INFO @ Fri, 15 Feb 2019 06:17:29: #2 finished! INFO @ Fri, 15 Feb 2019 06:17:29: #2 predicted fragment length is 163 bps INFO @ Fri, 15 Feb 2019 06:17:29: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 15 Feb 2019 06:17:29: #2.2 Generate R script for model : SRX3782443.05_model.r INFO @ Fri, 15 Feb 2019 06:17:29: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:17:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:17:45: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:17:46: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:17:51: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:17:58: #4 Write output xls file... SRX3782443.20_peaks.xls INFO @ Fri, 15 Feb 2019 06:17:58: #4 Write peak in narrowPeak format file... SRX3782443.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:17:58: #4 Write summits bed file... SRX3782443.20_summits.bed INFO @ Fri, 15 Feb 2019 06:17:58: Done! pass1 - making usageList (32 chroms): 13 millis pass2 - checking and writing primary data (543 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:17:59: #4 Write output xls file... SRX3782443.10_peaks.xls INFO @ Fri, 15 Feb 2019 06:17:59: #4 Write peak in narrowPeak format file... SRX3782443.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:17:59: #4 Write summits bed file... SRX3782443.10_summits.bed INFO @ Fri, 15 Feb 2019 06:17:59: Done! pass1 - making usageList (61 chroms): 3 millis pass2 - checking and writing primary data (5411 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:18:02: #4 Write output xls file... SRX3782443.05_peaks.xls INFO @ Fri, 15 Feb 2019 06:18:03: #4 Write peak in narrowPeak format file... SRX3782443.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:18:03: #4 Write summits bed file... SRX3782443.05_summits.bed INFO @ Fri, 15 Feb 2019 06:18:03: Done! pass1 - making usageList (107 chroms): 5 millis pass2 - checking and writing primary data (17124 records, 4 fields): 25 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。