Job ID = 11192561 sra ファイルのダウンロード中... Completed: 997660K bytes transferred in 10 seconds (770708K 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 31498582 spots for /home/okishinya/chipatlas/results/rn6/SRX2226575/SRR4374825.sra Written 31498582 spots for /home/okishinya/chipatlas/results/rn6/SRX2226575/SRR4374825.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: 00:18:39 31498582 reads; of these: 31498582 (100.00%) were unpaired; of these: 6201030 (19.69%) aligned 0 times 19272470 (61.19%) aligned exactly 1 time 6025082 (19.13%) aligned >1 times 80.31% overall alignment rate Time searching: 00:18:44 Overall time: 00:18:44 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 12 files... [bam_rmdupse_core] 13650270 / 25297552 = 0.5396 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 09:15:45: # Command line: callpeak -t SRX2226575.bam -f BAM -g 2.15e9 -n SRX2226575.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2226575.05 # format = BAM # ChIP-seq file = ['SRX2226575.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 @ Sat, 15 Sep 2018 09:15:45: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:15:45: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:15:45: # Command line: callpeak -t SRX2226575.bam -f BAM -g 2.15e9 -n SRX2226575.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2226575.20 # format = BAM # ChIP-seq file = ['SRX2226575.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 @ Sat, 15 Sep 2018 09:15:45: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:15:45: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:15:45: # Command line: callpeak -t SRX2226575.bam -f BAM -g 2.15e9 -n SRX2226575.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2226575.10 # format = BAM # ChIP-seq file = ['SRX2226575.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 @ Sat, 15 Sep 2018 09:15:45: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:15:45: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:15:52: 1000000 INFO @ Sat, 15 Sep 2018 09:15:53: 1000000 INFO @ Sat, 15 Sep 2018 09:15:53: 1000000 INFO @ Sat, 15 Sep 2018 09:15:59: 2000000 INFO @ Sat, 15 Sep 2018 09:16:01: 2000000 INFO @ Sat, 15 Sep 2018 09:16:01: 2000000 INFO @ Sat, 15 Sep 2018 09:16:07: 3000000 INFO @ Sat, 15 Sep 2018 09:16:09: 3000000 INFO @ Sat, 15 Sep 2018 09:16:09: 3000000 INFO @ Sat, 15 Sep 2018 09:16:15: 4000000 INFO @ Sat, 15 Sep 2018 09:16:17: 4000000 INFO @ Sat, 15 Sep 2018 09:16:17: 4000000 INFO @ Sat, 15 Sep 2018 09:16:22: 5000000 INFO @ Sat, 15 Sep 2018 09:16:25: 5000000 INFO @ Sat, 15 Sep 2018 09:16:25: 5000000 INFO @ Sat, 15 Sep 2018 09:16:29: 6000000 INFO @ Sat, 15 Sep 2018 09:16:33: 6000000 INFO @ Sat, 15 Sep 2018 09:16:33: 6000000 INFO @ Sat, 15 Sep 2018 09:16:37: 7000000 INFO @ Sat, 15 Sep 2018 09:16:41: 7000000 INFO @ Sat, 15 Sep 2018 09:16:41: 7000000 INFO @ Sat, 15 Sep 2018 09:16:44: 8000000 INFO @ Sat, 15 Sep 2018 09:16:48: 8000000 INFO @ Sat, 15 Sep 2018 09:16:48: 8000000 INFO @ Sat, 15 Sep 2018 09:16:52: 9000000 INFO @ Sat, 15 Sep 2018 09:16:57: 9000000 INFO @ Sat, 15 Sep 2018 09:16:57: 9000000 INFO @ Sat, 15 Sep 2018 09:17:01: 10000000 INFO @ Sat, 15 Sep 2018 09:17:05: 10000000 INFO @ Sat, 15 Sep 2018 09:17:05: 10000000 INFO @ Sat, 15 Sep 2018 09:17:08: 11000000 INFO @ Sat, 15 Sep 2018 09:17:13: 11000000 INFO @ Sat, 15 Sep 2018 09:17:13: 11000000 INFO @ Sat, 15 Sep 2018 09:17:14: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:17:14: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:17:14: #1 total tags in treatment: 11647282 INFO @ Sat, 15 Sep 2018 09:17:14: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:17:14: #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 09:17:14: #1 tags after filtering in treatment: 11647128 INFO @ Sat, 15 Sep 2018 09:17:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:17:14: #1 finished! INFO @ Sat, 15 Sep 2018 09:17:14: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:17:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:17:16: #2 number of paired peaks: 29307 INFO @ Sat, 15 Sep 2018 09:17:16: start model_add_line... INFO @ Sat, 15 Sep 2018 09:17:17: start X-correlation... INFO @ Sat, 15 Sep 2018 09:17:17: end of X-cor INFO @ Sat, 15 Sep 2018 09:17:17: #2 finished! INFO @ Sat, 15 Sep 2018 09:17:17: #2 predicted fragment length is 224 bps INFO @ Sat, 15 Sep 2018 09:17:17: #2 alternative fragment length(s) may be 224 bps INFO @ Sat, 15 Sep 2018 09:17:17: #2.2 Generate R script for model : SRX2226575.20_model.r INFO @ Sat, 15 Sep 2018 09:17:17: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:17:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:17:18: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:17:18: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:17:18: #1 total tags in treatment: 11647282 INFO @ Sat, 15 Sep 2018 09:17:18: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:17:18: #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 09:17:18: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:17:18: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:17:18: #1 total tags in treatment: 11647282 INFO @ Sat, 15 Sep 2018 09:17:18: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:17:18: #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 09:17:19: #1 tags after filtering in treatment: 11647128 INFO @ Sat, 15 Sep 2018 09:17:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:17:19: #1 finished! INFO @ Sat, 15 Sep 2018 09:17:19: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:17:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:17:19: #1 tags after filtering in treatment: 11647128 INFO @ Sat, 15 Sep 2018 09:17:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:17:19: #1 finished! INFO @ Sat, 15 Sep 2018 09:17:19: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:17:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:17:21: #2 number of paired peaks: 29307 INFO @ Sat, 15 Sep 2018 09:17:21: start model_add_line... INFO @ Sat, 15 Sep 2018 09:17:21: start X-correlation... INFO @ Sat, 15 Sep 2018 09:17:21: end of X-cor INFO @ Sat, 15 Sep 2018 09:17:21: #2 finished! INFO @ Sat, 15 Sep 2018 09:17:21: #2 predicted fragment length is 224 bps INFO @ Sat, 15 Sep 2018 09:17:21: #2 alternative fragment length(s) may be 224 bps INFO @ Sat, 15 Sep 2018 09:17:21: #2.2 Generate R script for model : SRX2226575.05_model.r INFO @ Sat, 15 Sep 2018 09:17:21: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:17:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:17:21: #2 number of paired peaks: 29307 INFO @ Sat, 15 Sep 2018 09:17:21: start model_add_line... INFO @ Sat, 15 Sep 2018 09:17:21: start X-correlation... INFO @ Sat, 15 Sep 2018 09:17:21: end of X-cor INFO @ Sat, 15 Sep 2018 09:17:21: #2 finished! INFO @ Sat, 15 Sep 2018 09:17:21: #2 predicted fragment length is 224 bps INFO @ Sat, 15 Sep 2018 09:17:21: #2 alternative fragment length(s) may be 224 bps INFO @ Sat, 15 Sep 2018 09:17:21: #2.2 Generate R script for model : SRX2226575.10_model.r INFO @ Sat, 15 Sep 2018 09:17:21: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:17:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:17:45: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:17:51: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:17:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:18:04: #4 Write output xls file... SRX2226575.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:18:04: #4 Write peak in narrowPeak format file... SRX2226575.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:18:04: #4 Write summits bed file... SRX2226575.20_summits.bed INFO @ Sat, 15 Sep 2018 09:18:04: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (2056 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:18:08: #4 Write output xls file... SRX2226575.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:18:08: #4 Write peak in narrowPeak format file... SRX2226575.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:18:08: #4 Write summits bed file... SRX2226575.05_summits.bed INFO @ Sat, 15 Sep 2018 09:18:08: Done! pass1 - making usageList (80 chroms): 2 millis pass2 - checking and writing primary data (7757 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:18:12: #4 Write output xls file... SRX2226575.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:18:12: #4 Write peak in narrowPeak format file... SRX2226575.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:18:12: #4 Write summits bed file... SRX2226575.10_summits.bed INFO @ Sat, 15 Sep 2018 09:18:12: Done! pass1 - making usageList (61 chroms): 2 millis pass2 - checking and writing primary data (4655 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。