Job ID = 11192574 sra ファイルのダウンロード中... Completed: 916313K bytes transferred in 11 seconds (670675K 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 28548890 spots for /home/okishinya/chipatlas/results/rn6/SRX2226586/SRR4374836.sra Written 28548890 spots for /home/okishinya/chipatlas/results/rn6/SRX2226586/SRR4374836.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:18:47 28548890 reads; of these: 28548890 (100.00%) were unpaired; of these: 4348578 (15.23%) aligned 0 times 18194529 (63.73%) aligned exactly 1 time 6005783 (21.04%) aligned >1 times 84.77% overall alignment rate Time searching: 00:18:49 Overall time: 00:18:49 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] 4069960 / 24200312 = 0.1682 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 09:26:26: # Command line: callpeak -t SRX2226586.bam -f BAM -g 2.15e9 -n SRX2226586.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2226586.20 # format = BAM # ChIP-seq file = ['SRX2226586.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 09:26:26: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:26:26: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:26:26: # Command line: callpeak -t SRX2226586.bam -f BAM -g 2.15e9 -n SRX2226586.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2226586.10 # format = BAM # ChIP-seq file = ['SRX2226586.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 09:26:26: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:26:26: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:26:26: # Command line: callpeak -t SRX2226586.bam -f BAM -g 2.15e9 -n SRX2226586.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2226586.05 # format = BAM # ChIP-seq file = ['SRX2226586.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 09:26:26: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:26:26: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:26:32: 1000000 INFO @ Sat, 15 Sep 2018 09:26:32: 1000000 INFO @ Sat, 15 Sep 2018 09:26:32: 1000000 INFO @ Sat, 15 Sep 2018 09:26:38: 2000000 INFO @ Sat, 15 Sep 2018 09:26:39: 2000000 INFO @ Sat, 15 Sep 2018 09:26:39: 2000000 INFO @ Sat, 15 Sep 2018 09:26:45: 3000000 INFO @ Sat, 15 Sep 2018 09:26:45: 3000000 INFO @ Sat, 15 Sep 2018 09:26:45: 3000000 INFO @ Sat, 15 Sep 2018 09:26:51: 4000000 INFO @ Sat, 15 Sep 2018 09:26:51: 4000000 INFO @ Sat, 15 Sep 2018 09:26:52: 4000000 INFO @ Sat, 15 Sep 2018 09:26:58: 5000000 INFO @ Sat, 15 Sep 2018 09:26:58: 5000000 INFO @ Sat, 15 Sep 2018 09:26:58: 5000000 INFO @ Sat, 15 Sep 2018 09:27:04: 6000000 INFO @ Sat, 15 Sep 2018 09:27:05: 6000000 INFO @ Sat, 15 Sep 2018 09:27:05: 6000000 INFO @ Sat, 15 Sep 2018 09:27:11: 7000000 INFO @ Sat, 15 Sep 2018 09:27:12: 7000000 INFO @ Sat, 15 Sep 2018 09:27:12: 7000000 INFO @ Sat, 15 Sep 2018 09:27:17: 8000000 INFO @ Sat, 15 Sep 2018 09:27:18: 8000000 INFO @ Sat, 15 Sep 2018 09:27:18: 8000000 INFO @ Sat, 15 Sep 2018 09:27:24: 9000000 INFO @ Sat, 15 Sep 2018 09:27:24: 9000000 INFO @ Sat, 15 Sep 2018 09:27:25: 9000000 INFO @ Sat, 15 Sep 2018 09:27:30: 10000000 INFO @ Sat, 15 Sep 2018 09:27:31: 10000000 INFO @ Sat, 15 Sep 2018 09:27:31: 10000000 INFO @ Sat, 15 Sep 2018 09:27:36: 11000000 INFO @ Sat, 15 Sep 2018 09:27:37: 11000000 INFO @ Sat, 15 Sep 2018 09:27:38: 11000000 INFO @ Sat, 15 Sep 2018 09:27:43: 12000000 INFO @ Sat, 15 Sep 2018 09:27:43: 12000000 INFO @ Sat, 15 Sep 2018 09:27:44: 12000000 INFO @ Sat, 15 Sep 2018 09:27:49: 13000000 INFO @ Sat, 15 Sep 2018 09:27:49: 13000000 INFO @ Sat, 15 Sep 2018 09:27:51: 13000000 INFO @ Sat, 15 Sep 2018 09:27:55: 14000000 INFO @ Sat, 15 Sep 2018 09:27:56: 14000000 INFO @ Sat, 15 Sep 2018 09:27:57: 14000000 INFO @ Sat, 15 Sep 2018 09:28:01: 15000000 INFO @ Sat, 15 Sep 2018 09:28:02: 15000000 INFO @ Sat, 15 Sep 2018 09:28:04: 15000000 INFO @ Sat, 15 Sep 2018 09:28:07: 16000000 INFO @ Sat, 15 Sep 2018 09:28:09: 16000000 INFO @ Sat, 15 Sep 2018 09:28:10: 16000000 INFO @ Sat, 15 Sep 2018 09:28:13: 17000000 INFO @ Sat, 15 Sep 2018 09:28:15: 17000000 INFO @ Sat, 15 Sep 2018 09:28:17: 17000000 INFO @ Sat, 15 Sep 2018 09:28:19: 18000000 INFO @ Sat, 15 Sep 2018 09:28:22: 18000000 INFO @ Sat, 15 Sep 2018 09:28:23: 18000000 INFO @ Sat, 15 Sep 2018 09:28:25: 19000000 INFO @ Sat, 15 Sep 2018 09:28:28: 19000000 INFO @ Sat, 15 Sep 2018 09:28:30: 19000000 INFO @ Sat, 15 Sep 2018 09:28:32: 20000000 INFO @ Sat, 15 Sep 2018 09:28:33: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:28:33: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:28:33: #1 total tags in treatment: 20130352 INFO @ Sat, 15 Sep 2018 09:28:33: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:28:33: #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 09:28:33: #1 tags after filtering in treatment: 20130233 INFO @ Sat, 15 Sep 2018 09:28:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:28:33: #1 finished! INFO @ Sat, 15 Sep 2018 09:28:33: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:28:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:28:35: 20000000 INFO @ Sat, 15 Sep 2018 09:28:36: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:28:36: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:28:36: #1 total tags in treatment: 20130352 INFO @ Sat, 15 Sep 2018 09:28:36: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:28:36: #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 09:28:36: #2 number of paired peaks: 17400 INFO @ Sat, 15 Sep 2018 09:28:36: start model_add_line... INFO @ Sat, 15 Sep 2018 09:28:36: start X-correlation... INFO @ Sat, 15 Sep 2018 09:28:36: end of X-cor INFO @ Sat, 15 Sep 2018 09:28:36: #2 finished! INFO @ Sat, 15 Sep 2018 09:28:36: #2 predicted fragment length is 129 bps INFO @ Sat, 15 Sep 2018 09:28:36: #2 alternative fragment length(s) may be 129 bps INFO @ Sat, 15 Sep 2018 09:28:36: #2.2 Generate R script for model : SRX2226586.20_model.r INFO @ Sat, 15 Sep 2018 09:28:36: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:28:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:28:36: #1 tags after filtering in treatment: 20130233 INFO @ Sat, 15 Sep 2018 09:28:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:28:36: #1 finished! INFO @ Sat, 15 Sep 2018 09:28:36: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:28:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:28:37: 20000000 INFO @ Sat, 15 Sep 2018 09:28:38: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:28:38: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:28:38: #1 total tags in treatment: 20130352 INFO @ Sat, 15 Sep 2018 09:28:38: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:28:38: #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 09:28:38: #1 tags after filtering in treatment: 20130233 INFO @ Sat, 15 Sep 2018 09:28:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:28:38: #1 finished! INFO @ Sat, 15 Sep 2018 09:28:38: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:28:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:28:39: #2 number of paired peaks: 17400 INFO @ Sat, 15 Sep 2018 09:28:39: start model_add_line... INFO @ Sat, 15 Sep 2018 09:28:39: start X-correlation... INFO @ Sat, 15 Sep 2018 09:28:39: end of X-cor INFO @ Sat, 15 Sep 2018 09:28:39: #2 finished! INFO @ Sat, 15 Sep 2018 09:28:39: #2 predicted fragment length is 129 bps INFO @ Sat, 15 Sep 2018 09:28:39: #2 alternative fragment length(s) may be 129 bps INFO @ Sat, 15 Sep 2018 09:28:39: #2.2 Generate R script for model : SRX2226586.05_model.r INFO @ Sat, 15 Sep 2018 09:28:39: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:28:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:28:41: #2 number of paired peaks: 17400 INFO @ Sat, 15 Sep 2018 09:28:41: start model_add_line... INFO @ Sat, 15 Sep 2018 09:28:41: start X-correlation... INFO @ Sat, 15 Sep 2018 09:28:41: end of X-cor INFO @ Sat, 15 Sep 2018 09:28:41: #2 finished! INFO @ Sat, 15 Sep 2018 09:28:41: #2 predicted fragment length is 129 bps INFO @ Sat, 15 Sep 2018 09:28:41: #2 alternative fragment length(s) may be 129 bps INFO @ Sat, 15 Sep 2018 09:28:41: #2.2 Generate R script for model : SRX2226586.10_model.r INFO @ Sat, 15 Sep 2018 09:28:41: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:28:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:29:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:29:29: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:29:32: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:29:53: #4 Write output xls file... SRX2226586.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:29:53: #4 Write peak in narrowPeak format file... SRX2226586.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:29:53: #4 Write summits bed file... SRX2226586.05_summits.bed INFO @ Sat, 15 Sep 2018 09:29:53: Done! pass1 - making usageList (74 chroms): 2 millis pass2 - checking and writing primary data (8126 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:30:02: #4 Write output xls file... SRX2226586.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:30:02: #4 Write peak in narrowPeak format file... SRX2226586.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:30:02: #4 Write summits bed file... SRX2226586.10_summits.bed INFO @ Sat, 15 Sep 2018 09:30:02: Done! INFO @ Sat, 15 Sep 2018 09:30:02: #4 Write output xls file... SRX2226586.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:30:02: #4 Write peak in narrowPeak format file... SRX2226586.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:30:02: #4 Write summits bed file... SRX2226586.20_summits.bed INFO @ Sat, 15 Sep 2018 09:30:02: Done! pass1 - making usageList (40 chroms): 10 millis pass1 - making usageList (56 chroms): 11 millis pass2 - checking and writing primary data (2298 records, 4 fields): 15 millis pass2 - checking and writing primary data (4357 records, 4 fields): 17 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。