Job ID = 11171219 sra ファイルのダウンロード中... Completed: 269524K bytes transferred in 11 seconds (189254K 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 13456519 spots for /home/okishinya/chipatlas/results/dm3/SRX2618528/SRR5319082.sra Written 13456519 spots for /home/okishinya/chipatlas/results/dm3/SRX2618528/SRR5319082.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: 00:03:47 13456519 reads; of these: 13456519 (100.00%) were unpaired; of these: 1060975 (7.88%) aligned 0 times 10757706 (79.94%) aligned exactly 1 time 1637838 (12.17%) aligned >1 times 92.12% overall alignment rate Time searching: 00:03:47 Overall time: 00:03:47 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1737856 / 12395544 = 0.1402 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, 08 Sep 2018 13:09:16: # Command line: callpeak -t SRX2618528.bam -f BAM -g dm -n SRX2618528.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2618528.20 # format = BAM # ChIP-seq file = ['SRX2618528.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 08 Sep 2018 13:09:16: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:09:16: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:09:16: # Command line: callpeak -t SRX2618528.bam -f BAM -g dm -n SRX2618528.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2618528.05 # format = BAM # ChIP-seq file = ['SRX2618528.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 08 Sep 2018 13:09:16: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:09:16: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:09:16: # Command line: callpeak -t SRX2618528.bam -f BAM -g dm -n SRX2618528.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2618528.10 # format = BAM # ChIP-seq file = ['SRX2618528.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 08 Sep 2018 13:09:16: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:09:16: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:09:22: 1000000 INFO @ Sat, 08 Sep 2018 13:09:22: 1000000 INFO @ Sat, 08 Sep 2018 13:09:22: 1000000 INFO @ Sat, 08 Sep 2018 13:09:28: 2000000 INFO @ Sat, 08 Sep 2018 13:09:29: 2000000 INFO @ Sat, 08 Sep 2018 13:09:29: 2000000 INFO @ Sat, 08 Sep 2018 13:09:35: 3000000 INFO @ Sat, 08 Sep 2018 13:09:35: 3000000 INFO @ Sat, 08 Sep 2018 13:09:35: 3000000 INFO @ Sat, 08 Sep 2018 13:09:41: 4000000 INFO @ Sat, 08 Sep 2018 13:09:41: 4000000 INFO @ Sat, 08 Sep 2018 13:09:42: 4000000 INFO @ Sat, 08 Sep 2018 13:09:47: 5000000 INFO @ Sat, 08 Sep 2018 13:09:48: 5000000 INFO @ Sat, 08 Sep 2018 13:09:48: 5000000 INFO @ Sat, 08 Sep 2018 13:09:54: 6000000 INFO @ Sat, 08 Sep 2018 13:09:54: 6000000 INFO @ Sat, 08 Sep 2018 13:09:54: 6000000 INFO @ Sat, 08 Sep 2018 13:10:00: 7000000 INFO @ Sat, 08 Sep 2018 13:10:01: 7000000 INFO @ Sat, 08 Sep 2018 13:10:01: 7000000 INFO @ Sat, 08 Sep 2018 13:10:07: 8000000 INFO @ Sat, 08 Sep 2018 13:10:07: 8000000 INFO @ Sat, 08 Sep 2018 13:10:08: 8000000 INFO @ Sat, 08 Sep 2018 13:10:13: 9000000 INFO @ Sat, 08 Sep 2018 13:10:14: 9000000 INFO @ Sat, 08 Sep 2018 13:10:14: 9000000 INFO @ Sat, 08 Sep 2018 13:10:20: 10000000 INFO @ Sat, 08 Sep 2018 13:10:20: 10000000 INFO @ Sat, 08 Sep 2018 13:10:21: 10000000 INFO @ Sat, 08 Sep 2018 13:10:24: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 13:10:24: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 13:10:24: #1 total tags in treatment: 10657688 INFO @ Sat, 08 Sep 2018 13:10:24: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:10:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:10:24: #1 tags after filtering in treatment: 10657688 INFO @ Sat, 08 Sep 2018 13:10:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:10:24: #1 finished! INFO @ Sat, 08 Sep 2018 13:10:24: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:10:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:10:24: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 13:10:24: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 13:10:24: #1 total tags in treatment: 10657688 INFO @ Sat, 08 Sep 2018 13:10:24: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:10:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:10:25: #1 tags after filtering in treatment: 10657688 INFO @ Sat, 08 Sep 2018 13:10:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:10:25: #1 finished! INFO @ Sat, 08 Sep 2018 13:10:25: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:10:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:10:25: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 13:10:25: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 13:10:25: #1 total tags in treatment: 10657688 INFO @ Sat, 08 Sep 2018 13:10:25: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:10:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:10:25: #2 number of paired peaks: 2848 INFO @ Sat, 08 Sep 2018 13:10:25: start model_add_line... INFO @ Sat, 08 Sep 2018 13:10:26: start X-correlation... INFO @ Sat, 08 Sep 2018 13:10:26: end of X-cor INFO @ Sat, 08 Sep 2018 13:10:26: #2 finished! INFO @ Sat, 08 Sep 2018 13:10:26: #2 predicted fragment length is 163 bps INFO @ Sat, 08 Sep 2018 13:10:26: #2 alternative fragment length(s) may be 163 bps INFO @ Sat, 08 Sep 2018 13:10:26: #2.2 Generate R script for model : SRX2618528.20_model.r INFO @ Sat, 08 Sep 2018 13:10:26: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:10:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:10:26: #1 tags after filtering in treatment: 10657688 INFO @ Sat, 08 Sep 2018 13:10:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:10:26: #1 finished! INFO @ Sat, 08 Sep 2018 13:10:26: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:10:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:10:26: #2 number of paired peaks: 2848 INFO @ Sat, 08 Sep 2018 13:10:26: start model_add_line... INFO @ Sat, 08 Sep 2018 13:10:26: start X-correlation... INFO @ Sat, 08 Sep 2018 13:10:26: end of X-cor INFO @ Sat, 08 Sep 2018 13:10:26: #2 finished! INFO @ Sat, 08 Sep 2018 13:10:26: #2 predicted fragment length is 163 bps INFO @ Sat, 08 Sep 2018 13:10:26: #2 alternative fragment length(s) may be 163 bps INFO @ Sat, 08 Sep 2018 13:10:26: #2.2 Generate R script for model : SRX2618528.05_model.r INFO @ Sat, 08 Sep 2018 13:10:26: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:10:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:10:27: #2 number of paired peaks: 2848 INFO @ Sat, 08 Sep 2018 13:10:27: start model_add_line... INFO @ Sat, 08 Sep 2018 13:10:27: start X-correlation... INFO @ Sat, 08 Sep 2018 13:10:27: end of X-cor INFO @ Sat, 08 Sep 2018 13:10:27: #2 finished! INFO @ Sat, 08 Sep 2018 13:10:27: #2 predicted fragment length is 163 bps INFO @ Sat, 08 Sep 2018 13:10:27: #2 alternative fragment length(s) may be 163 bps INFO @ Sat, 08 Sep 2018 13:10:27: #2.2 Generate R script for model : SRX2618528.10_model.r INFO @ Sat, 08 Sep 2018 13:10:27: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:10:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:10:53: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:10:54: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:10:55: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:11:08: #4 Write output xls file... SRX2618528.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:11:08: #4 Write output xls file... SRX2618528.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:11:08: #4 Write peak in narrowPeak format file... SRX2618528.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:11:08: #4 Write peak in narrowPeak format file... SRX2618528.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:11:08: #4 Write summits bed file... SRX2618528.05_summits.bed INFO @ Sat, 08 Sep 2018 13:11:08: Done! INFO @ Sat, 08 Sep 2018 13:11:08: #4 Write summits bed file... SRX2618528.10_summits.bed INFO @ Sat, 08 Sep 2018 13:11:08: Done! pass1 - making usageList (13 chroms): 3 millis pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (9464 records, 4 fields): 12 millis pass2 - checking and writing primary data (6616 records, 4 fields): 10 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:11:09: #4 Write output xls file... SRX2618528.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:11:09: #4 Write peak in narrowPeak format file... SRX2618528.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:11:09: #4 Write summits bed file... SRX2618528.20_summits.bed INFO @ Sat, 08 Sep 2018 13:11:09: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (3627 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。