Job ID = 11171107 sra ファイルのダウンロード中... Completed: 493626K bytes transferred in 7 seconds (572555K 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 26112720 spots for /home/okishinya/chipatlas/results/dm3/SRX1794241/SRR3575285.sra Written 26112720 spots for /home/okishinya/chipatlas/results/dm3/SRX1794241/SRR3575285.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: 00:08:31 26112720 reads; of these: 26112720 (100.00%) were unpaired; of these: 5153734 (19.74%) aligned 0 times 15840991 (60.66%) aligned exactly 1 time 5117995 (19.60%) aligned >1 times 80.26% overall alignment rate Time searching: 00:08:31 Overall time: 00:08:31 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 12 files... [bam_rmdupse_core] 4518639 / 20958986 = 0.2156 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 12:00:27: # Command line: callpeak -t SRX1794241.bam -f BAM -g dm -n SRX1794241.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794241.10 # format = BAM # ChIP-seq file = ['SRX1794241.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 12:00:27: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:00:27: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:00:27: # Command line: callpeak -t SRX1794241.bam -f BAM -g dm -n SRX1794241.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794241.05 # format = BAM # ChIP-seq file = ['SRX1794241.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 12:00:27: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:00:27: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:00:27: # Command line: callpeak -t SRX1794241.bam -f BAM -g dm -n SRX1794241.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794241.20 # format = BAM # ChIP-seq file = ['SRX1794241.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 12:00:27: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:00:27: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:00:34: 1000000 INFO @ Sat, 08 Sep 2018 12:00:34: 1000000 INFO @ Sat, 08 Sep 2018 12:00:34: 1000000 INFO @ Sat, 08 Sep 2018 12:00:41: 2000000 INFO @ Sat, 08 Sep 2018 12:00:41: 2000000 INFO @ Sat, 08 Sep 2018 12:00:41: 2000000 INFO @ Sat, 08 Sep 2018 12:00:48: 3000000 INFO @ Sat, 08 Sep 2018 12:00:48: 3000000 INFO @ Sat, 08 Sep 2018 12:00:49: 3000000 INFO @ Sat, 08 Sep 2018 12:00:55: 4000000 INFO @ Sat, 08 Sep 2018 12:00:55: 4000000 INFO @ Sat, 08 Sep 2018 12:00:56: 4000000 INFO @ Sat, 08 Sep 2018 12:01:02: 5000000 INFO @ Sat, 08 Sep 2018 12:01:02: 5000000 INFO @ Sat, 08 Sep 2018 12:01:03: 5000000 INFO @ Sat, 08 Sep 2018 12:01:09: 6000000 INFO @ Sat, 08 Sep 2018 12:01:09: 6000000 INFO @ Sat, 08 Sep 2018 12:01:10: 6000000 INFO @ Sat, 08 Sep 2018 12:01:16: 7000000 INFO @ Sat, 08 Sep 2018 12:01:16: 7000000 INFO @ Sat, 08 Sep 2018 12:01:17: 7000000 INFO @ Sat, 08 Sep 2018 12:01:23: 8000000 INFO @ Sat, 08 Sep 2018 12:01:24: 8000000 INFO @ Sat, 08 Sep 2018 12:01:24: 8000000 INFO @ Sat, 08 Sep 2018 12:01:30: 9000000 INFO @ Sat, 08 Sep 2018 12:01:31: 9000000 INFO @ Sat, 08 Sep 2018 12:01:32: 9000000 INFO @ Sat, 08 Sep 2018 12:01:37: 10000000 INFO @ Sat, 08 Sep 2018 12:01:38: 10000000 INFO @ Sat, 08 Sep 2018 12:01:39: 10000000 INFO @ Sat, 08 Sep 2018 12:01:44: 11000000 INFO @ Sat, 08 Sep 2018 12:01:45: 11000000 INFO @ Sat, 08 Sep 2018 12:01:46: 11000000 INFO @ Sat, 08 Sep 2018 12:01:51: 12000000 INFO @ Sat, 08 Sep 2018 12:01:53: 12000000 INFO @ Sat, 08 Sep 2018 12:01:53: 12000000 INFO @ Sat, 08 Sep 2018 12:01:59: 13000000 INFO @ Sat, 08 Sep 2018 12:02:00: 13000000 INFO @ Sat, 08 Sep 2018 12:02:00: 13000000 INFO @ Sat, 08 Sep 2018 12:02:06: 14000000 INFO @ Sat, 08 Sep 2018 12:02:07: 14000000 INFO @ Sat, 08 Sep 2018 12:02:07: 14000000 INFO @ Sat, 08 Sep 2018 12:02:13: 15000000 INFO @ Sat, 08 Sep 2018 12:02:15: 15000000 INFO @ Sat, 08 Sep 2018 12:02:15: 15000000 INFO @ Sat, 08 Sep 2018 12:02:20: 16000000 INFO @ Sat, 08 Sep 2018 12:02:22: 16000000 INFO @ Sat, 08 Sep 2018 12:02:22: 16000000 INFO @ Sat, 08 Sep 2018 12:02:23: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:02:23: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:02:23: #1 total tags in treatment: 16440347 INFO @ Sat, 08 Sep 2018 12:02:23: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:02:23: #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 12:02:24: #1 tags after filtering in treatment: 16440347 INFO @ Sat, 08 Sep 2018 12:02:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:02:24: #1 finished! INFO @ Sat, 08 Sep 2018 12:02:24: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:02:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:02:25: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:02:25: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:02:25: #1 total tags in treatment: 16440347 INFO @ Sat, 08 Sep 2018 12:02:25: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:02:25: #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 12:02:25: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:02:25: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:02:25: #1 total tags in treatment: 16440347 INFO @ Sat, 08 Sep 2018 12:02:25: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:02:25: #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 12:02:25: #1 tags after filtering in treatment: 16440347 INFO @ Sat, 08 Sep 2018 12:02:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:02:25: #1 finished! INFO @ Sat, 08 Sep 2018 12:02:25: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:02:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:02:25: #2 number of paired peaks: 4524 INFO @ Sat, 08 Sep 2018 12:02:25: start model_add_line... INFO @ Sat, 08 Sep 2018 12:02:26: #1 tags after filtering in treatment: 16440347 INFO @ Sat, 08 Sep 2018 12:02:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:02:26: #1 finished! INFO @ Sat, 08 Sep 2018 12:02:26: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:02:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:02:26: start X-correlation... INFO @ Sat, 08 Sep 2018 12:02:26: end of X-cor INFO @ Sat, 08 Sep 2018 12:02:26: #2 finished! INFO @ Sat, 08 Sep 2018 12:02:26: #2 predicted fragment length is 157 bps INFO @ Sat, 08 Sep 2018 12:02:26: #2 alternative fragment length(s) may be 4,157 bps INFO @ Sat, 08 Sep 2018 12:02:26: #2.2 Generate R script for model : SRX1794241.20_model.r INFO @ Sat, 08 Sep 2018 12:02:26: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:02:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:02:27: #2 number of paired peaks: 4524 INFO @ Sat, 08 Sep 2018 12:02:27: start model_add_line... INFO @ Sat, 08 Sep 2018 12:02:27: #2 number of paired peaks: 4524 INFO @ Sat, 08 Sep 2018 12:02:27: start model_add_line... INFO @ Sat, 08 Sep 2018 12:02:27: start X-correlation... INFO @ Sat, 08 Sep 2018 12:02:27: end of X-cor INFO @ Sat, 08 Sep 2018 12:02:27: #2 finished! INFO @ Sat, 08 Sep 2018 12:02:27: #2 predicted fragment length is 157 bps INFO @ Sat, 08 Sep 2018 12:02:27: #2 alternative fragment length(s) may be 4,157 bps INFO @ Sat, 08 Sep 2018 12:02:27: #2.2 Generate R script for model : SRX1794241.10_model.r INFO @ Sat, 08 Sep 2018 12:02:27: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:02:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:02:28: start X-correlation... INFO @ Sat, 08 Sep 2018 12:02:28: end of X-cor INFO @ Sat, 08 Sep 2018 12:02:28: #2 finished! INFO @ Sat, 08 Sep 2018 12:02:28: #2 predicted fragment length is 157 bps INFO @ Sat, 08 Sep 2018 12:02:28: #2 alternative fragment length(s) may be 4,157 bps INFO @ Sat, 08 Sep 2018 12:02:28: #2.2 Generate R script for model : SRX1794241.05_model.r INFO @ Sat, 08 Sep 2018 12:02:28: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:02:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:03:12: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:03:14: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:03:14: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:03:32: #4 Write output xls file... SRX1794241.20_peaks.xls INFO @ Sat, 08 Sep 2018 12:03:32: #4 Write peak in narrowPeak format file... SRX1794241.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:03:32: #4 Write summits bed file... SRX1794241.20_summits.bed INFO @ Sat, 08 Sep 2018 12:03:32: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5536 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:03:34: #4 Write output xls file... SRX1794241.10_peaks.xls INFO @ Sat, 08 Sep 2018 12:03:34: #4 Write peak in narrowPeak format file... SRX1794241.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:03:35: #4 Write summits bed file... SRX1794241.10_summits.bed INFO @ Sat, 08 Sep 2018 12:03:35: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9502 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:03:35: #4 Write output xls file... SRX1794241.05_peaks.xls INFO @ Sat, 08 Sep 2018 12:03:35: #4 Write peak in narrowPeak format file... SRX1794241.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:03:35: #4 Write summits bed file... SRX1794241.05_summits.bed INFO @ Sat, 08 Sep 2018 12:03:35: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12698 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。