Job ID = 11293660 sra ファイルのダウンロード中... Completed: 790565K bytes transferred in 26 seconds (246917K 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 22013082 spots for /home/okishinya/chipatlas/results/dm3/SRX4375822/SRR7506476.sra Written 22013082 spots for /home/okishinya/chipatlas/results/dm3/SRX4375822/SRR7506476.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: 00:05:28 22013082 reads; of these: 22013082 (100.00%) were unpaired; of these: 9650164 (43.84%) aligned 0 times 9837404 (44.69%) aligned exactly 1 time 2525514 (11.47%) aligned >1 times 56.16% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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] 7519328 / 12362918 = 0.6082 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 @ Sun, 04 Nov 2018 17:56:18: # Command line: callpeak -t SRX4375822.bam -f BAM -g dm -n SRX4375822.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4375822.20 # format = BAM # ChIP-seq file = ['SRX4375822.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 @ Sun, 04 Nov 2018 17:56:18: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:56:18: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:56:18: # Command line: callpeak -t SRX4375822.bam -f BAM -g dm -n SRX4375822.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4375822.05 # format = BAM # ChIP-seq file = ['SRX4375822.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 @ Sun, 04 Nov 2018 17:56:18: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:56:18: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:56:18: # Command line: callpeak -t SRX4375822.bam -f BAM -g dm -n SRX4375822.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4375822.10 # format = BAM # ChIP-seq file = ['SRX4375822.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 @ Sun, 04 Nov 2018 17:56:18: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:56:18: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:56:25: 1000000 INFO @ Sun, 04 Nov 2018 17:56:25: 1000000 INFO @ Sun, 04 Nov 2018 17:56:25: 1000000 INFO @ Sun, 04 Nov 2018 17:56:31: 2000000 INFO @ Sun, 04 Nov 2018 17:56:31: 2000000 INFO @ Sun, 04 Nov 2018 17:56:32: 2000000 INFO @ Sun, 04 Nov 2018 17:56:38: 3000000 INFO @ Sun, 04 Nov 2018 17:56:38: 3000000 INFO @ Sun, 04 Nov 2018 17:56:39: 3000000 INFO @ Sun, 04 Nov 2018 17:56:45: 4000000 INFO @ Sun, 04 Nov 2018 17:56:45: 4000000 INFO @ Sun, 04 Nov 2018 17:56:45: 4000000 INFO @ Sun, 04 Nov 2018 17:56:51: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:56:51: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:56:51: #1 total tags in treatment: 4843590 INFO @ Sun, 04 Nov 2018 17:56:51: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:56:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:56:51: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:56:51: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:56:51: #1 total tags in treatment: 4843590 INFO @ Sun, 04 Nov 2018 17:56:51: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:56:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:56:51: #1 tags after filtering in treatment: 4843590 INFO @ Sun, 04 Nov 2018 17:56:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:56:51: #1 finished! INFO @ Sun, 04 Nov 2018 17:56:51: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:56:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:56:51: #1 tags after filtering in treatment: 4843590 INFO @ Sun, 04 Nov 2018 17:56:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:56:51: #1 finished! INFO @ Sun, 04 Nov 2018 17:56:51: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:56:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:56:51: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:56:51: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:56:51: #1 total tags in treatment: 4843590 INFO @ Sun, 04 Nov 2018 17:56:51: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:56:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:56:51: #1 tags after filtering in treatment: 4843590 INFO @ Sun, 04 Nov 2018 17:56:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:56:51: #1 finished! INFO @ Sun, 04 Nov 2018 17:56:51: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:56:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:56:52: #2 number of paired peaks: 6923 INFO @ Sun, 04 Nov 2018 17:56:52: start model_add_line... INFO @ Sun, 04 Nov 2018 17:56:52: #2 number of paired peaks: 6923 INFO @ Sun, 04 Nov 2018 17:56:52: start model_add_line... INFO @ Sun, 04 Nov 2018 17:56:52: start X-correlation... INFO @ Sun, 04 Nov 2018 17:56:52: start X-correlation... INFO @ Sun, 04 Nov 2018 17:56:52: end of X-cor INFO @ Sun, 04 Nov 2018 17:56:52: #2 finished! INFO @ Sun, 04 Nov 2018 17:56:52: #2 predicted fragment length is 228 bps INFO @ Sun, 04 Nov 2018 17:56:52: #2 alternative fragment length(s) may be 228 bps INFO @ Sun, 04 Nov 2018 17:56:52: #2.2 Generate R script for model : SRX4375822.05_model.r INFO @ Sun, 04 Nov 2018 17:56:52: end of X-cor INFO @ Sun, 04 Nov 2018 17:56:52: #2 finished! INFO @ Sun, 04 Nov 2018 17:56:52: #2 predicted fragment length is 228 bps INFO @ Sun, 04 Nov 2018 17:56:52: #2 alternative fragment length(s) may be 228 bps INFO @ Sun, 04 Nov 2018 17:56:52: #2.2 Generate R script for model : SRX4375822.20_model.r INFO @ Sun, 04 Nov 2018 17:56:52: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:56:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:56:52: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:56:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:56:52: #2 number of paired peaks: 6923 INFO @ Sun, 04 Nov 2018 17:56:52: start model_add_line... INFO @ Sun, 04 Nov 2018 17:56:52: start X-correlation... INFO @ Sun, 04 Nov 2018 17:56:52: end of X-cor INFO @ Sun, 04 Nov 2018 17:56:52: #2 finished! INFO @ Sun, 04 Nov 2018 17:56:52: #2 predicted fragment length is 228 bps INFO @ Sun, 04 Nov 2018 17:56:52: #2 alternative fragment length(s) may be 228 bps INFO @ Sun, 04 Nov 2018 17:56:52: #2.2 Generate R script for model : SRX4375822.10_model.r INFO @ Sun, 04 Nov 2018 17:56:52: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:56:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:57:09: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:57:09: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:57:10: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:57:16: #4 Write output xls file... SRX4375822.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:57:16: #4 Write peak in narrowPeak format file... SRX4375822.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:57:16: #4 Write output xls file... SRX4375822.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:57:16: #4 Write summits bed file... SRX4375822.20_summits.bed INFO @ Sun, 04 Nov 2018 17:57:16: Done! INFO @ Sun, 04 Nov 2018 17:57:17: #4 Write peak in narrowPeak format file... SRX4375822.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:57:17: #4 Write output xls file... SRX4375822.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:57:17: #4 Write summits bed file... SRX4375822.10_summits.bed pass1 - making usageList (14 chroms): 1 millis INFO @ Sun, 04 Nov 2018 17:57:17: Done! pass2 - checking and writing primary data (5477 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:57:17: #4 Write peak in narrowPeak format file... SRX4375822.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:57:17: #4 Write summits bed file... SRX4375822.05_summits.bed INFO @ Sun, 04 Nov 2018 17:57:17: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7063 records, 4 fields): 11 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8415 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。