Job ID = 11293696 sra ファイルのダウンロード中... Completed: 510661K bytes transferred in 21 seconds (194776K 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 15466935 spots for /home/okishinya/chipatlas/results/dm3/SRX4375857/SRR7506511.sra Written 15466935 spots for /home/okishinya/chipatlas/results/dm3/SRX4375857/SRR7506511.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: 00:03:57 15466935 reads; of these: 15466935 (100.00%) were unpaired; of these: 4708063 (30.44%) aligned 0 times 8693506 (56.21%) aligned exactly 1 time 2065366 (13.35%) aligned >1 times 69.56% overall alignment rate Time searching: 00:03:57 Overall time: 00:03:57 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] 2762275 / 10758872 = 0.2567 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 17:55:32: # Command line: callpeak -t SRX4375857.bam -f BAM -g dm -n SRX4375857.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4375857.05 # format = BAM # ChIP-seq file = ['SRX4375857.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 17:55:32: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:55:32: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:55:32: # Command line: callpeak -t SRX4375857.bam -f BAM -g dm -n SRX4375857.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4375857.20 # format = BAM # ChIP-seq file = ['SRX4375857.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 17:55:32: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:55:32: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:55:32: # Command line: callpeak -t SRX4375857.bam -f BAM -g dm -n SRX4375857.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4375857.10 # format = BAM # ChIP-seq file = ['SRX4375857.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 17:55:32: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:55:32: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:55:41: 1000000 INFO @ Sun, 04 Nov 2018 17:55:41: 1000000 INFO @ Sun, 04 Nov 2018 17:55:41: 1000000 INFO @ Sun, 04 Nov 2018 17:55:49: 2000000 INFO @ Sun, 04 Nov 2018 17:55:49: 2000000 INFO @ Sun, 04 Nov 2018 17:55:49: 2000000 INFO @ Sun, 04 Nov 2018 17:55:57: 3000000 INFO @ Sun, 04 Nov 2018 17:55:57: 3000000 INFO @ Sun, 04 Nov 2018 17:55:58: 3000000 INFO @ Sun, 04 Nov 2018 17:56:05: 4000000 INFO @ Sun, 04 Nov 2018 17:56:06: 4000000 INFO @ Sun, 04 Nov 2018 17:56:06: 4000000 INFO @ Sun, 04 Nov 2018 17:56:12: 5000000 INFO @ Sun, 04 Nov 2018 17:56:13: 5000000 INFO @ Sun, 04 Nov 2018 17:56:13: 5000000 INFO @ Sun, 04 Nov 2018 17:56:19: 6000000 INFO @ Sun, 04 Nov 2018 17:56:20: 6000000 INFO @ Sun, 04 Nov 2018 17:56:20: 6000000 INFO @ Sun, 04 Nov 2018 17:56:25: 7000000 INFO @ Sun, 04 Nov 2018 17:56:27: 7000000 INFO @ Sun, 04 Nov 2018 17:56:27: 7000000 INFO @ Sun, 04 Nov 2018 17:56:32: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:56:32: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:56:32: #1 total tags in treatment: 7996597 INFO @ Sun, 04 Nov 2018 17:56:32: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:56:32: #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 17:56:32: #1 tags after filtering in treatment: 7996597 INFO @ Sun, 04 Nov 2018 17:56:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:56:32: #1 finished! INFO @ Sun, 04 Nov 2018 17:56:32: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:56:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:56:33: #2 number of paired peaks: 7649 INFO @ Sun, 04 Nov 2018 17:56:33: start model_add_line... INFO @ Sun, 04 Nov 2018 17:56:34: start X-correlation... INFO @ Sun, 04 Nov 2018 17:56:34: end of X-cor INFO @ Sun, 04 Nov 2018 17:56:34: #2 finished! INFO @ Sun, 04 Nov 2018 17:56:34: #2 predicted fragment length is 193 bps INFO @ Sun, 04 Nov 2018 17:56:34: #2 alternative fragment length(s) may be 193 bps INFO @ Sun, 04 Nov 2018 17:56:34: #2.2 Generate R script for model : SRX4375857.10_model.r INFO @ Sun, 04 Nov 2018 17:56:34: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:56:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:56:34: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:56:34: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:56:34: #1 total tags in treatment: 7996597 INFO @ Sun, 04 Nov 2018 17:56:34: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:56:34: #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 17:56:34: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:56:34: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:56:34: #1 total tags in treatment: 7996597 INFO @ Sun, 04 Nov 2018 17:56:34: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:56:34: #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 17:56:34: #1 tags after filtering in treatment: 7996597 INFO @ Sun, 04 Nov 2018 17:56:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:56:34: #1 finished! INFO @ Sun, 04 Nov 2018 17:56:34: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:56:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:56:34: #1 tags after filtering in treatment: 7996597 INFO @ Sun, 04 Nov 2018 17:56:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:56:34: #1 finished! INFO @ Sun, 04 Nov 2018 17:56:34: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:56:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:56:35: #2 number of paired peaks: 7649 INFO @ Sun, 04 Nov 2018 17:56:35: start model_add_line... INFO @ Sun, 04 Nov 2018 17:56:35: #2 number of paired peaks: 7649 INFO @ Sun, 04 Nov 2018 17:56:35: start model_add_line... INFO @ Sun, 04 Nov 2018 17:56:35: start X-correlation... INFO @ Sun, 04 Nov 2018 17:56:35: end of X-cor INFO @ Sun, 04 Nov 2018 17:56:35: #2 finished! INFO @ Sun, 04 Nov 2018 17:56:35: start X-correlation... INFO @ Sun, 04 Nov 2018 17:56:35: #2 predicted fragment length is 193 bps INFO @ Sun, 04 Nov 2018 17:56:35: #2 alternative fragment length(s) may be 193 bps INFO @ Sun, 04 Nov 2018 17:56:35: #2.2 Generate R script for model : SRX4375857.05_model.r INFO @ Sun, 04 Nov 2018 17:56:35: end of X-cor INFO @ Sun, 04 Nov 2018 17:56:35: #2 finished! INFO @ Sun, 04 Nov 2018 17:56:35: #2 predicted fragment length is 193 bps INFO @ Sun, 04 Nov 2018 17:56:35: #2 alternative fragment length(s) may be 193 bps INFO @ Sun, 04 Nov 2018 17:56:35: #2.2 Generate R script for model : SRX4375857.20_model.r INFO @ Sun, 04 Nov 2018 17:56:35: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:56:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:56:35: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:56:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:57:03: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:57:04: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:57:04: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:57:14: #4 Write output xls file... SRX4375857.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:57:14: #4 Write peak in narrowPeak format file... SRX4375857.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:57:14: #4 Write summits bed file... SRX4375857.10_summits.bed INFO @ Sun, 04 Nov 2018 17:57:14: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7541 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:57:15: #4 Write output xls file... SRX4375857.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:57:15: #4 Write peak in narrowPeak format file... SRX4375857.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:57:15: #4 Write summits bed file... SRX4375857.20_summits.bed INFO @ Sun, 04 Nov 2018 17:57:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5631 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:57:16: #4 Write output xls file... SRX4375857.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:57:16: #4 Write peak in narrowPeak format file... SRX4375857.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:57:16: #4 Write summits bed file... SRX4375857.05_summits.bed INFO @ Sun, 04 Nov 2018 17:57:16: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9505 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。