Job ID = 10175307 sra ファイルのダウンロード中... Completed: 174273K bytes transferred in 6 seconds (212211K 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... Written 10672478 spots for /home/okishinya/chipatlas/results/dm3/SRX3170980/SRR6019827.sra Written 10672478 spots total 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: 00:03:14 10672478 reads; of these: 10672478 (100.00%) were unpaired; of these: 289690 (2.71%) aligned 0 times 8107767 (75.97%) aligned exactly 1 time 2275021 (21.32%) aligned >1 times 97.29% overall alignment rate Time searching: 00:03:14 Overall time: 00:03:14 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] 2211611 / 10382788 = 0.2130 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 @ Mon, 06 Nov 2017 12:27:57: # Command line: callpeak -t SRX3170980.bam -f BAM -g dm -n SRX3170980.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3170980.10 # format = BAM # ChIP-seq file = ['SRX3170980.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 @ Mon, 06 Nov 2017 12:27:57: # Command line: callpeak -t SRX3170980.bam -f BAM -g dm -n SRX3170980.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3170980.20 # format = BAM # ChIP-seq file = ['SRX3170980.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 @ Mon, 06 Nov 2017 12:27:57: # Command line: callpeak -t SRX3170980.bam -f BAM -g dm -n SRX3170980.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3170980.05 # format = BAM # ChIP-seq file = ['SRX3170980.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 @ Mon, 06 Nov 2017 12:27:57: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:27:57: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:27:57: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:27:57: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:27:57: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:27:57: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:28:03: 1000000 INFO @ Mon, 06 Nov 2017 12:28:03: 1000000 INFO @ Mon, 06 Nov 2017 12:28:03: 1000000 INFO @ Mon, 06 Nov 2017 12:28:09: 2000000 INFO @ Mon, 06 Nov 2017 12:28:10: 2000000 INFO @ Mon, 06 Nov 2017 12:28:10: 2000000 INFO @ Mon, 06 Nov 2017 12:28:16: 3000000 INFO @ Mon, 06 Nov 2017 12:28:16: 3000000 INFO @ Mon, 06 Nov 2017 12:28:16: 3000000 INFO @ Mon, 06 Nov 2017 12:28:22: 4000000 INFO @ Mon, 06 Nov 2017 12:28:23: 4000000 INFO @ Mon, 06 Nov 2017 12:28:23: 4000000 INFO @ Mon, 06 Nov 2017 12:28:28: 5000000 INFO @ Mon, 06 Nov 2017 12:28:30: 5000000 INFO @ Mon, 06 Nov 2017 12:28:30: 5000000 INFO @ Mon, 06 Nov 2017 12:28:35: 6000000 INFO @ Mon, 06 Nov 2017 12:28:37: 6000000 INFO @ Mon, 06 Nov 2017 12:28:37: 6000000 INFO @ Mon, 06 Nov 2017 12:28:41: 7000000 INFO @ Mon, 06 Nov 2017 12:28:44: 7000000 INFO @ Mon, 06 Nov 2017 12:28:44: 7000000 INFO @ Mon, 06 Nov 2017 12:28:47: 8000000 INFO @ Mon, 06 Nov 2017 12:28:48: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 12:28:48: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 12:28:48: #1 total tags in treatment: 8171177 INFO @ Mon, 06 Nov 2017 12:28:48: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:28:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:28:49: #1 tags after filtering in treatment: 8171177 INFO @ Mon, 06 Nov 2017 12:28:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:28:49: #1 finished! INFO @ Mon, 06 Nov 2017 12:28:49: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:28:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:28:50: #2 number of paired peaks: 5309 INFO @ Mon, 06 Nov 2017 12:28:50: start model_add_line... INFO @ Mon, 06 Nov 2017 12:28:50: start X-correlation... INFO @ Mon, 06 Nov 2017 12:28:50: end of X-cor INFO @ Mon, 06 Nov 2017 12:28:50: #2 finished! INFO @ Mon, 06 Nov 2017 12:28:50: #2 predicted fragment length is 150 bps INFO @ Mon, 06 Nov 2017 12:28:50: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 06 Nov 2017 12:28:50: #2.2 Generate R script for model : SRX3170980.10_model.r INFO @ Mon, 06 Nov 2017 12:28:50: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:28:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:28:50: 8000000 INFO @ Mon, 06 Nov 2017 12:28:50: 8000000 INFO @ Mon, 06 Nov 2017 12:28:52: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 12:28:52: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 12:28:52: #1 total tags in treatment: 8171177 INFO @ Mon, 06 Nov 2017 12:28:52: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:28:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:28:52: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 12:28:52: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 12:28:52: #1 total tags in treatment: 8171177 INFO @ Mon, 06 Nov 2017 12:28:52: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:28:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:28:52: #1 tags after filtering in treatment: 8171177 INFO @ Mon, 06 Nov 2017 12:28:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:28:52: #1 finished! INFO @ Mon, 06 Nov 2017 12:28:52: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:28:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:28:52: #1 tags after filtering in treatment: 8171177 INFO @ Mon, 06 Nov 2017 12:28:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:28:52: #1 finished! INFO @ Mon, 06 Nov 2017 12:28:52: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:28:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:28:53: #2 number of paired peaks: 5309 INFO @ Mon, 06 Nov 2017 12:28:53: start model_add_line... INFO @ Mon, 06 Nov 2017 12:28:53: #2 number of paired peaks: 5309 INFO @ Mon, 06 Nov 2017 12:28:53: start model_add_line... INFO @ Mon, 06 Nov 2017 12:28:53: start X-correlation... INFO @ Mon, 06 Nov 2017 12:28:53: end of X-cor INFO @ Mon, 06 Nov 2017 12:28:53: #2 finished! INFO @ Mon, 06 Nov 2017 12:28:53: #2 predicted fragment length is 150 bps INFO @ Mon, 06 Nov 2017 12:28:53: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 06 Nov 2017 12:28:53: #2.2 Generate R script for model : SRX3170980.05_model.r INFO @ Mon, 06 Nov 2017 12:28:53: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:28:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:28:53: start X-correlation... INFO @ Mon, 06 Nov 2017 12:28:53: end of X-cor INFO @ Mon, 06 Nov 2017 12:28:53: #2 finished! INFO @ Mon, 06 Nov 2017 12:28:53: #2 predicted fragment length is 150 bps INFO @ Mon, 06 Nov 2017 12:28:53: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 06 Nov 2017 12:28:53: #2.2 Generate R script for model : SRX3170980.20_model.r INFO @ Mon, 06 Nov 2017 12:28:53: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:28:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:29:14: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:29:15: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:29:16: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:29:25: #4 Write output xls file... SRX3170980.10_peaks.xls INFO @ Mon, 06 Nov 2017 12:29:25: #4 Write peak in narrowPeak format file... SRX3170980.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:29:25: #4 Write summits bed file... SRX3170980.10_summits.bed INFO @ Mon, 06 Nov 2017 12:29:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4402 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:29:27: #4 Write output xls file... SRX3170980.05_peaks.xls INFO @ Mon, 06 Nov 2017 12:29:27: #4 Write peak in narrowPeak format file... SRX3170980.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:29:27: #4 Write summits bed file... SRX3170980.05_summits.bed INFO @ Mon, 06 Nov 2017 12:29:27: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9876 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:29:29: #4 Write output xls file... SRX3170980.20_peaks.xls INFO @ Mon, 06 Nov 2017 12:29:29: #4 Write peak in narrowPeak format file... SRX3170980.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:29:29: #4 Write summits bed file... SRX3170980.20_summits.bed INFO @ Mon, 06 Nov 2017 12:29:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1105 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。