Job ID = 10201973 sra ファイルのダウンロード中... Completed: 365941K bytes transferred in 13 seconds (215295K 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 20603440 spots for /home/okishinya/chipatlas/results/ce10/SRX2576642/SRR5272599.sra Written 20603440 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: 00:05:12 20603440 reads; of these: 20603440 (100.00%) were unpaired; of these: 853916 (4.14%) aligned 0 times 15569689 (75.57%) aligned exactly 1 time 4179835 (20.29%) aligned >1 times 95.86% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 10199095 / 19749524 = 0.5164 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, 13 Nov 2017 13:18:07: # Command line: callpeak -t SRX2576642.bam -f BAM -g ce -n SRX2576642.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576642.20 # format = BAM # ChIP-seq file = ['SRX2576642.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 13 Nov 2017 13:18:07: # Command line: callpeak -t SRX2576642.bam -f BAM -g ce -n SRX2576642.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576642.10 # format = BAM # ChIP-seq file = ['SRX2576642.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 13 Nov 2017 13:18:07: # Command line: callpeak -t SRX2576642.bam -f BAM -g ce -n SRX2576642.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576642.05 # format = BAM # ChIP-seq file = ['SRX2576642.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 13 Nov 2017 13:18:07: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:18:07: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:18:07: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:18:07: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:18:07: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:18:07: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:18:13: 1000000 INFO @ Mon, 13 Nov 2017 13:18:14: 1000000 INFO @ Mon, 13 Nov 2017 13:18:14: 1000000 INFO @ Mon, 13 Nov 2017 13:18:20: 2000000 INFO @ Mon, 13 Nov 2017 13:18:22: 2000000 INFO @ Mon, 13 Nov 2017 13:18:22: 2000000 INFO @ Mon, 13 Nov 2017 13:18:27: 3000000 INFO @ Mon, 13 Nov 2017 13:18:29: 3000000 INFO @ Mon, 13 Nov 2017 13:18:29: 3000000 INFO @ Mon, 13 Nov 2017 13:18:34: 4000000 INFO @ Mon, 13 Nov 2017 13:18:36: 4000000 INFO @ Mon, 13 Nov 2017 13:18:36: 4000000 INFO @ Mon, 13 Nov 2017 13:18:41: 5000000 INFO @ Mon, 13 Nov 2017 13:18:44: 5000000 INFO @ Mon, 13 Nov 2017 13:18:44: 5000000 INFO @ Mon, 13 Nov 2017 13:18:48: 6000000 INFO @ Mon, 13 Nov 2017 13:18:51: 6000000 INFO @ Mon, 13 Nov 2017 13:18:51: 6000000 INFO @ Mon, 13 Nov 2017 13:18:55: 7000000 INFO @ Mon, 13 Nov 2017 13:18:59: 7000000 INFO @ Mon, 13 Nov 2017 13:18:59: 7000000 INFO @ Mon, 13 Nov 2017 13:19:01: 8000000 INFO @ Mon, 13 Nov 2017 13:19:07: 8000000 INFO @ Mon, 13 Nov 2017 13:19:07: 8000000 INFO @ Mon, 13 Nov 2017 13:19:08: 9000000 INFO @ Mon, 13 Nov 2017 13:19:12: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:19:12: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:19:12: #1 total tags in treatment: 9550429 INFO @ Mon, 13 Nov 2017 13:19:12: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:19:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:19:12: #1 tags after filtering in treatment: 9550429 INFO @ Mon, 13 Nov 2017 13:19:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:19:12: #1 finished! INFO @ Mon, 13 Nov 2017 13:19:12: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:19:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:19:13: #2 number of paired peaks: 1589 INFO @ Mon, 13 Nov 2017 13:19:13: start model_add_line... INFO @ Mon, 13 Nov 2017 13:19:13: start X-correlation... INFO @ Mon, 13 Nov 2017 13:19:13: end of X-cor INFO @ Mon, 13 Nov 2017 13:19:13: #2 finished! INFO @ Mon, 13 Nov 2017 13:19:13: #2 predicted fragment length is 226 bps INFO @ Mon, 13 Nov 2017 13:19:13: #2 alternative fragment length(s) may be 226 bps INFO @ Mon, 13 Nov 2017 13:19:13: #2.2 Generate R script for model : SRX2576642.20_model.r INFO @ Mon, 13 Nov 2017 13:19:13: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:19:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:19:14: 9000000 INFO @ Mon, 13 Nov 2017 13:19:14: 9000000 INFO @ Mon, 13 Nov 2017 13:19:18: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:19:18: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:19:18: #1 total tags in treatment: 9550429 INFO @ Mon, 13 Nov 2017 13:19:18: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:19:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:19:18: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:19:18: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:19:18: #1 total tags in treatment: 9550429 INFO @ Mon, 13 Nov 2017 13:19:18: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:19:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:19:19: #1 tags after filtering in treatment: 9550429 INFO @ Mon, 13 Nov 2017 13:19:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:19:19: #1 finished! INFO @ Mon, 13 Nov 2017 13:19:19: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:19:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:19:19: #1 tags after filtering in treatment: 9550429 INFO @ Mon, 13 Nov 2017 13:19:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:19:19: #1 finished! INFO @ Mon, 13 Nov 2017 13:19:19: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:19:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:19:19: #2 number of paired peaks: 1589 INFO @ Mon, 13 Nov 2017 13:19:19: start model_add_line... INFO @ Mon, 13 Nov 2017 13:19:19: #2 number of paired peaks: 1589 INFO @ Mon, 13 Nov 2017 13:19:19: start model_add_line... INFO @ Mon, 13 Nov 2017 13:19:20: start X-correlation... INFO @ Mon, 13 Nov 2017 13:19:20: end of X-cor INFO @ Mon, 13 Nov 2017 13:19:20: #2 finished! INFO @ Mon, 13 Nov 2017 13:19:20: #2 predicted fragment length is 226 bps INFO @ Mon, 13 Nov 2017 13:19:20: #2 alternative fragment length(s) may be 226 bps INFO @ Mon, 13 Nov 2017 13:19:20: #2.2 Generate R script for model : SRX2576642.05_model.r INFO @ Mon, 13 Nov 2017 13:19:20: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:19:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:19:20: start X-correlation... INFO @ Mon, 13 Nov 2017 13:19:20: end of X-cor INFO @ Mon, 13 Nov 2017 13:19:20: #2 finished! INFO @ Mon, 13 Nov 2017 13:19:20: #2 predicted fragment length is 226 bps INFO @ Mon, 13 Nov 2017 13:19:20: #2 alternative fragment length(s) may be 226 bps INFO @ Mon, 13 Nov 2017 13:19:20: #2.2 Generate R script for model : SRX2576642.10_model.r INFO @ Mon, 13 Nov 2017 13:19:20: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:19:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:19:41: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:19:47: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:19:49: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:19:55: #4 Write output xls file... SRX2576642.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:19:55: #4 Write peak in narrowPeak format file... SRX2576642.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:19:55: #4 Write summits bed file... SRX2576642.20_summits.bed INFO @ Mon, 13 Nov 2017 13:19:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1708 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:19:59: #4 Write output xls file... SRX2576642.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:19:59: #4 Write peak in narrowPeak format file... SRX2576642.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:19:59: #4 Write summits bed file... SRX2576642.10_summits.bed INFO @ Mon, 13 Nov 2017 13:19:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2325 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:20:01: #4 Write output xls file... SRX2576642.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:20:01: #4 Write peak in narrowPeak format file... SRX2576642.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:20:01: #4 Write summits bed file... SRX2576642.05_summits.bed INFO @ Mon, 13 Nov 2017 13:20:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2943 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。