Job ID = 10714573 sra ファイルのダウンロード中... Completed: 410010K bytes transferred in 7 seconds (470502K 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 22610053 spots for /home/okishinya/chipatlas/results/dm3/SRX4053307/SRR7132406.sra Written 22610053 spots for /home/okishinya/chipatlas/results/dm3/SRX4053307/SRR7132406.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: 00:07:20 22610053 reads; of these: 22610053 (100.00%) were unpaired; of these: 4134857 (18.29%) aligned 0 times 14858378 (65.72%) aligned exactly 1 time 3616818 (16.00%) aligned >1 times 81.71% overall alignment rate Time searching: 00:07:20 Overall time: 00:07:20 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] 10696355 / 18475196 = 0.5790 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, 03 Jun 2018 13:42:48: # Command line: callpeak -t SRX4053307.bam -f BAM -g dm -n SRX4053307.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4053307.20 # format = BAM # ChIP-seq file = ['SRX4053307.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, 03 Jun 2018 13:42:48: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:42:48: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:42:48: # Command line: callpeak -t SRX4053307.bam -f BAM -g dm -n SRX4053307.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4053307.05 # format = BAM # ChIP-seq file = ['SRX4053307.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, 03 Jun 2018 13:42:48: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:42:48: # Command line: callpeak -t SRX4053307.bam -f BAM -g dm -n SRX4053307.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4053307.10 # format = BAM # ChIP-seq file = ['SRX4053307.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, 03 Jun 2018 13:42:48: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:42:48: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:42:48: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:42:57: 1000000 INFO @ Sun, 03 Jun 2018 13:42:58: 1000000 INFO @ Sun, 03 Jun 2018 13:42:58: 1000000 INFO @ Sun, 03 Jun 2018 13:43:05: 2000000 INFO @ Sun, 03 Jun 2018 13:43:07: 2000000 INFO @ Sun, 03 Jun 2018 13:43:07: 2000000 INFO @ Sun, 03 Jun 2018 13:43:14: 3000000 INFO @ Sun, 03 Jun 2018 13:43:16: 3000000 INFO @ Sun, 03 Jun 2018 13:43:16: 3000000 INFO @ Sun, 03 Jun 2018 13:43:22: 4000000 INFO @ Sun, 03 Jun 2018 13:43:26: 4000000 INFO @ Sun, 03 Jun 2018 13:43:26: 4000000 INFO @ Sun, 03 Jun 2018 13:43:30: 5000000 INFO @ Sun, 03 Jun 2018 13:43:35: 5000000 INFO @ Sun, 03 Jun 2018 13:43:35: 5000000 INFO @ Sun, 03 Jun 2018 13:43:39: 6000000 INFO @ Sun, 03 Jun 2018 13:43:44: 6000000 INFO @ Sun, 03 Jun 2018 13:43:44: 6000000 INFO @ Sun, 03 Jun 2018 13:43:48: 7000000 INFO @ Sun, 03 Jun 2018 13:43:54: 7000000 INFO @ Sun, 03 Jun 2018 13:43:54: 7000000 INFO @ Sun, 03 Jun 2018 13:43:54: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:43:54: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:43:54: #1 total tags in treatment: 7778841 INFO @ Sun, 03 Jun 2018 13:43:54: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:43:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:43:54: #1 tags after filtering in treatment: 7778841 INFO @ Sun, 03 Jun 2018 13:43:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:43:54: #1 finished! INFO @ Sun, 03 Jun 2018 13:43:54: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:43:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:43:55: #2 number of paired peaks: 5775 INFO @ Sun, 03 Jun 2018 13:43:55: start model_add_line... INFO @ Sun, 03 Jun 2018 13:43:56: start X-correlation... INFO @ Sun, 03 Jun 2018 13:43:56: end of X-cor INFO @ Sun, 03 Jun 2018 13:43:56: #2 finished! INFO @ Sun, 03 Jun 2018 13:43:56: #2 predicted fragment length is 193 bps INFO @ Sun, 03 Jun 2018 13:43:56: #2 alternative fragment length(s) may be 3,193 bps INFO @ Sun, 03 Jun 2018 13:43:56: #2.2 Generate R script for model : SRX4053307.20_model.r INFO @ Sun, 03 Jun 2018 13:43:56: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:43:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:44:01: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:44:01: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:44:01: #1 total tags in treatment: 7778841 INFO @ Sun, 03 Jun 2018 13:44:01: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:44:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:44:01: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:44:01: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:44:01: #1 total tags in treatment: 7778841 INFO @ Sun, 03 Jun 2018 13:44:01: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:44:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:44:01: #1 tags after filtering in treatment: 7778841 INFO @ Sun, 03 Jun 2018 13:44:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:44:01: #1 finished! INFO @ Sun, 03 Jun 2018 13:44:01: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:44:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:44:01: #1 tags after filtering in treatment: 7778841 INFO @ Sun, 03 Jun 2018 13:44:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:44:01: #1 finished! INFO @ Sun, 03 Jun 2018 13:44:01: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:44:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:44:02: #2 number of paired peaks: 5775 INFO @ Sun, 03 Jun 2018 13:44:02: start model_add_line... INFO @ Sun, 03 Jun 2018 13:44:02: #2 number of paired peaks: 5775 INFO @ Sun, 03 Jun 2018 13:44:02: start model_add_line... INFO @ Sun, 03 Jun 2018 13:44:02: start X-correlation... INFO @ Sun, 03 Jun 2018 13:44:02: end of X-cor INFO @ Sun, 03 Jun 2018 13:44:02: #2 finished! INFO @ Sun, 03 Jun 2018 13:44:02: #2 predicted fragment length is 193 bps INFO @ Sun, 03 Jun 2018 13:44:02: #2 alternative fragment length(s) may be 3,193 bps INFO @ Sun, 03 Jun 2018 13:44:02: #2.2 Generate R script for model : SRX4053307.05_model.r INFO @ Sun, 03 Jun 2018 13:44:02: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:44:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:44:02: start X-correlation... INFO @ Sun, 03 Jun 2018 13:44:02: end of X-cor INFO @ Sun, 03 Jun 2018 13:44:02: #2 finished! INFO @ Sun, 03 Jun 2018 13:44:02: #2 predicted fragment length is 193 bps INFO @ Sun, 03 Jun 2018 13:44:02: #2 alternative fragment length(s) may be 3,193 bps INFO @ Sun, 03 Jun 2018 13:44:02: #2.2 Generate R script for model : SRX4053307.10_model.r INFO @ Sun, 03 Jun 2018 13:44:02: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:44:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:44:20: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:44:26: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:44:27: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:44:30: #4 Write output xls file... SRX4053307.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:44:30: #4 Write peak in narrowPeak format file... SRX4053307.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:44:30: #4 Write summits bed file... SRX4053307.20_summits.bed INFO @ Sun, 03 Jun 2018 13:44:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (761 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:44:37: #4 Write output xls file... SRX4053307.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:44:37: #4 Write peak in narrowPeak format file... SRX4053307.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:44:37: #4 Write summits bed file... SRX4053307.10_summits.bed INFO @ Sun, 03 Jun 2018 13:44:37: Done! INFO @ Sun, 03 Jun 2018 13:44:37: #4 Write output xls file... SRX4053307.05_peaks.xls pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1290 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:44:37: #4 Write peak in narrowPeak format file... SRX4053307.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:44:37: #4 Write summits bed file... SRX4053307.05_summits.bed INFO @ Sun, 03 Jun 2018 13:44:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2369 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。