Job ID = 10480742 sra ファイルのダウンロード中... Completed: 369337K bytes transferred in 8 seconds (343599K 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 12007729 spots for /home/okishinya/chipatlas/results/dm3/SRX3380801/SRR6278164.sra Written 12007729 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: 00:04:31 12007729 reads; of these: 12007729 (100.00%) were unpaired; of these: 448555 (3.74%) aligned 0 times 8566850 (71.34%) aligned exactly 1 time 2992324 (24.92%) aligned >1 times 96.26% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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] 2322830 / 11559174 = 0.2010 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 @ Fri, 16 Mar 2018 07:54:27: # Command line: callpeak -t SRX3380801.bam -f BAM -g dm -n SRX3380801.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3380801.20 # format = BAM # ChIP-seq file = ['SRX3380801.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 @ Fri, 16 Mar 2018 07:54:27: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:54:27: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:54:27: # Command line: callpeak -t SRX3380801.bam -f BAM -g dm -n SRX3380801.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3380801.05 # format = BAM # ChIP-seq file = ['SRX3380801.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 @ Fri, 16 Mar 2018 07:54:27: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:54:27: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:54:27: # Command line: callpeak -t SRX3380801.bam -f BAM -g dm -n SRX3380801.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3380801.10 # format = BAM # ChIP-seq file = ['SRX3380801.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 @ Fri, 16 Mar 2018 07:54:27: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:54:27: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:54:33: 1000000 INFO @ Fri, 16 Mar 2018 07:54:33: 1000000 INFO @ Fri, 16 Mar 2018 07:54:33: 1000000 INFO @ Fri, 16 Mar 2018 07:54:39: 2000000 INFO @ Fri, 16 Mar 2018 07:54:39: 2000000 INFO @ Fri, 16 Mar 2018 07:54:39: 2000000 INFO @ Fri, 16 Mar 2018 07:54:45: 3000000 INFO @ Fri, 16 Mar 2018 07:54:45: 3000000 INFO @ Fri, 16 Mar 2018 07:54:45: 3000000 INFO @ Fri, 16 Mar 2018 07:54:51: 4000000 INFO @ Fri, 16 Mar 2018 07:54:51: 4000000 INFO @ Fri, 16 Mar 2018 07:54:51: 4000000 INFO @ Fri, 16 Mar 2018 07:54:57: 5000000 INFO @ Fri, 16 Mar 2018 07:54:58: 5000000 INFO @ Fri, 16 Mar 2018 07:54:58: 5000000 INFO @ Fri, 16 Mar 2018 07:55:04: 6000000 INFO @ Fri, 16 Mar 2018 07:55:04: 6000000 INFO @ Fri, 16 Mar 2018 07:55:04: 6000000 INFO @ Fri, 16 Mar 2018 07:55:10: 7000000 INFO @ Fri, 16 Mar 2018 07:55:10: 7000000 INFO @ Fri, 16 Mar 2018 07:55:10: 7000000 INFO @ Fri, 16 Mar 2018 07:55:16: 8000000 INFO @ Fri, 16 Mar 2018 07:55:17: 8000000 INFO @ Fri, 16 Mar 2018 07:55:17: 8000000 INFO @ Fri, 16 Mar 2018 07:55:22: 9000000 INFO @ Fri, 16 Mar 2018 07:55:23: 9000000 INFO @ Fri, 16 Mar 2018 07:55:23: 9000000 INFO @ Fri, 16 Mar 2018 07:55:24: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:55:24: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:55:24: #1 total tags in treatment: 9236344 INFO @ Fri, 16 Mar 2018 07:55:24: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:55:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:55:24: #1 tags after filtering in treatment: 9236344 INFO @ Fri, 16 Mar 2018 07:55:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:55:24: #1 finished! INFO @ Fri, 16 Mar 2018 07:55:24: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:55:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:55:24: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:55:24: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:55:24: #1 total tags in treatment: 9236344 INFO @ Fri, 16 Mar 2018 07:55:24: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:55:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:55:25: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:55:25: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:55:25: #1 total tags in treatment: 9236344 INFO @ Fri, 16 Mar 2018 07:55:25: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:55:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:55:25: #1 tags after filtering in treatment: 9236344 INFO @ Fri, 16 Mar 2018 07:55:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:55:25: #1 finished! INFO @ Fri, 16 Mar 2018 07:55:25: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:55:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:55:25: #1 tags after filtering in treatment: 9236344 INFO @ Fri, 16 Mar 2018 07:55:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:55:25: #1 finished! INFO @ Fri, 16 Mar 2018 07:55:25: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:55:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:55:25: #2 number of paired peaks: 7929 INFO @ Fri, 16 Mar 2018 07:55:25: start model_add_line... INFO @ Fri, 16 Mar 2018 07:55:26: start X-correlation... INFO @ Fri, 16 Mar 2018 07:55:26: end of X-cor INFO @ Fri, 16 Mar 2018 07:55:26: #2 finished! INFO @ Fri, 16 Mar 2018 07:55:26: #2 predicted fragment length is 163 bps INFO @ Fri, 16 Mar 2018 07:55:26: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 16 Mar 2018 07:55:26: #2.2 Generate R script for model : SRX3380801.10_model.r INFO @ Fri, 16 Mar 2018 07:55:26: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:55:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:55:26: #2 number of paired peaks: 7929 INFO @ Fri, 16 Mar 2018 07:55:26: start model_add_line... INFO @ Fri, 16 Mar 2018 07:55:26: #2 number of paired peaks: 7929 INFO @ Fri, 16 Mar 2018 07:55:26: start model_add_line... INFO @ Fri, 16 Mar 2018 07:55:26: start X-correlation... INFO @ Fri, 16 Mar 2018 07:55:26: end of X-cor INFO @ Fri, 16 Mar 2018 07:55:26: #2 finished! INFO @ Fri, 16 Mar 2018 07:55:26: #2 predicted fragment length is 163 bps INFO @ Fri, 16 Mar 2018 07:55:26: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 16 Mar 2018 07:55:26: #2.2 Generate R script for model : SRX3380801.20_model.r INFO @ Fri, 16 Mar 2018 07:55:26: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:55:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:55:26: start X-correlation... INFO @ Fri, 16 Mar 2018 07:55:26: end of X-cor INFO @ Fri, 16 Mar 2018 07:55:26: #2 finished! INFO @ Fri, 16 Mar 2018 07:55:26: #2 predicted fragment length is 163 bps INFO @ Fri, 16 Mar 2018 07:55:26: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 16 Mar 2018 07:55:26: #2.2 Generate R script for model : SRX3380801.05_model.r INFO @ Fri, 16 Mar 2018 07:55:26: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:55:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:55:57: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:55:57: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:55:57: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:56:10: #4 Write output xls file... SRX3380801.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:56:10: #4 Write peak in narrowPeak format file... SRX3380801.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:56:10: #4 Write summits bed file... SRX3380801.20_summits.bed INFO @ Fri, 16 Mar 2018 07:56:10: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4711 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:56:10: #4 Write output xls file... SRX3380801.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:56:10: #4 Write peak in narrowPeak format file... SRX3380801.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:56:10: #4 Write summits bed file... SRX3380801.05_summits.bed INFO @ Fri, 16 Mar 2018 07:56:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10754 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:56:11: #4 Write output xls file... SRX3380801.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:56:11: #4 Write peak in narrowPeak format file... SRX3380801.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:56:11: #4 Write summits bed file... SRX3380801.10_summits.bed INFO @ Fri, 16 Mar 2018 07:56:11: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7981 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。