Job ID = 11240759 sra ファイルのダウンロード中... Completed: 469846K bytes transferred in 10 seconds (358791K 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 27535452 spots for /home/okishinya/chipatlas/results/dm3/SRX4669043/SRR7817568.sra Written 27535452 spots for /home/okishinya/chipatlas/results/dm3/SRX4669043/SRR7817568.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: 00:09:38 27535452 reads; of these: 27535452 (100.00%) were unpaired; of these: 2631010 (9.55%) aligned 0 times 17427794 (63.29%) aligned exactly 1 time 7476648 (27.15%) aligned >1 times 90.45% overall alignment rate Time searching: 00:09:38 Overall time: 00:09:38 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 12 files... [bam_rmdupse_core] 9270368 / 24904442 = 0.3722 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, 07 Oct 2018 20:45:28: # Command line: callpeak -t SRX4669043.bam -f BAM -g dm -n SRX4669043.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669043.20 # format = BAM # ChIP-seq file = ['SRX4669043.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, 07 Oct 2018 20:45:28: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:45:28: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:45:28: # Command line: callpeak -t SRX4669043.bam -f BAM -g dm -n SRX4669043.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669043.10 # format = BAM # ChIP-seq file = ['SRX4669043.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, 07 Oct 2018 20:45:28: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:45:28: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:45:28: # Command line: callpeak -t SRX4669043.bam -f BAM -g dm -n SRX4669043.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669043.05 # format = BAM # ChIP-seq file = ['SRX4669043.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, 07 Oct 2018 20:45:28: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:45:28: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:45:35: 1000000 INFO @ Sun, 07 Oct 2018 20:45:35: 1000000 INFO @ Sun, 07 Oct 2018 20:45:35: 1000000 INFO @ Sun, 07 Oct 2018 20:45:43: 2000000 INFO @ Sun, 07 Oct 2018 20:45:43: 2000000 INFO @ Sun, 07 Oct 2018 20:45:43: 2000000 INFO @ Sun, 07 Oct 2018 20:45:50: 3000000 INFO @ Sun, 07 Oct 2018 20:45:50: 3000000 INFO @ Sun, 07 Oct 2018 20:45:50: 3000000 INFO @ Sun, 07 Oct 2018 20:45:57: 4000000 INFO @ Sun, 07 Oct 2018 20:45:58: 4000000 INFO @ Sun, 07 Oct 2018 20:45:58: 4000000 INFO @ Sun, 07 Oct 2018 20:46:05: 5000000 INFO @ Sun, 07 Oct 2018 20:46:05: 5000000 INFO @ Sun, 07 Oct 2018 20:46:05: 5000000 INFO @ Sun, 07 Oct 2018 20:46:12: 6000000 INFO @ Sun, 07 Oct 2018 20:46:12: 6000000 INFO @ Sun, 07 Oct 2018 20:46:12: 6000000 INFO @ Sun, 07 Oct 2018 20:46:19: 7000000 INFO @ Sun, 07 Oct 2018 20:46:20: 7000000 INFO @ Sun, 07 Oct 2018 20:46:20: 7000000 INFO @ Sun, 07 Oct 2018 20:46:27: 8000000 INFO @ Sun, 07 Oct 2018 20:46:27: 8000000 INFO @ Sun, 07 Oct 2018 20:46:27: 8000000 INFO @ Sun, 07 Oct 2018 20:46:34: 9000000 INFO @ Sun, 07 Oct 2018 20:46:35: 9000000 INFO @ Sun, 07 Oct 2018 20:46:35: 9000000 INFO @ Sun, 07 Oct 2018 20:46:41: 10000000 INFO @ Sun, 07 Oct 2018 20:46:42: 10000000 INFO @ Sun, 07 Oct 2018 20:46:42: 10000000 INFO @ Sun, 07 Oct 2018 20:46:48: 11000000 INFO @ Sun, 07 Oct 2018 20:46:49: 11000000 INFO @ Sun, 07 Oct 2018 20:46:49: 11000000 INFO @ Sun, 07 Oct 2018 20:46:57: 12000000 INFO @ Sun, 07 Oct 2018 20:46:58: 12000000 INFO @ Sun, 07 Oct 2018 20:46:58: 12000000 INFO @ Sun, 07 Oct 2018 20:47:06: 13000000 INFO @ Sun, 07 Oct 2018 20:47:06: 13000000 INFO @ Sun, 07 Oct 2018 20:47:06: 13000000 INFO @ Sun, 07 Oct 2018 20:47:14: 14000000 INFO @ Sun, 07 Oct 2018 20:47:15: 14000000 INFO @ Sun, 07 Oct 2018 20:47:15: 14000000 INFO @ Sun, 07 Oct 2018 20:47:23: 15000000 INFO @ Sun, 07 Oct 2018 20:47:23: 15000000 INFO @ Sun, 07 Oct 2018 20:47:23: 15000000 INFO @ Sun, 07 Oct 2018 20:47:28: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:47:28: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:47:28: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:47:28: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:47:28: #1 total tags in treatment: 15634074 INFO @ Sun, 07 Oct 2018 20:47:28: #1 total tags in treatment: 15634074 INFO @ Sun, 07 Oct 2018 20:47:28: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:47:28: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:47:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:47:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:47:28: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:47:28: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:47:28: #1 total tags in treatment: 15634074 INFO @ Sun, 07 Oct 2018 20:47:28: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:47:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:47:28: #1 tags after filtering in treatment: 15634074 INFO @ Sun, 07 Oct 2018 20:47:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:47:28: #1 finished! INFO @ Sun, 07 Oct 2018 20:47:28: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:47:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:47:28: #1 tags after filtering in treatment: 15634074 INFO @ Sun, 07 Oct 2018 20:47:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:47:28: #1 finished! INFO @ Sun, 07 Oct 2018 20:47:28: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:47:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:47:29: #1 tags after filtering in treatment: 15634074 INFO @ Sun, 07 Oct 2018 20:47:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:47:29: #1 finished! INFO @ Sun, 07 Oct 2018 20:47:29: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:47:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:47:30: #2 number of paired peaks: 1474 INFO @ Sun, 07 Oct 2018 20:47:30: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:30: #2 number of paired peaks: 1474 INFO @ Sun, 07 Oct 2018 20:47:30: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:30: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:30: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:30: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:30: #2 predicted fragment length is 146 bps INFO @ Sun, 07 Oct 2018 20:47:30: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 07 Oct 2018 20:47:30: #2.2 Generate R script for model : SRX4669043.05_model.r INFO @ Sun, 07 Oct 2018 20:47:30: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:47:30: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:30: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:30: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:30: #2 predicted fragment length is 146 bps INFO @ Sun, 07 Oct 2018 20:47:30: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 07 Oct 2018 20:47:30: #2.2 Generate R script for model : SRX4669043.10_model.r INFO @ Sun, 07 Oct 2018 20:47:30: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:47:30: #2 number of paired peaks: 1474 INFO @ Sun, 07 Oct 2018 20:47:30: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:30: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:30: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:30: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:30: #2 predicted fragment length is 146 bps INFO @ Sun, 07 Oct 2018 20:47:30: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 07 Oct 2018 20:47:30: #2.2 Generate R script for model : SRX4669043.20_model.r INFO @ Sun, 07 Oct 2018 20:47:30: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:48:10: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:48:12: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:48:12: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:48:33: #4 Write output xls file... SRX4669043.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:48:33: #4 Write peak in narrowPeak format file... SRX4669043.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:48:33: #4 Write summits bed file... SRX4669043.20_summits.bed INFO @ Sun, 07 Oct 2018 20:48:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2452 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:48:33: #4 Write output xls file... SRX4669043.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:48:33: #4 Write peak in narrowPeak format file... SRX4669043.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:48:33: #4 Write summits bed file... SRX4669043.05_summits.bed INFO @ Sun, 07 Oct 2018 20:48:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9097 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:48:35: #4 Write output xls file... SRX4669043.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:48:35: #4 Write peak in narrowPeak format file... SRX4669043.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:48:35: #4 Write summits bed file... SRX4669043.10_summits.bed INFO @ Sun, 07 Oct 2018 20:48:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5207 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。