Job ID = 11597979 sra ファイルのダウンロード中... Completed: 411379K bytes transferred in 5 seconds (582341K 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 18255858 spots for /home/okishinya/chipatlas/results/dm3/SRX4664646/SRR7813073.sra Written 18255858 spots for /home/okishinya/chipatlas/results/dm3/SRX4664646/SRR7813073.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: 00:07:16 18255858 reads; of these: 18255858 (100.00%) were unpaired; of these: 532447 (2.92%) aligned 0 times 13117380 (71.85%) aligned exactly 1 time 4606031 (25.23%) aligned >1 times 97.08% overall alignment rate Time searching: 00:07:16 Overall time: 00:07:16 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] 4219101 / 17723411 = 0.2381 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 @ Wed, 30 Jan 2019 18:37:45: # Command line: callpeak -t SRX4664646.bam -f BAM -g dm -n SRX4664646.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664646.05 # format = BAM # ChIP-seq file = ['SRX4664646.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 @ Wed, 30 Jan 2019 18:37:45: #1 read tag files... INFO @ Wed, 30 Jan 2019 18:37:45: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 18:37:45: # Command line: callpeak -t SRX4664646.bam -f BAM -g dm -n SRX4664646.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664646.20 # format = BAM # ChIP-seq file = ['SRX4664646.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 @ Wed, 30 Jan 2019 18:37:45: #1 read tag files... INFO @ Wed, 30 Jan 2019 18:37:45: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 18:37:45: # Command line: callpeak -t SRX4664646.bam -f BAM -g dm -n SRX4664646.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664646.10 # format = BAM # ChIP-seq file = ['SRX4664646.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 @ Wed, 30 Jan 2019 18:37:45: #1 read tag files... INFO @ Wed, 30 Jan 2019 18:37:45: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 18:37:52: 1000000 INFO @ Wed, 30 Jan 2019 18:37:52: 1000000 INFO @ Wed, 30 Jan 2019 18:37:52: 1000000 INFO @ Wed, 30 Jan 2019 18:37:59: 2000000 INFO @ Wed, 30 Jan 2019 18:37:59: 2000000 INFO @ Wed, 30 Jan 2019 18:37:59: 2000000 INFO @ Wed, 30 Jan 2019 18:38:06: 3000000 INFO @ Wed, 30 Jan 2019 18:38:06: 3000000 INFO @ Wed, 30 Jan 2019 18:38:06: 3000000 INFO @ Wed, 30 Jan 2019 18:38:13: 4000000 INFO @ Wed, 30 Jan 2019 18:38:13: 4000000 INFO @ Wed, 30 Jan 2019 18:38:13: 4000000 INFO @ Wed, 30 Jan 2019 18:38:20: 5000000 INFO @ Wed, 30 Jan 2019 18:38:20: 5000000 INFO @ Wed, 30 Jan 2019 18:38:20: 5000000 INFO @ Wed, 30 Jan 2019 18:38:27: 6000000 INFO @ Wed, 30 Jan 2019 18:38:27: 6000000 INFO @ Wed, 30 Jan 2019 18:38:27: 6000000 INFO @ Wed, 30 Jan 2019 18:38:34: 7000000 INFO @ Wed, 30 Jan 2019 18:38:34: 7000000 INFO @ Wed, 30 Jan 2019 18:38:34: 7000000 INFO @ Wed, 30 Jan 2019 18:38:41: 8000000 INFO @ Wed, 30 Jan 2019 18:38:41: 8000000 INFO @ Wed, 30 Jan 2019 18:38:41: 8000000 INFO @ Wed, 30 Jan 2019 18:38:47: 9000000 INFO @ Wed, 30 Jan 2019 18:38:48: 9000000 INFO @ Wed, 30 Jan 2019 18:38:48: 9000000 INFO @ Wed, 30 Jan 2019 18:38:54: 10000000 INFO @ Wed, 30 Jan 2019 18:38:55: 10000000 INFO @ Wed, 30 Jan 2019 18:38:55: 10000000 INFO @ Wed, 30 Jan 2019 18:39:01: 11000000 INFO @ Wed, 30 Jan 2019 18:39:02: 11000000 INFO @ Wed, 30 Jan 2019 18:39:02: 11000000 INFO @ Wed, 30 Jan 2019 18:39:08: 12000000 INFO @ Wed, 30 Jan 2019 18:39:09: 12000000 INFO @ Wed, 30 Jan 2019 18:39:09: 12000000 INFO @ Wed, 30 Jan 2019 18:39:15: 13000000 INFO @ Wed, 30 Jan 2019 18:39:16: 13000000 INFO @ Wed, 30 Jan 2019 18:39:16: 13000000 INFO @ Wed, 30 Jan 2019 18:39:19: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 18:39:19: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 18:39:19: #1 total tags in treatment: 13504310 INFO @ Wed, 30 Jan 2019 18:39:19: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 18:39:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 18:39:19: #1 tags after filtering in treatment: 13504310 INFO @ Wed, 30 Jan 2019 18:39:19: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 18:39:19: #1 finished! INFO @ Wed, 30 Jan 2019 18:39:19: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 18:39:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 18:39:19: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 18:39:19: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 18:39:19: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 18:39:19: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 18:39:19: #1 total tags in treatment: 13504310 INFO @ Wed, 30 Jan 2019 18:39:19: #1 total tags in treatment: 13504310 INFO @ Wed, 30 Jan 2019 18:39:19: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 18:39:19: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 18:39:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 18:39:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 18:39:19: #1 tags after filtering in treatment: 13504310 INFO @ Wed, 30 Jan 2019 18:39:19: #1 tags after filtering in treatment: 13504310 INFO @ Wed, 30 Jan 2019 18:39:19: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 18:39:19: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 18:39:19: #1 finished! INFO @ Wed, 30 Jan 2019 18:39:19: #1 finished! INFO @ Wed, 30 Jan 2019 18:39:19: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 18:39:19: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 18:39:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 18:39:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 18:39:20: #2 number of paired peaks: 2778 INFO @ Wed, 30 Jan 2019 18:39:20: start model_add_line... INFO @ Wed, 30 Jan 2019 18:39:20: start X-correlation... INFO @ Wed, 30 Jan 2019 18:39:20: end of X-cor INFO @ Wed, 30 Jan 2019 18:39:20: #2 finished! INFO @ Wed, 30 Jan 2019 18:39:20: #2 predicted fragment length is 128 bps INFO @ Wed, 30 Jan 2019 18:39:20: #2 alternative fragment length(s) may be 128 bps INFO @ Wed, 30 Jan 2019 18:39:20: #2.2 Generate R script for model : SRX4664646.10_model.r INFO @ Wed, 30 Jan 2019 18:39:20: #3 Call peaks... INFO @ Wed, 30 Jan 2019 18:39:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 18:39:21: #2 number of paired peaks: 2778 INFO @ Wed, 30 Jan 2019 18:39:21: start model_add_line... INFO @ Wed, 30 Jan 2019 18:39:21: #2 number of paired peaks: 2778 INFO @ Wed, 30 Jan 2019 18:39:21: start model_add_line... INFO @ Wed, 30 Jan 2019 18:39:21: start X-correlation... INFO @ Wed, 30 Jan 2019 18:39:21: end of X-cor INFO @ Wed, 30 Jan 2019 18:39:21: #2 finished! INFO @ Wed, 30 Jan 2019 18:39:21: #2 predicted fragment length is 128 bps INFO @ Wed, 30 Jan 2019 18:39:21: #2 alternative fragment length(s) may be 128 bps INFO @ Wed, 30 Jan 2019 18:39:21: #2.2 Generate R script for model : SRX4664646.05_model.r INFO @ Wed, 30 Jan 2019 18:39:21: #3 Call peaks... INFO @ Wed, 30 Jan 2019 18:39:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 18:39:21: start X-correlation... INFO @ Wed, 30 Jan 2019 18:39:21: end of X-cor INFO @ Wed, 30 Jan 2019 18:39:21: #2 finished! INFO @ Wed, 30 Jan 2019 18:39:21: #2 predicted fragment length is 128 bps INFO @ Wed, 30 Jan 2019 18:39:21: #2 alternative fragment length(s) may be 128 bps INFO @ Wed, 30 Jan 2019 18:39:21: #2.2 Generate R script for model : SRX4664646.20_model.r INFO @ Wed, 30 Jan 2019 18:39:21: #3 Call peaks... INFO @ Wed, 30 Jan 2019 18:39:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 18:39:53: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 18:39:55: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 18:39:56: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 18:40:11: #4 Write output xls file... SRX4664646.10_peaks.xls INFO @ Wed, 30 Jan 2019 18:40:11: #4 Write peak in narrowPeak format file... SRX4664646.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 18:40:12: #4 Write summits bed file... SRX4664646.10_summits.bed INFO @ Wed, 30 Jan 2019 18:40:12: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9865 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 18:40:13: #4 Write output xls file... SRX4664646.20_peaks.xls INFO @ Wed, 30 Jan 2019 18:40:13: #4 Write peak in narrowPeak format file... SRX4664646.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 18:40:13: #4 Write summits bed file... SRX4664646.20_summits.bed INFO @ Wed, 30 Jan 2019 18:40:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6815 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 18:40:14: #4 Write output xls file... SRX4664646.05_peaks.xls INFO @ Wed, 30 Jan 2019 18:40:15: #4 Write peak in narrowPeak format file... SRX4664646.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 18:40:15: #4 Write summits bed file... SRX4664646.05_summits.bed INFO @ Wed, 30 Jan 2019 18:40:15: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12758 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。