Job ID = 11293685 sra ファイルのダウンロード中... Completed: 620766K bytes transferred in 27 seconds (182379K 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 18364945 spots for /home/okishinya/chipatlas/results/dm3/SRX4375847/SRR7506501.sra Written 18364945 spots for /home/okishinya/chipatlas/results/dm3/SRX4375847/SRR7506501.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: 00:04:38 18364945 reads; of these: 18364945 (100.00%) were unpaired; of these: 4358836 (23.73%) aligned 0 times 11394002 (62.04%) aligned exactly 1 time 2612107 (14.22%) aligned >1 times 76.27% overall alignment rate Time searching: 00:04:38 Overall time: 00:04:38 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 8 files... [bam_rmdupse_core] 3473032 / 14006109 = 0.2480 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, 04 Nov 2018 17:56:57: # Command line: callpeak -t SRX4375847.bam -f BAM -g dm -n SRX4375847.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4375847.20 # format = BAM # ChIP-seq file = ['SRX4375847.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, 04 Nov 2018 17:56:57: # Command line: callpeak -t SRX4375847.bam -f BAM -g dm -n SRX4375847.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4375847.05 # format = BAM # ChIP-seq file = ['SRX4375847.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, 04 Nov 2018 17:56:57: # Command line: callpeak -t SRX4375847.bam -f BAM -g dm -n SRX4375847.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4375847.10 # format = BAM # ChIP-seq file = ['SRX4375847.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, 04 Nov 2018 17:56:57: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:56:57: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:56:57: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:56:57: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:56:57: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:56:57: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:57:04: 1000000 INFO @ Sun, 04 Nov 2018 17:57:05: 1000000 INFO @ Sun, 04 Nov 2018 17:57:05: 1000000 INFO @ Sun, 04 Nov 2018 17:57:11: 2000000 INFO @ Sun, 04 Nov 2018 17:57:12: 2000000 INFO @ Sun, 04 Nov 2018 17:57:12: 2000000 INFO @ Sun, 04 Nov 2018 17:57:18: 3000000 INFO @ Sun, 04 Nov 2018 17:57:19: 3000000 INFO @ Sun, 04 Nov 2018 17:57:19: 3000000 INFO @ Sun, 04 Nov 2018 17:57:25: 4000000 INFO @ Sun, 04 Nov 2018 17:57:26: 4000000 INFO @ Sun, 04 Nov 2018 17:57:27: 4000000 INFO @ Sun, 04 Nov 2018 17:57:32: 5000000 INFO @ Sun, 04 Nov 2018 17:57:34: 5000000 INFO @ Sun, 04 Nov 2018 17:57:34: 5000000 INFO @ Sun, 04 Nov 2018 17:57:39: 6000000 INFO @ Sun, 04 Nov 2018 17:57:41: 6000000 INFO @ Sun, 04 Nov 2018 17:57:41: 6000000 INFO @ Sun, 04 Nov 2018 17:57:46: 7000000 INFO @ Sun, 04 Nov 2018 17:57:48: 7000000 INFO @ Sun, 04 Nov 2018 17:57:49: 7000000 INFO @ Sun, 04 Nov 2018 17:57:53: 8000000 INFO @ Sun, 04 Nov 2018 17:57:56: 8000000 INFO @ Sun, 04 Nov 2018 17:57:57: 8000000 INFO @ Sun, 04 Nov 2018 17:58:00: 9000000 INFO @ Sun, 04 Nov 2018 17:58:03: 9000000 INFO @ Sun, 04 Nov 2018 17:58:04: 9000000 INFO @ Sun, 04 Nov 2018 17:58:07: 10000000 INFO @ Sun, 04 Nov 2018 17:58:11: 10000000 INFO @ Sun, 04 Nov 2018 17:58:11: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:58:11: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:58:11: #1 total tags in treatment: 10533077 INFO @ Sun, 04 Nov 2018 17:58:11: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:58:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:58:11: #1 tags after filtering in treatment: 10533077 INFO @ Sun, 04 Nov 2018 17:58:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:58:11: #1 finished! INFO @ Sun, 04 Nov 2018 17:58:11: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:58:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:58:12: 10000000 INFO @ Sun, 04 Nov 2018 17:58:13: #2 number of paired peaks: 7101 INFO @ Sun, 04 Nov 2018 17:58:13: start model_add_line... INFO @ Sun, 04 Nov 2018 17:58:13: start X-correlation... INFO @ Sun, 04 Nov 2018 17:58:13: end of X-cor INFO @ Sun, 04 Nov 2018 17:58:13: #2 finished! INFO @ Sun, 04 Nov 2018 17:58:13: #2 predicted fragment length is 189 bps INFO @ Sun, 04 Nov 2018 17:58:13: #2 alternative fragment length(s) may be 189 bps INFO @ Sun, 04 Nov 2018 17:58:13: #2.2 Generate R script for model : SRX4375847.20_model.r INFO @ Sun, 04 Nov 2018 17:58:13: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:58:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:58:15: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:58:15: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:58:15: #1 total tags in treatment: 10533077 INFO @ Sun, 04 Nov 2018 17:58:15: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:58:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:58:15: #1 tags after filtering in treatment: 10533077 INFO @ Sun, 04 Nov 2018 17:58:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:58:15: #1 finished! INFO @ Sun, 04 Nov 2018 17:58:15: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:58:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:58:16: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:58:16: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:58:16: #1 total tags in treatment: 10533077 INFO @ Sun, 04 Nov 2018 17:58:16: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:58:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:58:16: #1 tags after filtering in treatment: 10533077 INFO @ Sun, 04 Nov 2018 17:58:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:58:16: #1 finished! INFO @ Sun, 04 Nov 2018 17:58:16: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:58:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:58:16: #2 number of paired peaks: 7101 INFO @ Sun, 04 Nov 2018 17:58:16: start model_add_line... INFO @ Sun, 04 Nov 2018 17:58:17: start X-correlation... INFO @ Sun, 04 Nov 2018 17:58:17: end of X-cor INFO @ Sun, 04 Nov 2018 17:58:17: #2 finished! INFO @ Sun, 04 Nov 2018 17:58:17: #2 predicted fragment length is 189 bps INFO @ Sun, 04 Nov 2018 17:58:17: #2 alternative fragment length(s) may be 189 bps INFO @ Sun, 04 Nov 2018 17:58:17: #2.2 Generate R script for model : SRX4375847.10_model.r INFO @ Sun, 04 Nov 2018 17:58:17: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:58:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:58:17: #2 number of paired peaks: 7101 INFO @ Sun, 04 Nov 2018 17:58:17: start model_add_line... INFO @ Sun, 04 Nov 2018 17:58:18: start X-correlation... INFO @ Sun, 04 Nov 2018 17:58:18: end of X-cor INFO @ Sun, 04 Nov 2018 17:58:18: #2 finished! INFO @ Sun, 04 Nov 2018 17:58:18: #2 predicted fragment length is 189 bps INFO @ Sun, 04 Nov 2018 17:58:18: #2 alternative fragment length(s) may be 189 bps INFO @ Sun, 04 Nov 2018 17:58:18: #2.2 Generate R script for model : SRX4375847.05_model.r INFO @ Sun, 04 Nov 2018 17:58:18: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:58:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:58:48: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:58:53: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:58:54: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:59:03: #4 Write output xls file... SRX4375847.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:59:03: #4 Write peak in narrowPeak format file... SRX4375847.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:59:03: #4 Write summits bed file... SRX4375847.20_summits.bed INFO @ Sun, 04 Nov 2018 17:59:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5428 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:59:08: #4 Write output xls file... SRX4375847.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:59:08: #4 Write peak in narrowPeak format file... SRX4375847.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:59:08: #4 Write summits bed file... SRX4375847.10_summits.bed INFO @ Sun, 04 Nov 2018 17:59:08: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8086 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:59:09: #4 Write output xls file... SRX4375847.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:59:09: #4 Write peak in narrowPeak format file... SRX4375847.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:59:09: #4 Write summits bed file... SRX4375847.05_summits.bed INFO @ Sun, 04 Nov 2018 17:59:09: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (10888 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。