Job ID = 10924612 sra ファイルのダウンロード中... Completed: 485807K bytes transferred in 12 seconds (311356K 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: PAIRED fastq に変換中... Read 8188577 spots for /home/okishinya/chipatlas/results/dm3/SRX2396699/SRR5078069.sra Written 8188577 spots for /home/okishinya/chipatlas/results/dm3/SRX2396699/SRR5078069.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:11 8188577 reads; of these: 8188577 (100.00%) were paired; of these: 655822 (8.01%) aligned concordantly 0 times 7047545 (86.07%) aligned concordantly exactly 1 time 485210 (5.93%) aligned concordantly >1 times ---- 655822 pairs aligned concordantly 0 times; of these: 135849 (20.71%) aligned discordantly 1 time ---- 519973 pairs aligned 0 times concordantly or discordantly; of these: 1039946 mates make up the pairs; of these: 841454 (80.91%) aligned 0 times 149933 (14.42%) aligned exactly 1 time 48559 (4.67%) aligned >1 times 94.86% overall alignment rate Time searching: 00:09:12 Overall time: 00:09:12 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 87951 / 7665728 = 0.0115 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 @ Mon, 06 Aug 2018 10:40:26: # Command line: callpeak -t SRX2396699.bam -f BAM -g dm -n SRX2396699.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2396699.05 # format = BAM # ChIP-seq file = ['SRX2396699.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 @ Mon, 06 Aug 2018 10:40:26: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:40:26: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:40:26: # Command line: callpeak -t SRX2396699.bam -f BAM -g dm -n SRX2396699.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2396699.10 # format = BAM # ChIP-seq file = ['SRX2396699.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 @ Mon, 06 Aug 2018 10:40:26: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:40:26: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:40:26: # Command line: callpeak -t SRX2396699.bam -f BAM -g dm -n SRX2396699.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2396699.20 # format = BAM # ChIP-seq file = ['SRX2396699.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 @ Mon, 06 Aug 2018 10:40:26: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:40:26: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:40:32: 1000000 INFO @ Mon, 06 Aug 2018 10:40:32: 1000000 INFO @ Mon, 06 Aug 2018 10:40:32: 1000000 INFO @ Mon, 06 Aug 2018 10:40:37: 2000000 INFO @ Mon, 06 Aug 2018 10:40:37: 2000000 INFO @ Mon, 06 Aug 2018 10:40:37: 2000000 INFO @ Mon, 06 Aug 2018 10:40:43: 3000000 INFO @ Mon, 06 Aug 2018 10:40:43: 3000000 INFO @ Mon, 06 Aug 2018 10:40:43: 3000000 INFO @ Mon, 06 Aug 2018 10:40:48: 4000000 INFO @ Mon, 06 Aug 2018 10:40:48: 4000000 INFO @ Mon, 06 Aug 2018 10:40:49: 4000000 INFO @ Mon, 06 Aug 2018 10:40:54: 5000000 INFO @ Mon, 06 Aug 2018 10:40:54: 5000000 INFO @ Mon, 06 Aug 2018 10:40:54: 5000000 INFO @ Mon, 06 Aug 2018 10:40:59: 6000000 INFO @ Mon, 06 Aug 2018 10:41:00: 6000000 INFO @ Mon, 06 Aug 2018 10:41:00: 6000000 INFO @ Mon, 06 Aug 2018 10:41:05: 7000000 INFO @ Mon, 06 Aug 2018 10:41:05: 7000000 INFO @ Mon, 06 Aug 2018 10:41:05: 7000000 INFO @ Mon, 06 Aug 2018 10:41:10: 8000000 INFO @ Mon, 06 Aug 2018 10:41:11: 8000000 INFO @ Mon, 06 Aug 2018 10:41:11: 8000000 INFO @ Mon, 06 Aug 2018 10:41:16: 9000000 INFO @ Mon, 06 Aug 2018 10:41:17: 9000000 INFO @ Mon, 06 Aug 2018 10:41:17: 9000000 INFO @ Mon, 06 Aug 2018 10:41:22: 10000000 INFO @ Mon, 06 Aug 2018 10:41:22: 10000000 INFO @ Mon, 06 Aug 2018 10:41:23: 10000000 INFO @ Mon, 06 Aug 2018 10:41:27: 11000000 INFO @ Mon, 06 Aug 2018 10:41:28: 11000000 INFO @ Mon, 06 Aug 2018 10:41:28: 11000000 INFO @ Mon, 06 Aug 2018 10:41:33: 12000000 INFO @ Mon, 06 Aug 2018 10:41:33: 12000000 INFO @ Mon, 06 Aug 2018 10:41:34: 12000000 INFO @ Mon, 06 Aug 2018 10:41:38: 13000000 INFO @ Mon, 06 Aug 2018 10:41:39: 13000000 INFO @ Mon, 06 Aug 2018 10:41:40: 13000000 INFO @ Mon, 06 Aug 2018 10:41:44: 14000000 INFO @ Mon, 06 Aug 2018 10:41:44: 14000000 INFO @ Mon, 06 Aug 2018 10:41:45: 14000000 INFO @ Mon, 06 Aug 2018 10:41:50: 15000000 INFO @ Mon, 06 Aug 2018 10:41:50: 15000000 INFO @ Mon, 06 Aug 2018 10:41:51: 15000000 INFO @ Mon, 06 Aug 2018 10:41:52: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:41:52: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:41:52: #1 total tags in treatment: 7445455 INFO @ Mon, 06 Aug 2018 10:41:52: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:41:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:41:52: #1 tags after filtering in treatment: 7071767 INFO @ Mon, 06 Aug 2018 10:41:52: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 06 Aug 2018 10:41:52: #1 finished! INFO @ Mon, 06 Aug 2018 10:41:52: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:41:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:41:52: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:41:52: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:41:52: #1 total tags in treatment: 7445455 INFO @ Mon, 06 Aug 2018 10:41:52: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:41:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:41:52: #1 tags after filtering in treatment: 7071767 INFO @ Mon, 06 Aug 2018 10:41:52: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 06 Aug 2018 10:41:52: #1 finished! INFO @ Mon, 06 Aug 2018 10:41:52: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:41:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:41:53: #2 number of paired peaks: 3102 INFO @ Mon, 06 Aug 2018 10:41:53: start model_add_line... INFO @ Mon, 06 Aug 2018 10:41:53: start X-correlation... INFO @ Mon, 06 Aug 2018 10:41:53: end of X-cor INFO @ Mon, 06 Aug 2018 10:41:53: #2 finished! INFO @ Mon, 06 Aug 2018 10:41:53: #2 predicted fragment length is 187 bps INFO @ Mon, 06 Aug 2018 10:41:53: #2 alternative fragment length(s) may be 187 bps INFO @ Mon, 06 Aug 2018 10:41:53: #2.2 Generate R script for model : SRX2396699.10_model.r INFO @ Mon, 06 Aug 2018 10:41:53: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:41:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:41:53: #2 number of paired peaks: 3102 INFO @ Mon, 06 Aug 2018 10:41:53: start model_add_line... INFO @ Mon, 06 Aug 2018 10:41:53: start X-correlation... INFO @ Mon, 06 Aug 2018 10:41:53: end of X-cor INFO @ Mon, 06 Aug 2018 10:41:53: #2 finished! INFO @ Mon, 06 Aug 2018 10:41:53: #2 predicted fragment length is 187 bps INFO @ Mon, 06 Aug 2018 10:41:53: #2 alternative fragment length(s) may be 187 bps INFO @ Mon, 06 Aug 2018 10:41:53: #2.2 Generate R script for model : SRX2396699.20_model.r INFO @ Mon, 06 Aug 2018 10:41:53: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:41:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:41:53: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:41:53: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:41:53: #1 total tags in treatment: 7445455 INFO @ Mon, 06 Aug 2018 10:41:53: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:41:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:41:53: #1 tags after filtering in treatment: 7071767 INFO @ Mon, 06 Aug 2018 10:41:53: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 06 Aug 2018 10:41:53: #1 finished! INFO @ Mon, 06 Aug 2018 10:41:53: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:41:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:41:54: #2 number of paired peaks: 3102 INFO @ Mon, 06 Aug 2018 10:41:54: start model_add_line... INFO @ Mon, 06 Aug 2018 10:41:54: start X-correlation... INFO @ Mon, 06 Aug 2018 10:41:54: end of X-cor INFO @ Mon, 06 Aug 2018 10:41:54: #2 finished! INFO @ Mon, 06 Aug 2018 10:41:54: #2 predicted fragment length is 187 bps INFO @ Mon, 06 Aug 2018 10:41:54: #2 alternative fragment length(s) may be 187 bps INFO @ Mon, 06 Aug 2018 10:41:54: #2.2 Generate R script for model : SRX2396699.05_model.r INFO @ Mon, 06 Aug 2018 10:41:54: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:41:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:42:12: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:42:12: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:42:14: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:42:22: #4 Write output xls file... SRX2396699.10_peaks.xls INFO @ Mon, 06 Aug 2018 10:42:22: #4 Write peak in narrowPeak format file... SRX2396699.10_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:42:22: #4 Write summits bed file... SRX2396699.10_summits.bed INFO @ Mon, 06 Aug 2018 10:42:22: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (3179 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:42:23: #4 Write output xls file... SRX2396699.20_peaks.xls INFO @ Mon, 06 Aug 2018 10:42:23: #4 Write peak in narrowPeak format file... SRX2396699.20_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:42:23: #4 Write summits bed file... SRX2396699.20_summits.bed INFO @ Mon, 06 Aug 2018 10:42:23: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (913 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:42:23: #4 Write output xls file... SRX2396699.05_peaks.xls INFO @ Mon, 06 Aug 2018 10:42:24: #4 Write peak in narrowPeak format file... SRX2396699.05_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:42:24: #4 Write summits bed file... SRX2396699.05_summits.bed INFO @ Mon, 06 Aug 2018 10:42:24: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6358 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。