Job ID = 10924609 sra ファイルのダウンロード中... Completed: 407545K bytes transferred in 11 seconds (281437K 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 6841104 spots for /home/okishinya/chipatlas/results/dm3/SRX2396696/SRR5078066.sra Written 6841104 spots for /home/okishinya/chipatlas/results/dm3/SRX2396696/SRR5078066.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: 00:00:01 Multiseed full-index search: 00:07:33 6841104 reads; of these: 6841104 (100.00%) were paired; of these: 2744466 (40.12%) aligned concordantly 0 times 3746345 (54.76%) aligned concordantly exactly 1 time 350293 (5.12%) aligned concordantly >1 times ---- 2744466 pairs aligned concordantly 0 times; of these: 94251 (3.43%) aligned discordantly 1 time ---- 2650215 pairs aligned 0 times concordantly or discordantly; of these: 5300430 mates make up the pairs; of these: 5141733 (97.01%) aligned 0 times 117464 (2.22%) aligned exactly 1 time 41233 (0.78%) aligned >1 times 62.42% overall alignment rate Time searching: 00:07:34 Overall time: 00:07:34 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_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] 1718532 / 4190132 = 0.4101 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 10:35:45: # Command line: callpeak -t SRX2396696.bam -f BAM -g dm -n SRX2396696.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2396696.05 # format = BAM # ChIP-seq file = ['SRX2396696.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 10:35:45: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:35:45: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:35:45: # Command line: callpeak -t SRX2396696.bam -f BAM -g dm -n SRX2396696.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2396696.20 # format = BAM # ChIP-seq file = ['SRX2396696.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 10:35:45: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:35:45: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:35:45: # Command line: callpeak -t SRX2396696.bam -f BAM -g dm -n SRX2396696.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2396696.10 # format = BAM # ChIP-seq file = ['SRX2396696.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 10:35:45: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:35:45: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:35:51: 1000000 INFO @ Mon, 06 Aug 2018 10:35:51: 1000000 INFO @ Mon, 06 Aug 2018 10:35:51: 1000000 INFO @ Mon, 06 Aug 2018 10:35:58: 2000000 INFO @ Mon, 06 Aug 2018 10:35:58: 2000000 INFO @ Mon, 06 Aug 2018 10:35:58: 2000000 INFO @ Mon, 06 Aug 2018 10:36:04: 3000000 INFO @ Mon, 06 Aug 2018 10:36:05: 3000000 INFO @ Mon, 06 Aug 2018 10:36:05: 3000000 INFO @ Mon, 06 Aug 2018 10:36:10: 4000000 INFO @ Mon, 06 Aug 2018 10:36:11: 4000000 INFO @ Mon, 06 Aug 2018 10:36:11: 4000000 INFO @ Mon, 06 Aug 2018 10:36:16: 5000000 INFO @ Mon, 06 Aug 2018 10:36:17: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:36:17: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:36:17: #1 total tags in treatment: 2388779 INFO @ Mon, 06 Aug 2018 10:36:17: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:36:17: #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 10:36:17: #1 tags after filtering in treatment: 2347247 INFO @ Mon, 06 Aug 2018 10:36:17: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 06 Aug 2018 10:36:17: #1 finished! INFO @ Mon, 06 Aug 2018 10:36:17: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:36:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:36:17: 5000000 INFO @ Mon, 06 Aug 2018 10:36:17: 5000000 INFO @ Mon, 06 Aug 2018 10:36:17: #2 number of paired peaks: 3707 INFO @ Mon, 06 Aug 2018 10:36:17: start model_add_line... INFO @ Mon, 06 Aug 2018 10:36:18: start X-correlation... INFO @ Mon, 06 Aug 2018 10:36:18: end of X-cor INFO @ Mon, 06 Aug 2018 10:36:18: #2 finished! INFO @ Mon, 06 Aug 2018 10:36:18: #2 predicted fragment length is 234 bps INFO @ Mon, 06 Aug 2018 10:36:18: #2 alternative fragment length(s) may be 234 bps INFO @ Mon, 06 Aug 2018 10:36:18: #2.2 Generate R script for model : SRX2396696.05_model.r INFO @ Mon, 06 Aug 2018 10:36:18: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:36:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:36:18: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:36:18: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:36:18: #1 total tags in treatment: 2388779 INFO @ Mon, 06 Aug 2018 10:36:18: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:36:18: #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 10:36:18: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:36:18: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:36:18: #1 total tags in treatment: 2388779 INFO @ Mon, 06 Aug 2018 10:36:18: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:36:18: #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 10:36:18: #1 tags after filtering in treatment: 2347247 INFO @ Mon, 06 Aug 2018 10:36:18: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 06 Aug 2018 10:36:18: #1 finished! INFO @ Mon, 06 Aug 2018 10:36:18: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:36:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:36:18: #1 tags after filtering in treatment: 2347247 INFO @ Mon, 06 Aug 2018 10:36:18: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 06 Aug 2018 10:36:18: #1 finished! INFO @ Mon, 06 Aug 2018 10:36:18: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:36:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:36:18: #2 number of paired peaks: 3707 INFO @ Mon, 06 Aug 2018 10:36:18: start model_add_line... INFO @ Mon, 06 Aug 2018 10:36:18: #2 number of paired peaks: 3707 INFO @ Mon, 06 Aug 2018 10:36:18: start model_add_line... INFO @ Mon, 06 Aug 2018 10:36:18: start X-correlation... INFO @ Mon, 06 Aug 2018 10:36:18: end of X-cor INFO @ Mon, 06 Aug 2018 10:36:18: #2 finished! INFO @ Mon, 06 Aug 2018 10:36:18: #2 predicted fragment length is 234 bps INFO @ Mon, 06 Aug 2018 10:36:18: #2 alternative fragment length(s) may be 234 bps INFO @ Mon, 06 Aug 2018 10:36:18: #2.2 Generate R script for model : SRX2396696.20_model.r INFO @ Mon, 06 Aug 2018 10:36:18: start X-correlation... INFO @ Mon, 06 Aug 2018 10:36:18: end of X-cor INFO @ Mon, 06 Aug 2018 10:36:18: #2 finished! INFO @ Mon, 06 Aug 2018 10:36:18: #2 predicted fragment length is 234 bps INFO @ Mon, 06 Aug 2018 10:36:18: #2 alternative fragment length(s) may be 234 bps INFO @ Mon, 06 Aug 2018 10:36:18: #2.2 Generate R script for model : SRX2396696.10_model.r INFO @ Mon, 06 Aug 2018 10:36:18: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:36:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:36:18: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:36:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:36:23: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:36:24: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:36:24: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:36:27: #4 Write output xls file... SRX2396696.05_peaks.xls INFO @ Mon, 06 Aug 2018 10:36:27: #4 Write peak in narrowPeak format file... SRX2396696.05_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:36:27: #4 Write summits bed file... SRX2396696.05_summits.bed INFO @ Mon, 06 Aug 2018 10:36:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3469 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:36:28: #4 Write output xls file... SRX2396696.20_peaks.xls INFO @ Mon, 06 Aug 2018 10:36:28: #4 Write peak in narrowPeak format file... SRX2396696.20_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:36:28: #4 Write summits bed file... SRX2396696.20_summits.bed INFO @ Mon, 06 Aug 2018 10:36:28: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (213 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:36:28: #4 Write output xls file... SRX2396696.10_peaks.xls INFO @ Mon, 06 Aug 2018 10:36:28: #4 Write peak in narrowPeak format file... SRX2396696.10_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:36:28: #4 Write summits bed file... SRX2396696.10_summits.bed INFO @ Mon, 06 Aug 2018 10:36:28: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1330 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。