Job ID = 11293720 sra ファイルのダウンロード中... Completed: 294034K bytes transferred in 5 seconds (466486K 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 3655173 spots for /home/okishinya/chipatlas/results/dm3/SRX4940251/SRR8113884.sra Written 3655173 spots for /home/okishinya/chipatlas/results/dm3/SRX4940251/SRR8113884.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: 00:06:48 3655173 reads; of these: 3655173 (100.00%) were paired; of these: 711216 (19.46%) aligned concordantly 0 times 2518728 (68.91%) aligned concordantly exactly 1 time 425229 (11.63%) aligned concordantly >1 times ---- 711216 pairs aligned concordantly 0 times; of these: 165659 (23.29%) aligned discordantly 1 time ---- 545557 pairs aligned 0 times concordantly or discordantly; of these: 1091114 mates make up the pairs; of these: 932036 (85.42%) aligned 0 times 88407 (8.10%) aligned exactly 1 time 70671 (6.48%) aligned >1 times 87.25% overall alignment rate Time searching: 00:06:48 Overall time: 00:06:48 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] 181738 / 3096520 = 0.0587 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 17:58:35: # Command line: callpeak -t SRX4940251.bam -f BAM -g dm -n SRX4940251.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4940251.20 # format = BAM # ChIP-seq file = ['SRX4940251.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 17:58:35: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:58:35: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:58:35: # Command line: callpeak -t SRX4940251.bam -f BAM -g dm -n SRX4940251.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4940251.05 # format = BAM # ChIP-seq file = ['SRX4940251.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 17:58:35: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:58:35: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:58:35: # Command line: callpeak -t SRX4940251.bam -f BAM -g dm -n SRX4940251.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4940251.10 # format = BAM # ChIP-seq file = ['SRX4940251.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 17:58:35: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:58:35: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:58:42: 1000000 INFO @ Sun, 04 Nov 2018 17:58:42: 1000000 INFO @ Sun, 04 Nov 2018 17:58:42: 1000000 INFO @ Sun, 04 Nov 2018 17:58:48: 2000000 INFO @ Sun, 04 Nov 2018 17:58:48: 2000000 INFO @ Sun, 04 Nov 2018 17:58:48: 2000000 INFO @ Sun, 04 Nov 2018 17:58:54: 3000000 INFO @ Sun, 04 Nov 2018 17:58:55: 3000000 INFO @ Sun, 04 Nov 2018 17:58:55: 3000000 INFO @ Sun, 04 Nov 2018 17:59:00: 4000000 INFO @ Sun, 04 Nov 2018 17:59:01: 4000000 INFO @ Sun, 04 Nov 2018 17:59:01: 4000000 INFO @ Sun, 04 Nov 2018 17:59:07: 5000000 INFO @ Sun, 04 Nov 2018 17:59:07: 5000000 INFO @ Sun, 04 Nov 2018 17:59:07: 5000000 INFO @ Sun, 04 Nov 2018 17:59:13: 6000000 INFO @ Sun, 04 Nov 2018 17:59:13: #1 tag size is determined as 75 bps INFO @ Sun, 04 Nov 2018 17:59:13: #1 tag size = 75 INFO @ Sun, 04 Nov 2018 17:59:13: #1 total tags in treatment: 2765193 INFO @ Sun, 04 Nov 2018 17:59:13: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:59:13: #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 17:59:13: #1 tags after filtering in treatment: 2631353 INFO @ Sun, 04 Nov 2018 17:59:13: #1 Redundant rate of treatment: 0.05 INFO @ Sun, 04 Nov 2018 17:59:13: #1 finished! INFO @ Sun, 04 Nov 2018 17:59:13: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:59:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:59:13: #2 number of paired peaks: 2139 INFO @ Sun, 04 Nov 2018 17:59:13: start model_add_line... INFO @ Sun, 04 Nov 2018 17:59:13: start X-correlation... INFO @ Sun, 04 Nov 2018 17:59:13: end of X-cor INFO @ Sun, 04 Nov 2018 17:59:13: #2 finished! INFO @ Sun, 04 Nov 2018 17:59:13: #2 predicted fragment length is 262 bps INFO @ Sun, 04 Nov 2018 17:59:13: #2 alternative fragment length(s) may be 262 bps INFO @ Sun, 04 Nov 2018 17:59:13: #2.2 Generate R script for model : SRX4940251.10_model.r INFO @ Sun, 04 Nov 2018 17:59:13: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:59:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:59:14: 6000000 INFO @ Sun, 04 Nov 2018 17:59:14: 6000000 INFO @ Sun, 04 Nov 2018 17:59:14: #1 tag size is determined as 75 bps INFO @ Sun, 04 Nov 2018 17:59:14: #1 tag size = 75 INFO @ Sun, 04 Nov 2018 17:59:14: #1 total tags in treatment: 2765193 INFO @ Sun, 04 Nov 2018 17:59:14: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:59:14: #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 17:59:14: #1 tag size is determined as 75 bps INFO @ Sun, 04 Nov 2018 17:59:14: #1 tag size = 75 INFO @ Sun, 04 Nov 2018 17:59:14: #1 total tags in treatment: 2765193 INFO @ Sun, 04 Nov 2018 17:59:14: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:59:14: #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 17:59:14: #1 tags after filtering in treatment: 2631353 INFO @ Sun, 04 Nov 2018 17:59:14: #1 Redundant rate of treatment: 0.05 INFO @ Sun, 04 Nov 2018 17:59:14: #1 finished! INFO @ Sun, 04 Nov 2018 17:59:14: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:59:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:59:14: #1 tags after filtering in treatment: 2631353 INFO @ Sun, 04 Nov 2018 17:59:14: #1 Redundant rate of treatment: 0.05 INFO @ Sun, 04 Nov 2018 17:59:14: #1 finished! INFO @ Sun, 04 Nov 2018 17:59:14: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:59:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:59:14: #2 number of paired peaks: 2139 INFO @ Sun, 04 Nov 2018 17:59:14: start model_add_line... INFO @ Sun, 04 Nov 2018 17:59:14: #2 number of paired peaks: 2139 INFO @ Sun, 04 Nov 2018 17:59:14: start model_add_line... INFO @ Sun, 04 Nov 2018 17:59:14: start X-correlation... INFO @ Sun, 04 Nov 2018 17:59:14: end of X-cor INFO @ Sun, 04 Nov 2018 17:59:14: #2 finished! INFO @ Sun, 04 Nov 2018 17:59:14: #2 predicted fragment length is 262 bps INFO @ Sun, 04 Nov 2018 17:59:14: #2 alternative fragment length(s) may be 262 bps INFO @ Sun, 04 Nov 2018 17:59:14: #2.2 Generate R script for model : SRX4940251.20_model.r INFO @ Sun, 04 Nov 2018 17:59:14: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:59:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:59:14: start X-correlation... INFO @ Sun, 04 Nov 2018 17:59:14: end of X-cor INFO @ Sun, 04 Nov 2018 17:59:14: #2 finished! INFO @ Sun, 04 Nov 2018 17:59:14: #2 predicted fragment length is 262 bps INFO @ Sun, 04 Nov 2018 17:59:14: #2 alternative fragment length(s) may be 262 bps INFO @ Sun, 04 Nov 2018 17:59:14: #2.2 Generate R script for model : SRX4940251.05_model.r INFO @ Sun, 04 Nov 2018 17:59:14: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:59:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:59:20: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:59:20: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:59:21: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:59:23: #4 Write output xls file... SRX4940251.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:59:23: #4 Write peak in narrowPeak format file... SRX4940251.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:59:23: #4 Write summits bed file... SRX4940251.10_summits.bed INFO @ Sun, 04 Nov 2018 17:59:23: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (824 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:59:24: #4 Write output xls file... SRX4940251.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:59:24: #4 Write peak in narrowPeak format file... SRX4940251.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:59:24: #4 Write summits bed file... SRX4940251.05_summits.bed INFO @ Sun, 04 Nov 2018 17:59:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3320 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:59:24: #4 Write output xls file... SRX4940251.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:59:24: #4 Write peak in narrowPeak format file... SRX4940251.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:59:24: #4 Write summits bed file... SRX4940251.20_summits.bed INFO @ Sun, 04 Nov 2018 17:59:24: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (36 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。