Job ID = 11158496 sra ファイルのダウンロード中... Completed: 2044626K bytes transferred in 42 seconds (397607K 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 31766288 spots for /home/okishinya/chipatlas/results/dm3/SRX4279679/SRR7408123.sra Written 31766288 spots for /home/okishinya/chipatlas/results/dm3/SRX4279679/SRR7408123.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: 02:21:35 31766288 reads; of these: 31766288 (100.00%) were paired; of these: 10748453 (33.84%) aligned concordantly 0 times 16560665 (52.13%) aligned concordantly exactly 1 time 4457170 (14.03%) aligned concordantly >1 times ---- 10748453 pairs aligned concordantly 0 times; of these: 14758 (0.14%) aligned discordantly 1 time ---- 10733695 pairs aligned 0 times concordantly or discordantly; of these: 21467390 mates make up the pairs; of these: 18643115 (86.84%) aligned 0 times 783764 (3.65%) aligned exactly 1 time 2040511 (9.51%) aligned >1 times 70.66% overall alignment rate Time searching: 02:21:35 Overall time: 02:21:35 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 20 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] 17119250 / 20995642 = 0.8154 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 @ Tue, 04 Sep 2018 12:12:57: # Command line: callpeak -t SRX4279679.bam -f BAM -g dm -n SRX4279679.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4279679.05 # format = BAM # ChIP-seq file = ['SRX4279679.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 @ Tue, 04 Sep 2018 12:12:57: # Command line: callpeak -t SRX4279679.bam -f BAM -g dm -n SRX4279679.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4279679.10 # format = BAM # ChIP-seq file = ['SRX4279679.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 @ Tue, 04 Sep 2018 12:12:57: # Command line: callpeak -t SRX4279679.bam -f BAM -g dm -n SRX4279679.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4279679.20 # format = BAM # ChIP-seq file = ['SRX4279679.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 @ Tue, 04 Sep 2018 12:12:57: #1 read tag files... INFO @ Tue, 04 Sep 2018 12:12:57: #1 read tag files... INFO @ Tue, 04 Sep 2018 12:12:57: #1 read tag files... INFO @ Tue, 04 Sep 2018 12:12:57: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 12:12:57: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 12:12:57: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 12:13:03: 1000000 INFO @ Tue, 04 Sep 2018 12:13:03: 1000000 INFO @ Tue, 04 Sep 2018 12:13:04: 1000000 INFO @ Tue, 04 Sep 2018 12:13:10: 2000000 INFO @ Tue, 04 Sep 2018 12:13:10: 2000000 INFO @ Tue, 04 Sep 2018 12:13:11: 2000000 INFO @ Tue, 04 Sep 2018 12:13:16: 3000000 INFO @ Tue, 04 Sep 2018 12:13:16: 3000000 INFO @ Tue, 04 Sep 2018 12:13:18: 3000000 INFO @ Tue, 04 Sep 2018 12:13:23: 4000000 INFO @ Tue, 04 Sep 2018 12:13:23: 4000000 INFO @ Tue, 04 Sep 2018 12:13:26: 4000000 INFO @ Tue, 04 Sep 2018 12:13:29: 5000000 INFO @ Tue, 04 Sep 2018 12:13:30: 5000000 INFO @ Tue, 04 Sep 2018 12:13:33: 5000000 INFO @ Tue, 04 Sep 2018 12:13:35: 6000000 INFO @ Tue, 04 Sep 2018 12:13:36: 6000000 INFO @ Tue, 04 Sep 2018 12:13:40: 6000000 INFO @ Tue, 04 Sep 2018 12:13:42: 7000000 INFO @ Tue, 04 Sep 2018 12:13:42: 7000000 INFO @ Tue, 04 Sep 2018 12:13:48: 7000000 INFO @ Tue, 04 Sep 2018 12:13:49: 8000000 INFO @ Tue, 04 Sep 2018 12:13:49: 8000000 INFO @ Tue, 04 Sep 2018 12:13:56: 9000000 INFO @ Tue, 04 Sep 2018 12:13:56: 8000000 INFO @ Tue, 04 Sep 2018 12:13:56: 9000000 INFO @ Tue, 04 Sep 2018 12:14:02: 10000000 INFO @ Tue, 04 Sep 2018 12:14:02: 10000000 INFO @ Tue, 04 Sep 2018 12:14:03: 9000000 INFO @ Tue, 04 Sep 2018 12:14:07: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 12:14:07: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 12:14:07: #1 total tags in treatment: 3905051 INFO @ Tue, 04 Sep 2018 12:14:07: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 12:14:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 12:14:07: #1 tags after filtering in treatment: 3717886 INFO @ Tue, 04 Sep 2018 12:14:07: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 04 Sep 2018 12:14:07: #1 finished! INFO @ Tue, 04 Sep 2018 12:14:07: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 12:14:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 12:14:07: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 12:14:07: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 12:14:07: #1 total tags in treatment: 3905051 INFO @ Tue, 04 Sep 2018 12:14:07: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 12:14:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 12:14:07: #1 tags after filtering in treatment: 3717886 INFO @ Tue, 04 Sep 2018 12:14:07: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 04 Sep 2018 12:14:07: #1 finished! INFO @ Tue, 04 Sep 2018 12:14:07: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 12:14:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 12:14:07: #2 number of paired peaks: 3513 INFO @ Tue, 04 Sep 2018 12:14:07: start model_add_line... INFO @ Tue, 04 Sep 2018 12:14:07: start X-correlation... INFO @ Tue, 04 Sep 2018 12:14:07: end of X-cor INFO @ Tue, 04 Sep 2018 12:14:07: #2 finished! INFO @ Tue, 04 Sep 2018 12:14:07: #2 predicted fragment length is 181 bps INFO @ Tue, 04 Sep 2018 12:14:07: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 04 Sep 2018 12:14:07: #2.2 Generate R script for model : SRX4279679.10_model.r INFO @ Tue, 04 Sep 2018 12:14:07: #3 Call peaks... INFO @ Tue, 04 Sep 2018 12:14:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 12:14:07: #2 number of paired peaks: 3513 INFO @ Tue, 04 Sep 2018 12:14:07: start model_add_line... INFO @ Tue, 04 Sep 2018 12:14:07: start X-correlation... INFO @ Tue, 04 Sep 2018 12:14:07: end of X-cor INFO @ Tue, 04 Sep 2018 12:14:07: #2 finished! INFO @ Tue, 04 Sep 2018 12:14:07: #2 predicted fragment length is 181 bps INFO @ Tue, 04 Sep 2018 12:14:07: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 04 Sep 2018 12:14:07: #2.2 Generate R script for model : SRX4279679.05_model.r INFO @ Tue, 04 Sep 2018 12:14:08: #3 Call peaks... INFO @ Tue, 04 Sep 2018 12:14:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 12:14:09: 10000000 INFO @ Tue, 04 Sep 2018 12:14:14: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 12:14:14: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 12:14:14: #1 total tags in treatment: 3905051 INFO @ Tue, 04 Sep 2018 12:14:14: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 12:14:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 12:14:14: #1 tags after filtering in treatment: 3717886 INFO @ Tue, 04 Sep 2018 12:14:14: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 04 Sep 2018 12:14:14: #1 finished! INFO @ Tue, 04 Sep 2018 12:14:14: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 12:14:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 12:14:14: #2 number of paired peaks: 3513 INFO @ Tue, 04 Sep 2018 12:14:14: start model_add_line... INFO @ Tue, 04 Sep 2018 12:14:14: start X-correlation... INFO @ Tue, 04 Sep 2018 12:14:14: end of X-cor INFO @ Tue, 04 Sep 2018 12:14:14: #2 finished! INFO @ Tue, 04 Sep 2018 12:14:14: #2 predicted fragment length is 181 bps INFO @ Tue, 04 Sep 2018 12:14:14: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 04 Sep 2018 12:14:14: #2.2 Generate R script for model : SRX4279679.20_model.r INFO @ Tue, 04 Sep 2018 12:14:14: #3 Call peaks... INFO @ Tue, 04 Sep 2018 12:14:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 12:14:17: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 12:14:17: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 12:14:22: #4 Write output xls file... SRX4279679.05_peaks.xls INFO @ Tue, 04 Sep 2018 12:14:22: #4 Write peak in narrowPeak format file... SRX4279679.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 12:14:22: #4 Write output xls file... SRX4279679.10_peaks.xls INFO @ Tue, 04 Sep 2018 12:14:22: #4 Write summits bed file... SRX4279679.05_summits.bed INFO @ Tue, 04 Sep 2018 12:14:22: #4 Write peak in narrowPeak format file... SRX4279679.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 12:14:22: Done! INFO @ Tue, 04 Sep 2018 12:14:22: #4 Write summits bed file... SRX4279679.10_summits.bed INFO @ Tue, 04 Sep 2018 12:14:22: Done! pass1 - making usageList (15 chroms): 2 millis pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3643 records, 4 fields): 7 millis pass2 - checking and writing primary data (6198 records, 4 fields): 9 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 12:14:24: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 12:14:29: #4 Write output xls file... SRX4279679.20_peaks.xls INFO @ Tue, 04 Sep 2018 12:14:29: #4 Write peak in narrowPeak format file... SRX4279679.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 12:14:29: #4 Write summits bed file... SRX4279679.20_summits.bed INFO @ Tue, 04 Sep 2018 12:14:29: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1027 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。