Job ID = 11158505 sra ファイルのダウンロード中... Completed: 2344539K bytes transferred in 49 seconds (388106K 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 36634362 spots for /home/okishinya/chipatlas/results/dm3/SRX4279698/SRR7408104.sra Written 36634362 spots for /home/okishinya/chipatlas/results/dm3/SRX4279698/SRR7408104.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: 06:30:07 36634362 reads; of these: 36634362 (100.00%) were paired; of these: 15442057 (42.15%) aligned concordantly 0 times 17199062 (46.95%) aligned concordantly exactly 1 time 3993243 (10.90%) aligned concordantly >1 times ---- 15442057 pairs aligned concordantly 0 times; of these: 69146 (0.45%) aligned discordantly 1 time ---- 15372911 pairs aligned 0 times concordantly or discordantly; of these: 30745822 mates make up the pairs; of these: 24743651 (80.48%) aligned 0 times 883030 (2.87%) aligned exactly 1 time 5119141 (16.65%) aligned >1 times 66.23% overall alignment rate Time searching: 06:30:07 Overall time: 06:30:07 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] 15162991 / 21238677 = 0.7139 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 16:24:52: # Command line: callpeak -t SRX4279698.bam -f BAM -g dm -n SRX4279698.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4279698.05 # format = BAM # ChIP-seq file = ['SRX4279698.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 16:24:52: # Command line: callpeak -t SRX4279698.bam -f BAM -g dm -n SRX4279698.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4279698.10 # format = BAM # ChIP-seq file = ['SRX4279698.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 16:24:52: # Command line: callpeak -t SRX4279698.bam -f BAM -g dm -n SRX4279698.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4279698.20 # format = BAM # ChIP-seq file = ['SRX4279698.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 16:24:52: #1 read tag files... INFO @ Tue, 04 Sep 2018 16:24:52: #1 read tag files... INFO @ Tue, 04 Sep 2018 16:24:52: #1 read tag files... INFO @ Tue, 04 Sep 2018 16:24:52: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 16:24:52: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 16:24:52: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 16:24:59: 1000000 INFO @ Tue, 04 Sep 2018 16:24:59: 1000000 INFO @ Tue, 04 Sep 2018 16:24:59: 1000000 INFO @ Tue, 04 Sep 2018 16:25:05: 2000000 INFO @ Tue, 04 Sep 2018 16:25:05: 2000000 INFO @ Tue, 04 Sep 2018 16:25:05: 2000000 INFO @ Tue, 04 Sep 2018 16:25:11: 3000000 INFO @ Tue, 04 Sep 2018 16:25:11: 3000000 INFO @ Tue, 04 Sep 2018 16:25:12: 3000000 INFO @ Tue, 04 Sep 2018 16:25:18: 4000000 INFO @ Tue, 04 Sep 2018 16:25:18: 4000000 INFO @ Tue, 04 Sep 2018 16:25:18: 4000000 INFO @ Tue, 04 Sep 2018 16:25:24: 5000000 INFO @ Tue, 04 Sep 2018 16:25:24: 5000000 INFO @ Tue, 04 Sep 2018 16:25:25: 5000000 INFO @ Tue, 04 Sep 2018 16:25:30: 6000000 INFO @ Tue, 04 Sep 2018 16:25:31: 6000000 INFO @ Tue, 04 Sep 2018 16:25:32: 6000000 INFO @ Tue, 04 Sep 2018 16:25:36: 7000000 INFO @ Tue, 04 Sep 2018 16:25:37: 7000000 INFO @ Tue, 04 Sep 2018 16:25:39: 7000000 INFO @ Tue, 04 Sep 2018 16:25:42: 8000000 INFO @ Tue, 04 Sep 2018 16:25:44: 8000000 INFO @ Tue, 04 Sep 2018 16:25:46: 8000000 INFO @ Tue, 04 Sep 2018 16:25:48: 9000000 INFO @ Tue, 04 Sep 2018 16:25:51: 9000000 INFO @ Tue, 04 Sep 2018 16:25:53: 9000000 INFO @ Tue, 04 Sep 2018 16:25:53: 10000000 INFO @ Tue, 04 Sep 2018 16:25:56: 10000000 INFO @ Tue, 04 Sep 2018 16:25:58: 11000000 INFO @ Tue, 04 Sep 2018 16:25:59: 10000000 INFO @ Tue, 04 Sep 2018 16:26:02: 11000000 INFO @ Tue, 04 Sep 2018 16:26:04: 12000000 INFO @ Tue, 04 Sep 2018 16:26:05: 11000000 INFO @ Tue, 04 Sep 2018 16:26:08: 12000000 INFO @ Tue, 04 Sep 2018 16:26:10: 13000000 INFO @ Tue, 04 Sep 2018 16:26:11: 12000000 INFO @ Tue, 04 Sep 2018 16:26:15: 13000000 INFO @ Tue, 04 Sep 2018 16:26:16: 14000000 INFO @ Tue, 04 Sep 2018 16:26:18: 13000000 INFO @ Tue, 04 Sep 2018 16:26:21: 14000000 INFO @ Tue, 04 Sep 2018 16:26:21: 15000000 INFO @ Tue, 04 Sep 2018 16:26:25: 14000000 INFO @ Tue, 04 Sep 2018 16:26:27: 16000000 INFO @ Tue, 04 Sep 2018 16:26:27: 15000000 INFO @ Tue, 04 Sep 2018 16:26:31: 15000000 INFO @ Tue, 04 Sep 2018 16:26:32: 17000000 INFO @ Tue, 04 Sep 2018 16:26:32: 16000000 INFO @ Tue, 04 Sep 2018 16:26:37: 16000000 INFO @ Tue, 04 Sep 2018 16:26:38: 18000000 INFO @ Tue, 04 Sep 2018 16:26:39: 17000000 INFO @ Tue, 04 Sep 2018 16:26:40: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 16:26:40: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 16:26:40: #1 total tags in treatment: 6064637 INFO @ Tue, 04 Sep 2018 16:26:40: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 16:26:40: #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 16:26:40: #1 tags after filtering in treatment: 5861429 INFO @ Tue, 04 Sep 2018 16:26:40: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 04 Sep 2018 16:26:40: #1 finished! INFO @ Tue, 04 Sep 2018 16:26:40: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 16:26:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 16:26:40: #2 number of paired peaks: 1212 INFO @ Tue, 04 Sep 2018 16:26:40: start model_add_line... INFO @ Tue, 04 Sep 2018 16:26:41: start X-correlation... INFO @ Tue, 04 Sep 2018 16:26:41: end of X-cor INFO @ Tue, 04 Sep 2018 16:26:41: #2 finished! INFO @ Tue, 04 Sep 2018 16:26:41: #2 predicted fragment length is 178 bps INFO @ Tue, 04 Sep 2018 16:26:41: #2 alternative fragment length(s) may be 178,191 bps INFO @ Tue, 04 Sep 2018 16:26:41: #2.2 Generate R script for model : SRX4279698.05_model.r INFO @ Tue, 04 Sep 2018 16:26:41: #3 Call peaks... INFO @ Tue, 04 Sep 2018 16:26:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 16:26:44: 17000000 INFO @ Tue, 04 Sep 2018 16:26:46: 18000000 INFO @ Tue, 04 Sep 2018 16:26:47: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 16:26:47: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 16:26:47: #1 total tags in treatment: 6064637 INFO @ Tue, 04 Sep 2018 16:26:47: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 16:26:47: #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 16:26:47: #1 tags after filtering in treatment: 5861429 INFO @ Tue, 04 Sep 2018 16:26:47: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 04 Sep 2018 16:26:47: #1 finished! INFO @ Tue, 04 Sep 2018 16:26:47: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 16:26:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 16:26:47: #2 number of paired peaks: 1212 INFO @ Tue, 04 Sep 2018 16:26:47: start model_add_line... INFO @ Tue, 04 Sep 2018 16:26:48: start X-correlation... INFO @ Tue, 04 Sep 2018 16:26:48: end of X-cor INFO @ Tue, 04 Sep 2018 16:26:48: #2 finished! INFO @ Tue, 04 Sep 2018 16:26:48: #2 predicted fragment length is 178 bps INFO @ Tue, 04 Sep 2018 16:26:48: #2 alternative fragment length(s) may be 178,191 bps INFO @ Tue, 04 Sep 2018 16:26:48: #2.2 Generate R script for model : SRX4279698.20_model.r INFO @ Tue, 04 Sep 2018 16:26:48: #3 Call peaks... INFO @ Tue, 04 Sep 2018 16:26:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 16:26:50: 18000000 INFO @ Tue, 04 Sep 2018 16:26:52: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 16:26:52: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 16:26:52: #1 total tags in treatment: 6064637 INFO @ Tue, 04 Sep 2018 16:26:52: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 16:26:52: #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 16:26:52: #1 tags after filtering in treatment: 5861429 INFO @ Tue, 04 Sep 2018 16:26:52: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 04 Sep 2018 16:26:52: #1 finished! INFO @ Tue, 04 Sep 2018 16:26:52: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 16:26:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 16:26:52: #2 number of paired peaks: 1212 INFO @ Tue, 04 Sep 2018 16:26:52: start model_add_line... INFO @ Tue, 04 Sep 2018 16:26:52: start X-correlation... INFO @ Tue, 04 Sep 2018 16:26:52: end of X-cor INFO @ Tue, 04 Sep 2018 16:26:52: #2 finished! INFO @ Tue, 04 Sep 2018 16:26:52: #2 predicted fragment length is 178 bps INFO @ Tue, 04 Sep 2018 16:26:52: #2 alternative fragment length(s) may be 178,191 bps INFO @ Tue, 04 Sep 2018 16:26:52: #2.2 Generate R script for model : SRX4279698.10_model.r INFO @ Tue, 04 Sep 2018 16:26:52: #3 Call peaks... INFO @ Tue, 04 Sep 2018 16:26:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 16:26:56: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 16:27:02: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 16:27:04: #4 Write output xls file... SRX4279698.05_peaks.xls INFO @ Tue, 04 Sep 2018 16:27:04: #4 Write peak in narrowPeak format file... SRX4279698.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 16:27:04: #4 Write summits bed file... SRX4279698.05_summits.bed INFO @ Tue, 04 Sep 2018 16:27:04: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4518 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 16:27:08: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 16:27:10: #4 Write output xls file... SRX4279698.20_peaks.xls INFO @ Tue, 04 Sep 2018 16:27:10: #4 Write peak in narrowPeak format file... SRX4279698.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 16:27:10: #4 Write summits bed file... SRX4279698.20_summits.bed INFO @ Tue, 04 Sep 2018 16:27:10: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (482 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 16:27:15: #4 Write output xls file... SRX4279698.10_peaks.xls INFO @ Tue, 04 Sep 2018 16:27:15: #4 Write peak in narrowPeak format file... SRX4279698.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 16:27:15: #4 Write summits bed file... SRX4279698.10_summits.bed INFO @ Tue, 04 Sep 2018 16:27:15: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1771 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。