Job ID = 11158501 sra ファイルのダウンロード中... Completed: 1955907K bytes transferred in 47 seconds (336834K 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 30100905 spots for /home/okishinya/chipatlas/results/dm3/SRX4279687/SRR7408115.sra Written 30100905 spots for /home/okishinya/chipatlas/results/dm3/SRX4279687/SRR7408115.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: 06:50:17 30100905 reads; of these: 30100905 (100.00%) were paired; of these: 17050274 (56.64%) aligned concordantly 0 times 10287293 (34.18%) aligned concordantly exactly 1 time 2763338 (9.18%) aligned concordantly >1 times ---- 17050274 pairs aligned concordantly 0 times; of these: 60753 (0.36%) aligned discordantly 1 time ---- 16989521 pairs aligned 0 times concordantly or discordantly; of these: 33979042 mates make up the pairs; of these: 27861786 (82.00%) aligned 0 times 582192 (1.71%) aligned exactly 1 time 5535064 (16.29%) aligned >1 times 53.72% overall alignment rate Time searching: 06:50:17 Overall time: 06:50:17 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 16 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] 9563378 / 13087175 = 0.7307 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 16:39:33: # Command line: callpeak -t SRX4279687.bam -f BAM -g dm -n SRX4279687.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4279687.05 # format = BAM # ChIP-seq file = ['SRX4279687.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 16:39:33: # Command line: callpeak -t SRX4279687.bam -f BAM -g dm -n SRX4279687.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4279687.10 # format = BAM # ChIP-seq file = ['SRX4279687.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 16:39:33: #1 read tag files... INFO @ Tue, 04 Sep 2018 16:39:33: #1 read tag files... INFO @ Tue, 04 Sep 2018 16:39:33: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 16:39:33: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 16:39:33: # Command line: callpeak -t SRX4279687.bam -f BAM -g dm -n SRX4279687.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4279687.20 # format = BAM # ChIP-seq file = ['SRX4279687.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 16:39:33: #1 read tag files... INFO @ Tue, 04 Sep 2018 16:39:33: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 16:39:41: 1000000 INFO @ Tue, 04 Sep 2018 16:39:41: 1000000 INFO @ Tue, 04 Sep 2018 16:39:41: 1000000 INFO @ Tue, 04 Sep 2018 16:39:48: 2000000 INFO @ Tue, 04 Sep 2018 16:39:48: 2000000 INFO @ Tue, 04 Sep 2018 16:39:48: 2000000 INFO @ Tue, 04 Sep 2018 16:39:55: 3000000 INFO @ Tue, 04 Sep 2018 16:39:55: 3000000 INFO @ Tue, 04 Sep 2018 16:39:55: 3000000 INFO @ Tue, 04 Sep 2018 16:40:02: 4000000 INFO @ Tue, 04 Sep 2018 16:40:02: 4000000 INFO @ Tue, 04 Sep 2018 16:40:03: 4000000 INFO @ Tue, 04 Sep 2018 16:40:09: 5000000 INFO @ Tue, 04 Sep 2018 16:40:09: 5000000 INFO @ Tue, 04 Sep 2018 16:40:10: 5000000 INFO @ Tue, 04 Sep 2018 16:40:16: 6000000 INFO @ Tue, 04 Sep 2018 16:40:16: 6000000 INFO @ Tue, 04 Sep 2018 16:40:16: 6000000 INFO @ Tue, 04 Sep 2018 16:40:22: 7000000 INFO @ Tue, 04 Sep 2018 16:40:22: 7000000 INFO @ Tue, 04 Sep 2018 16:40:22: 7000000 INFO @ Tue, 04 Sep 2018 16:40:28: 8000000 INFO @ Tue, 04 Sep 2018 16:40:28: 8000000 INFO @ Tue, 04 Sep 2018 16:40:29: 8000000 INFO @ Tue, 04 Sep 2018 16:40:36: 9000000 INFO @ Tue, 04 Sep 2018 16:40:36: 9000000 INFO @ Tue, 04 Sep 2018 16:40:36: 9000000 INFO @ Tue, 04 Sep 2018 16:40:42: 10000000 INFO @ Tue, 04 Sep 2018 16:40:42: 10000000 INFO @ Tue, 04 Sep 2018 16:40:43: 10000000 INFO @ Tue, 04 Sep 2018 16:40:49: 11000000 INFO @ Tue, 04 Sep 2018 16:40:49: 11000000 INFO @ Tue, 04 Sep 2018 16:40:49: 11000000 INFO @ Tue, 04 Sep 2018 16:40:55: 12000000 INFO @ Tue, 04 Sep 2018 16:40:55: 12000000 INFO @ Tue, 04 Sep 2018 16:40:55: 12000000 INFO @ Tue, 04 Sep 2018 16:41:02: 13000000 INFO @ Tue, 04 Sep 2018 16:41:02: 13000000 INFO @ Tue, 04 Sep 2018 16:41:02: 13000000 INFO @ Tue, 04 Sep 2018 16:41:03: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 16:41:03: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 16:41:03: #1 total tags in treatment: 3519828 INFO @ Tue, 04 Sep 2018 16:41:03: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 16:41:03: #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 16:41:03: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 16:41:03: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 16:41:03: #1 total tags in treatment: 3519828 INFO @ Tue, 04 Sep 2018 16:41:03: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 16:41:03: #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 16:41:03: #1 tags after filtering in treatment: 3407489 INFO @ Tue, 04 Sep 2018 16:41:03: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 04 Sep 2018 16:41:03: #1 finished! INFO @ Tue, 04 Sep 2018 16:41:03: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 16:41:03: #1 tags after filtering in treatment: 3407489 INFO @ Tue, 04 Sep 2018 16:41:03: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 04 Sep 2018 16:41:03: #1 finished! INFO @ Tue, 04 Sep 2018 16:41:03: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 16:41:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 16:41:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 16:41:04: #2 number of paired peaks: 1781 INFO @ Tue, 04 Sep 2018 16:41:04: start model_add_line... INFO @ Tue, 04 Sep 2018 16:41:04: #2 number of paired peaks: 1781 INFO @ Tue, 04 Sep 2018 16:41:04: start model_add_line... INFO @ Tue, 04 Sep 2018 16:41:04: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 16:41:04: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 16:41:04: #1 total tags in treatment: 3519828 INFO @ Tue, 04 Sep 2018 16:41:04: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 16:41:04: #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 16:41:04: start X-correlation... INFO @ Tue, 04 Sep 2018 16:41:04: start X-correlation... INFO @ Tue, 04 Sep 2018 16:41:04: #1 tags after filtering in treatment: 3407489 INFO @ Tue, 04 Sep 2018 16:41:04: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 04 Sep 2018 16:41:04: #1 finished! INFO @ Tue, 04 Sep 2018 16:41:04: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 16:41:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 16:41:04: end of X-cor INFO @ Tue, 04 Sep 2018 16:41:04: end of X-cor INFO @ Tue, 04 Sep 2018 16:41:04: #2 finished! INFO @ Tue, 04 Sep 2018 16:41:04: #2 finished! INFO @ Tue, 04 Sep 2018 16:41:04: #2 predicted fragment length is 181 bps INFO @ Tue, 04 Sep 2018 16:41:04: #2 predicted fragment length is 181 bps INFO @ Tue, 04 Sep 2018 16:41:04: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 04 Sep 2018 16:41:04: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 04 Sep 2018 16:41:04: #2.2 Generate R script for model : SRX4279687.10_model.r INFO @ Tue, 04 Sep 2018 16:41:04: #2.2 Generate R script for model : SRX4279687.05_model.r INFO @ Tue, 04 Sep 2018 16:41:04: #3 Call peaks... INFO @ Tue, 04 Sep 2018 16:41:04: #3 Call peaks... INFO @ Tue, 04 Sep 2018 16:41:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 16:41:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 16:41:04: #2 number of paired peaks: 1781 INFO @ Tue, 04 Sep 2018 16:41:04: start model_add_line... INFO @ Tue, 04 Sep 2018 16:41:04: start X-correlation... INFO @ Tue, 04 Sep 2018 16:41:04: end of X-cor INFO @ Tue, 04 Sep 2018 16:41:04: #2 finished! INFO @ Tue, 04 Sep 2018 16:41:04: #2 predicted fragment length is 181 bps INFO @ Tue, 04 Sep 2018 16:41:04: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 04 Sep 2018 16:41:04: #2.2 Generate R script for model : SRX4279687.20_model.r INFO @ Tue, 04 Sep 2018 16:41:04: #3 Call peaks... INFO @ Tue, 04 Sep 2018 16:41:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 16:41:13: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 16:41:13: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 16:41:14: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 16:41:17: #4 Write output xls file... SRX4279687.05_peaks.xls INFO @ Tue, 04 Sep 2018 16:41:17: #4 Write peak in narrowPeak format file... SRX4279687.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 16:41:17: #4 Write summits bed file... SRX4279687.05_summits.bed INFO @ Tue, 04 Sep 2018 16:41:17: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3075 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 16:41:18: #4 Write output xls file... SRX4279687.20_peaks.xls INFO @ Tue, 04 Sep 2018 16:41:18: #4 Write peak in narrowPeak format file... SRX4279687.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 16:41:18: #4 Write summits bed file... SRX4279687.20_summits.bed INFO @ Tue, 04 Sep 2018 16:41:18: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (376 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 16:41:19: #4 Write output xls file... SRX4279687.10_peaks.xls INFO @ Tue, 04 Sep 2018 16:41:19: #4 Write peak in narrowPeak format file... SRX4279687.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 16:41:19: #4 Write summits bed file... SRX4279687.10_summits.bed INFO @ Tue, 04 Sep 2018 16:41:19: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (1066 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。