Job ID = 11171276 sra ファイルのダウンロード中... Completed: 2651834K bytes transferred in 68 seconds (316201K 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 39636082 spots for /home/okishinya/chipatlas/results/dm3/SRX2982444/SRR5803101.sra Written 39636082 spots for /home/okishinya/chipatlas/results/dm3/SRX2982444/SRR5803101.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: 01:26:53 39636082 reads; of these: 39636082 (100.00%) were paired; of these: 9632714 (24.30%) aligned concordantly 0 times 23744463 (59.91%) aligned concordantly exactly 1 time 6258905 (15.79%) aligned concordantly >1 times ---- 9632714 pairs aligned concordantly 0 times; of these: 41387 (0.43%) aligned discordantly 1 time ---- 9591327 pairs aligned 0 times concordantly or discordantly; of these: 19182654 mates make up the pairs; of these: 17522846 (91.35%) aligned 0 times 980957 (5.11%) aligned exactly 1 time 678851 (3.54%) aligned >1 times 77.90% overall alignment rate Time searching: 01:26:53 Overall time: 01:26:53 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 28 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] 22015143 / 30005229 = 0.7337 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 @ Sat, 08 Sep 2018 15:13:20: # Command line: callpeak -t SRX2982444.bam -f BAM -g dm -n SRX2982444.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2982444.20 # format = BAM # ChIP-seq file = ['SRX2982444.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 @ Sat, 08 Sep 2018 15:13:20: # Command line: callpeak -t SRX2982444.bam -f BAM -g dm -n SRX2982444.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2982444.10 # format = BAM # ChIP-seq file = ['SRX2982444.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 @ Sat, 08 Sep 2018 15:13:20: # Command line: callpeak -t SRX2982444.bam -f BAM -g dm -n SRX2982444.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2982444.05 # format = BAM # ChIP-seq file = ['SRX2982444.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 @ Sat, 08 Sep 2018 15:13:20: #1 read tag files... INFO @ Sat, 08 Sep 2018 15:13:20: #1 read tag files... INFO @ Sat, 08 Sep 2018 15:13:20: #1 read tag files... INFO @ Sat, 08 Sep 2018 15:13:20: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 15:13:20: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 15:13:20: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 15:13:27: 1000000 INFO @ Sat, 08 Sep 2018 15:13:27: 1000000 INFO @ Sat, 08 Sep 2018 15:13:27: 1000000 INFO @ Sat, 08 Sep 2018 15:13:34: 2000000 INFO @ Sat, 08 Sep 2018 15:13:34: 2000000 INFO @ Sat, 08 Sep 2018 15:13:34: 2000000 INFO @ Sat, 08 Sep 2018 15:13:41: 3000000 INFO @ Sat, 08 Sep 2018 15:13:41: 3000000 INFO @ Sat, 08 Sep 2018 15:13:42: 3000000 INFO @ Sat, 08 Sep 2018 15:13:48: 4000000 INFO @ Sat, 08 Sep 2018 15:13:48: 4000000 INFO @ Sat, 08 Sep 2018 15:13:49: 4000000 INFO @ Sat, 08 Sep 2018 15:13:55: 5000000 INFO @ Sat, 08 Sep 2018 15:13:55: 5000000 INFO @ Sat, 08 Sep 2018 15:13:57: 5000000 INFO @ Sat, 08 Sep 2018 15:14:02: 6000000 INFO @ Sat, 08 Sep 2018 15:14:02: 6000000 INFO @ Sat, 08 Sep 2018 15:14:04: 6000000 INFO @ Sat, 08 Sep 2018 15:14:09: 7000000 INFO @ Sat, 08 Sep 2018 15:14:10: 7000000 INFO @ Sat, 08 Sep 2018 15:14:12: 7000000 INFO @ Sat, 08 Sep 2018 15:14:17: 8000000 INFO @ Sat, 08 Sep 2018 15:14:17: 8000000 INFO @ Sat, 08 Sep 2018 15:14:19: 8000000 INFO @ Sat, 08 Sep 2018 15:14:24: 9000000 INFO @ Sat, 08 Sep 2018 15:14:24: 9000000 INFO @ Sat, 08 Sep 2018 15:14:26: 9000000 INFO @ Sat, 08 Sep 2018 15:14:31: 10000000 INFO @ Sat, 08 Sep 2018 15:14:31: 10000000 INFO @ Sat, 08 Sep 2018 15:14:34: 10000000 INFO @ Sat, 08 Sep 2018 15:14:38: 11000000 INFO @ Sat, 08 Sep 2018 15:14:38: 11000000 INFO @ Sat, 08 Sep 2018 15:14:41: 11000000 INFO @ Sat, 08 Sep 2018 15:14:45: 12000000 INFO @ Sat, 08 Sep 2018 15:14:45: 12000000 INFO @ Sat, 08 Sep 2018 15:14:49: 12000000 INFO @ Sat, 08 Sep 2018 15:14:52: 13000000 INFO @ Sat, 08 Sep 2018 15:14:52: 13000000 INFO @ Sat, 08 Sep 2018 15:14:56: 13000000 INFO @ Sat, 08 Sep 2018 15:15:00: 14000000 INFO @ Sat, 08 Sep 2018 15:15:00: 14000000 INFO @ Sat, 08 Sep 2018 15:15:04: 14000000 INFO @ Sat, 08 Sep 2018 15:15:07: 15000000 INFO @ Sat, 08 Sep 2018 15:15:07: 15000000 INFO @ Sat, 08 Sep 2018 15:15:12: 15000000 INFO @ Sat, 08 Sep 2018 15:15:14: 16000000 INFO @ Sat, 08 Sep 2018 15:15:14: 16000000 INFO @ Sat, 08 Sep 2018 15:15:19: 16000000 INFO @ Sat, 08 Sep 2018 15:15:21: 17000000 INFO @ Sat, 08 Sep 2018 15:15:21: 17000000 INFO @ Sat, 08 Sep 2018 15:15:26: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 15:15:26: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 15:15:26: #1 total tags in treatment: 8007704 INFO @ Sat, 08 Sep 2018 15:15:26: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 15:15:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 15:15:26: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 15:15:26: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 15:15:26: #1 total tags in treatment: 8007704 INFO @ Sat, 08 Sep 2018 15:15:26: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 15:15:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 15:15:26: #1 tags after filtering in treatment: 7507744 INFO @ Sat, 08 Sep 2018 15:15:26: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Sep 2018 15:15:26: #1 finished! INFO @ Sat, 08 Sep 2018 15:15:26: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 15:15:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 15:15:27: #1 tags after filtering in treatment: 7507744 INFO @ Sat, 08 Sep 2018 15:15:27: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Sep 2018 15:15:27: #1 finished! INFO @ Sat, 08 Sep 2018 15:15:27: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 15:15:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 15:15:27: 17000000 INFO @ Sat, 08 Sep 2018 15:15:27: #2 number of paired peaks: 1045 INFO @ Sat, 08 Sep 2018 15:15:27: start model_add_line... INFO @ Sat, 08 Sep 2018 15:15:27: #2 number of paired peaks: 1045 INFO @ Sat, 08 Sep 2018 15:15:27: start model_add_line... INFO @ Sat, 08 Sep 2018 15:15:27: start X-correlation... INFO @ Sat, 08 Sep 2018 15:15:27: end of X-cor INFO @ Sat, 08 Sep 2018 15:15:27: #2 finished! INFO @ Sat, 08 Sep 2018 15:15:27: #2 predicted fragment length is 201 bps INFO @ Sat, 08 Sep 2018 15:15:27: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 08 Sep 2018 15:15:27: #2.2 Generate R script for model : SRX2982444.10_model.r INFO @ Sat, 08 Sep 2018 15:15:27: #3 Call peaks... INFO @ Sat, 08 Sep 2018 15:15:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 15:15:27: start X-correlation... INFO @ Sat, 08 Sep 2018 15:15:27: end of X-cor INFO @ Sat, 08 Sep 2018 15:15:27: #2 finished! INFO @ Sat, 08 Sep 2018 15:15:27: #2 predicted fragment length is 201 bps INFO @ Sat, 08 Sep 2018 15:15:27: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 08 Sep 2018 15:15:27: #2.2 Generate R script for model : SRX2982444.20_model.r INFO @ Sat, 08 Sep 2018 15:15:27: #3 Call peaks... INFO @ Sat, 08 Sep 2018 15:15:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 15:15:31: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 15:15:31: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 15:15:31: #1 total tags in treatment: 8007704 INFO @ Sat, 08 Sep 2018 15:15:31: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 15:15:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 15:15:31: #1 tags after filtering in treatment: 7507744 INFO @ Sat, 08 Sep 2018 15:15:31: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Sep 2018 15:15:31: #1 finished! INFO @ Sat, 08 Sep 2018 15:15:31: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 15:15:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 15:15:32: #2 number of paired peaks: 1045 INFO @ Sat, 08 Sep 2018 15:15:32: start model_add_line... INFO @ Sat, 08 Sep 2018 15:15:32: start X-correlation... INFO @ Sat, 08 Sep 2018 15:15:32: end of X-cor INFO @ Sat, 08 Sep 2018 15:15:32: #2 finished! INFO @ Sat, 08 Sep 2018 15:15:32: #2 predicted fragment length is 201 bps INFO @ Sat, 08 Sep 2018 15:15:32: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 08 Sep 2018 15:15:32: #2.2 Generate R script for model : SRX2982444.05_model.r INFO @ Sat, 08 Sep 2018 15:15:32: #3 Call peaks... INFO @ Sat, 08 Sep 2018 15:15:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 15:15:46: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 15:15:47: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 15:15:52: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 15:15:55: #4 Write output xls file... SRX2982444.20_peaks.xls INFO @ Sat, 08 Sep 2018 15:15:55: #4 Write peak in narrowPeak format file... SRX2982444.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 15:15:55: #4 Write summits bed file... SRX2982444.20_summits.bed INFO @ Sat, 08 Sep 2018 15:15:55: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (923 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 15:15:57: #4 Write output xls file... SRX2982444.10_peaks.xls INFO @ Sat, 08 Sep 2018 15:15:57: #4 Write peak in narrowPeak format file... SRX2982444.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 15:15:57: #4 Write summits bed file... SRX2982444.10_summits.bed INFO @ Sat, 08 Sep 2018 15:15:57: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2997 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 15:16:02: #4 Write output xls file... SRX2982444.05_peaks.xls INFO @ Sat, 08 Sep 2018 15:16:02: #4 Write peak in narrowPeak format file... SRX2982444.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 15:16:02: #4 Write summits bed file... SRX2982444.05_summits.bed INFO @ Sat, 08 Sep 2018 15:16:02: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5877 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。