Job ID = 9159838 sra ファイルのダウンロード中... Completed: 1240121K bytes transferred in 12 seconds (827626K bits/sec), in 1 file, 2 directories. 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... Written 20230265 spots for /home/okishinya/chipatlas/results/dm3/SRX749021/SRR1636749.sra Written 20230265 spots total 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:26:33 20230265 reads; of these: 20230265 (100.00%) were paired; of these: 1172653 (5.80%) aligned concordantly 0 times 17090074 (84.48%) aligned concordantly exactly 1 time 1967538 (9.73%) aligned concordantly >1 times ---- 1172653 pairs aligned concordantly 0 times; of these: 13354 (1.14%) aligned discordantly 1 time ---- 1159299 pairs aligned 0 times concordantly or discordantly; of these: 2318598 mates make up the pairs; of these: 1872072 (80.74%) aligned 0 times 376921 (16.26%) aligned exactly 1 time 69605 (3.00%) aligned >1 times 95.37% overall alignment rate Time searching: 00:26:34 Overall time: 00:26:34 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] 11802699 / 19060261 = 0.6192 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 @ Wed, 28 Jun 2017 00:46:27: # Command line: callpeak -t SRX749021.bam -f BAM -g dm -n SRX749021.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749021.20 # format = BAM # ChIP-seq file = ['SRX749021.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 @ Wed, 28 Jun 2017 00:46:27: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:46:27: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:46:27: # Command line: callpeak -t SRX749021.bam -f BAM -g dm -n SRX749021.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749021.10 # format = BAM # ChIP-seq file = ['SRX749021.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 @ Wed, 28 Jun 2017 00:46:27: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:46:27: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:46:27: # Command line: callpeak -t SRX749021.bam -f BAM -g dm -n SRX749021.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749021.05 # format = BAM # ChIP-seq file = ['SRX749021.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 @ Wed, 28 Jun 2017 00:46:27: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:46:27: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:46:33: 1000000 INFO @ Wed, 28 Jun 2017 00:46:33: 1000000 INFO @ Wed, 28 Jun 2017 00:46:33: 1000000 INFO @ Wed, 28 Jun 2017 00:46:39: 2000000 INFO @ Wed, 28 Jun 2017 00:46:39: 2000000 INFO @ Wed, 28 Jun 2017 00:46:39: 2000000 INFO @ Wed, 28 Jun 2017 00:46:45: 3000000 INFO @ Wed, 28 Jun 2017 00:46:45: 3000000 INFO @ Wed, 28 Jun 2017 00:46:45: 3000000 INFO @ Wed, 28 Jun 2017 00:46:51: 4000000 INFO @ Wed, 28 Jun 2017 00:46:51: 4000000 INFO @ Wed, 28 Jun 2017 00:46:52: 4000000 INFO @ Wed, 28 Jun 2017 00:46:57: 5000000 INFO @ Wed, 28 Jun 2017 00:46:57: 5000000 INFO @ Wed, 28 Jun 2017 00:46:58: 5000000 INFO @ Wed, 28 Jun 2017 00:47:03: 6000000 INFO @ Wed, 28 Jun 2017 00:47:04: 6000000 INFO @ Wed, 28 Jun 2017 00:47:05: 6000000 INFO @ Wed, 28 Jun 2017 00:47:09: 7000000 INFO @ Wed, 28 Jun 2017 00:47:10: 7000000 INFO @ Wed, 28 Jun 2017 00:47:11: 7000000 INFO @ Wed, 28 Jun 2017 00:47:16: 8000000 INFO @ Wed, 28 Jun 2017 00:47:16: 8000000 INFO @ Wed, 28 Jun 2017 00:47:18: 8000000 INFO @ Wed, 28 Jun 2017 00:47:22: 9000000 INFO @ Wed, 28 Jun 2017 00:47:23: 9000000 INFO @ Wed, 28 Jun 2017 00:47:25: 9000000 INFO @ Wed, 28 Jun 2017 00:47:28: 10000000 INFO @ Wed, 28 Jun 2017 00:47:29: 10000000 INFO @ Wed, 28 Jun 2017 00:47:31: 10000000 INFO @ Wed, 28 Jun 2017 00:47:35: 11000000 INFO @ Wed, 28 Jun 2017 00:47:36: 11000000 INFO @ Wed, 28 Jun 2017 00:47:38: 11000000 INFO @ Wed, 28 Jun 2017 00:47:41: 12000000 INFO @ Wed, 28 Jun 2017 00:47:43: 12000000 INFO @ Wed, 28 Jun 2017 00:47:45: 12000000 INFO @ Wed, 28 Jun 2017 00:47:48: 13000000 INFO @ Wed, 28 Jun 2017 00:47:49: 13000000 INFO @ Wed, 28 Jun 2017 00:47:51: 13000000 INFO @ Wed, 28 Jun 2017 00:47:54: 14000000 INFO @ Wed, 28 Jun 2017 00:47:56: 14000000 INFO @ Wed, 28 Jun 2017 00:47:58: 14000000 INFO @ Wed, 28 Jun 2017 00:48:00: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:48:00: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:48:00: #1 total tags in treatment: 7258398 INFO @ Wed, 28 Jun 2017 00:48:00: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:48:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:48:01: #1 tags after filtering in treatment: 3947621 INFO @ Wed, 28 Jun 2017 00:48:01: #1 Redundant rate of treatment: 0.46 INFO @ Wed, 28 Jun 2017 00:48:01: #1 finished! INFO @ Wed, 28 Jun 2017 00:48:01: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:48:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:48:01: #2 number of paired peaks: 5532 INFO @ Wed, 28 Jun 2017 00:48:01: start model_add_line... INFO @ Wed, 28 Jun 2017 00:48:01: start X-correlation... INFO @ Wed, 28 Jun 2017 00:48:01: end of X-cor INFO @ Wed, 28 Jun 2017 00:48:01: #2 finished! INFO @ Wed, 28 Jun 2017 00:48:01: #2 predicted fragment length is 163 bps INFO @ Wed, 28 Jun 2017 00:48:01: #2 alternative fragment length(s) may be 163 bps INFO @ Wed, 28 Jun 2017 00:48:01: #2.2 Generate R script for model : SRX749021.20_model.r INFO @ Wed, 28 Jun 2017 00:48:01: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:48:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:48:02: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:48:02: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:48:02: #1 total tags in treatment: 7258398 INFO @ Wed, 28 Jun 2017 00:48:02: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:48:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:48:02: #1 tags after filtering in treatment: 3947621 INFO @ Wed, 28 Jun 2017 00:48:02: #1 Redundant rate of treatment: 0.46 INFO @ Wed, 28 Jun 2017 00:48:02: #1 finished! INFO @ Wed, 28 Jun 2017 00:48:02: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:48:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:48:03: #2 number of paired peaks: 5532 INFO @ Wed, 28 Jun 2017 00:48:03: start model_add_line... INFO @ Wed, 28 Jun 2017 00:48:03: start X-correlation... INFO @ Wed, 28 Jun 2017 00:48:03: end of X-cor INFO @ Wed, 28 Jun 2017 00:48:03: #2 finished! INFO @ Wed, 28 Jun 2017 00:48:03: #2 predicted fragment length is 163 bps INFO @ Wed, 28 Jun 2017 00:48:03: #2 alternative fragment length(s) may be 163 bps INFO @ Wed, 28 Jun 2017 00:48:03: #2.2 Generate R script for model : SRX749021.10_model.r INFO @ Wed, 28 Jun 2017 00:48:03: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:48:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:48:04: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:48:04: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:48:04: #1 total tags in treatment: 7258398 INFO @ Wed, 28 Jun 2017 00:48:04: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:48:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:48:04: #1 tags after filtering in treatment: 3947621 INFO @ Wed, 28 Jun 2017 00:48:04: #1 Redundant rate of treatment: 0.46 INFO @ Wed, 28 Jun 2017 00:48:04: #1 finished! INFO @ Wed, 28 Jun 2017 00:48:04: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:48:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:48:05: #2 number of paired peaks: 5532 INFO @ Wed, 28 Jun 2017 00:48:05: start model_add_line... INFO @ Wed, 28 Jun 2017 00:48:05: start X-correlation... INFO @ Wed, 28 Jun 2017 00:48:05: end of X-cor INFO @ Wed, 28 Jun 2017 00:48:05: #2 finished! INFO @ Wed, 28 Jun 2017 00:48:05: #2 predicted fragment length is 163 bps INFO @ Wed, 28 Jun 2017 00:48:05: #2 alternative fragment length(s) may be 163 bps INFO @ Wed, 28 Jun 2017 00:48:05: #2.2 Generate R script for model : SRX749021.05_model.r INFO @ Wed, 28 Jun 2017 00:48:05: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:48:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:48:14: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:48:16: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:48:18: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:48:20: #4 Write output xls file... SRX749021.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:48:20: #4 Write peak in narrowPeak format file... SRX749021.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:48:20: #4 Write summits bed file... SRX749021.20_summits.bed INFO @ Wed, 28 Jun 2017 00:48:20: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4263 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:48:23: #4 Write output xls file... SRX749021.10_peaks.xls INFO @ Wed, 28 Jun 2017 00:48:23: #4 Write peak in narrowPeak format file... SRX749021.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:48:23: #4 Write summits bed file... SRX749021.10_summits.bed INFO @ Wed, 28 Jun 2017 00:48:23: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5487 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:48:24: #4 Write output xls file... SRX749021.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:48:24: #4 Write peak in narrowPeak format file... SRX749021.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:48:24: #4 Write summits bed file... SRX749021.05_summits.bed INFO @ Wed, 28 Jun 2017 00:48:24: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7090 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。