Job ID = 9730442 sra ファイルのダウンロード中... Completed: 329239K bytes transferred in 7 seconds (361213K 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 8761962 spots for /home/okishinya/chipatlas/results/dm3/SRX2559030/SRR5253494.sra Written 8761962 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:22:11 8761962 reads; of these: 8761962 (100.00%) were paired; of these: 433393 (4.95%) aligned concordantly 0 times 6092645 (69.54%) aligned concordantly exactly 1 time 2235924 (25.52%) aligned concordantly >1 times ---- 433393 pairs aligned concordantly 0 times; of these: 79773 (18.41%) aligned discordantly 1 time ---- 353620 pairs aligned 0 times concordantly or discordantly; of these: 707240 mates make up the pairs; of these: 449614 (63.57%) aligned 0 times 160567 (22.70%) aligned exactly 1 time 97059 (13.72%) aligned >1 times 97.43% overall alignment rate Time searching: 00:22:11 Overall time: 00:22:11 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 8 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] 258809 / 8401293 = 0.0308 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 @ Sun, 03 Sep 2017 01:21:34: # Command line: callpeak -t SRX2559030.bam -f BAM -g dm -n SRX2559030.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2559030.10 # format = BAM # ChIP-seq file = ['SRX2559030.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 @ Sun, 03 Sep 2017 01:21:34: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:21:34: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:21:34: # Command line: callpeak -t SRX2559030.bam -f BAM -g dm -n SRX2559030.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2559030.20 # format = BAM # ChIP-seq file = ['SRX2559030.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 @ Sun, 03 Sep 2017 01:21:34: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:21:34: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:21:34: # Command line: callpeak -t SRX2559030.bam -f BAM -g dm -n SRX2559030.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2559030.05 # format = BAM # ChIP-seq file = ['SRX2559030.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 @ Sun, 03 Sep 2017 01:21:34: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:21:34: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:21:39: 1000000 INFO @ Sun, 03 Sep 2017 01:21:39: 1000000 INFO @ Sun, 03 Sep 2017 01:21:40: 1000000 INFO @ Sun, 03 Sep 2017 01:21:45: 2000000 INFO @ Sun, 03 Sep 2017 01:21:45: 2000000 INFO @ Sun, 03 Sep 2017 01:21:46: 2000000 INFO @ Sun, 03 Sep 2017 01:21:50: 3000000 INFO @ Sun, 03 Sep 2017 01:21:50: 3000000 INFO @ Sun, 03 Sep 2017 01:21:52: 3000000 INFO @ Sun, 03 Sep 2017 01:21:55: 4000000 INFO @ Sun, 03 Sep 2017 01:21:56: 4000000 INFO @ Sun, 03 Sep 2017 01:21:58: 4000000 INFO @ Sun, 03 Sep 2017 01:22:00: 5000000 INFO @ Sun, 03 Sep 2017 01:22:01: 5000000 INFO @ Sun, 03 Sep 2017 01:22:04: 5000000 INFO @ Sun, 03 Sep 2017 01:22:06: 6000000 INFO @ Sun, 03 Sep 2017 01:22:07: 6000000 INFO @ Sun, 03 Sep 2017 01:22:10: 6000000 INFO @ Sun, 03 Sep 2017 01:22:11: 7000000 INFO @ Sun, 03 Sep 2017 01:22:12: 7000000 INFO @ Sun, 03 Sep 2017 01:22:16: 7000000 INFO @ Sun, 03 Sep 2017 01:22:16: 8000000 INFO @ Sun, 03 Sep 2017 01:22:18: 8000000 INFO @ Sun, 03 Sep 2017 01:22:21: 9000000 INFO @ Sun, 03 Sep 2017 01:22:21: 8000000 INFO @ Sun, 03 Sep 2017 01:22:23: 9000000 INFO @ Sun, 03 Sep 2017 01:22:26: 10000000 INFO @ Sun, 03 Sep 2017 01:22:27: 9000000 INFO @ Sun, 03 Sep 2017 01:22:29: 10000000 INFO @ Sun, 03 Sep 2017 01:22:31: 11000000 INFO @ Sun, 03 Sep 2017 01:22:33: 10000000 INFO @ Sun, 03 Sep 2017 01:22:34: 11000000 INFO @ Sun, 03 Sep 2017 01:22:37: 12000000 INFO @ Sun, 03 Sep 2017 01:22:39: 11000000 INFO @ Sun, 03 Sep 2017 01:22:40: 12000000 INFO @ Sun, 03 Sep 2017 01:22:42: 13000000 INFO @ Sun, 03 Sep 2017 01:22:45: 12000000 INFO @ Sun, 03 Sep 2017 01:22:45: 13000000 INFO @ Sun, 03 Sep 2017 01:22:47: 14000000 INFO @ Sun, 03 Sep 2017 01:22:51: 14000000 INFO @ Sun, 03 Sep 2017 01:22:51: 13000000 INFO @ Sun, 03 Sep 2017 01:22:52: 15000000 INFO @ Sun, 03 Sep 2017 01:22:56: 15000000 INFO @ Sun, 03 Sep 2017 01:22:57: 14000000 INFO @ Sun, 03 Sep 2017 01:22:58: 16000000 INFO @ Sun, 03 Sep 2017 01:23:01: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:23:01: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:23:01: #1 total tags in treatment: 8070312 INFO @ Sun, 03 Sep 2017 01:23:01: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:23:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:23:01: #1 tags after filtering in treatment: 7679055 INFO @ Sun, 03 Sep 2017 01:23:01: #1 Redundant rate of treatment: 0.05 INFO @ Sun, 03 Sep 2017 01:23:01: #1 finished! INFO @ Sun, 03 Sep 2017 01:23:01: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:23:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:23:01: 16000000 INFO @ Sun, 03 Sep 2017 01:23:02: #2 number of paired peaks: 767 WARNING @ Sun, 03 Sep 2017 01:23:02: Fewer paired peaks (767) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 767 pairs to build model! INFO @ Sun, 03 Sep 2017 01:23:02: start model_add_line... INFO @ Sun, 03 Sep 2017 01:23:02: start X-correlation... INFO @ Sun, 03 Sep 2017 01:23:02: end of X-cor INFO @ Sun, 03 Sep 2017 01:23:02: #2 finished! INFO @ Sun, 03 Sep 2017 01:23:02: #2 predicted fragment length is 160 bps INFO @ Sun, 03 Sep 2017 01:23:02: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 03 Sep 2017 01:23:02: #2.2 Generate R script for model : SRX2559030.20_model.r INFO @ Sun, 03 Sep 2017 01:23:02: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:23:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:23:03: 15000000 INFO @ Sun, 03 Sep 2017 01:23:04: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:23:04: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:23:04: #1 total tags in treatment: 8070312 INFO @ Sun, 03 Sep 2017 01:23:04: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:23:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:23:04: #1 tags after filtering in treatment: 7679055 INFO @ Sun, 03 Sep 2017 01:23:04: #1 Redundant rate of treatment: 0.05 INFO @ Sun, 03 Sep 2017 01:23:04: #1 finished! INFO @ Sun, 03 Sep 2017 01:23:04: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:23:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:23:05: #2 number of paired peaks: 767 WARNING @ Sun, 03 Sep 2017 01:23:05: Fewer paired peaks (767) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 767 pairs to build model! INFO @ Sun, 03 Sep 2017 01:23:05: start model_add_line... INFO @ Sun, 03 Sep 2017 01:23:05: start X-correlation... INFO @ Sun, 03 Sep 2017 01:23:05: end of X-cor INFO @ Sun, 03 Sep 2017 01:23:05: #2 finished! INFO @ Sun, 03 Sep 2017 01:23:05: #2 predicted fragment length is 160 bps INFO @ Sun, 03 Sep 2017 01:23:05: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 03 Sep 2017 01:23:05: #2.2 Generate R script for model : SRX2559030.10_model.r INFO @ Sun, 03 Sep 2017 01:23:05: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:23:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:23:09: 16000000 INFO @ Sun, 03 Sep 2017 01:23:12: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:23:12: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:23:12: #1 total tags in treatment: 8070312 INFO @ Sun, 03 Sep 2017 01:23:12: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:23:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:23:12: #1 tags after filtering in treatment: 7679055 INFO @ Sun, 03 Sep 2017 01:23:12: #1 Redundant rate of treatment: 0.05 INFO @ Sun, 03 Sep 2017 01:23:12: #1 finished! INFO @ Sun, 03 Sep 2017 01:23:12: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:23:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:23:13: #2 number of paired peaks: 767 WARNING @ Sun, 03 Sep 2017 01:23:13: Fewer paired peaks (767) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 767 pairs to build model! INFO @ Sun, 03 Sep 2017 01:23:13: start model_add_line... INFO @ Sun, 03 Sep 2017 01:23:13: start X-correlation... INFO @ Sun, 03 Sep 2017 01:23:13: end of X-cor INFO @ Sun, 03 Sep 2017 01:23:13: #2 finished! INFO @ Sun, 03 Sep 2017 01:23:13: #2 predicted fragment length is 160 bps INFO @ Sun, 03 Sep 2017 01:23:13: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 03 Sep 2017 01:23:13: #2.2 Generate R script for model : SRX2559030.05_model.r INFO @ Sun, 03 Sep 2017 01:23:13: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:23:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:23:20: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:23:26: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:23:31: #4 Write output xls file... SRX2559030.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:23:31: #4 Write peak in narrowPeak format file... SRX2559030.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:23:31: #4 Write summits bed file... SRX2559030.20_summits.bed INFO @ Sun, 03 Sep 2017 01:23:31: Done! INFO @ Sun, 03 Sep 2017 01:23:31: #3 Call peaks for each chromosome... pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (537 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:23:37: #4 Write output xls file... SRX2559030.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:23:37: #4 Write peak in narrowPeak format file... SRX2559030.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:23:37: #4 Write summits bed file... SRX2559030.10_summits.bed INFO @ Sun, 03 Sep 2017 01:23:37: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1290 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:23:42: #4 Write output xls file... SRX2559030.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:23:42: #4 Write peak in narrowPeak format file... SRX2559030.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:23:42: #4 Write summits bed file... SRX2559030.05_summits.bed INFO @ Sun, 03 Sep 2017 01:23:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2912 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。