Job ID = 9159837 sra ファイルのダウンロード中... Completed: 811778K bytes transferred in 9 seconds (687788K 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 12676495 spots for /home/okishinya/chipatlas/results/dm3/SRX749020/SRR1636748.sra Written 12676495 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: 00:18:42 12676495 reads; of these: 12676495 (100.00%) were paired; of these: 579934 (4.57%) aligned concordantly 0 times 10447841 (82.42%) aligned concordantly exactly 1 time 1648720 (13.01%) aligned concordantly >1 times ---- 579934 pairs aligned concordantly 0 times; of these: 6924 (1.19%) aligned discordantly 1 time ---- 573010 pairs aligned 0 times concordantly or discordantly; of these: 1146020 mates make up the pairs; of these: 947219 (82.65%) aligned 0 times 162046 (14.14%) aligned exactly 1 time 36755 (3.21%) aligned >1 times 96.26% overall alignment rate Time searching: 00:18:42 Overall time: 00:18:42 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 12 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] 6869628 / 12097061 = 0.5679 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 00:34:51: # Command line: callpeak -t SRX749020.bam -f BAM -g dm -n SRX749020.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749020.20 # format = BAM # ChIP-seq file = ['SRX749020.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 00:34:51: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:34:51: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:34:51: # Command line: callpeak -t SRX749020.bam -f BAM -g dm -n SRX749020.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749020.05 # format = BAM # ChIP-seq file = ['SRX749020.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 00:34:51: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:34:51: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:34:51: # Command line: callpeak -t SRX749020.bam -f BAM -g dm -n SRX749020.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749020.10 # format = BAM # ChIP-seq file = ['SRX749020.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 00:34:51: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:34:51: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:34:56: 1000000 INFO @ Wed, 28 Jun 2017 00:34:56: 1000000 INFO @ Wed, 28 Jun 2017 00:34:57: 1000000 INFO @ Wed, 28 Jun 2017 00:35:02: 2000000 INFO @ Wed, 28 Jun 2017 00:35:02: 2000000 INFO @ Wed, 28 Jun 2017 00:35:03: 2000000 INFO @ Wed, 28 Jun 2017 00:35:08: 3000000 INFO @ Wed, 28 Jun 2017 00:35:08: 3000000 INFO @ Wed, 28 Jun 2017 00:35:09: 3000000 INFO @ Wed, 28 Jun 2017 00:35:13: 4000000 INFO @ Wed, 28 Jun 2017 00:35:15: 4000000 INFO @ Wed, 28 Jun 2017 00:35:15: 4000000 INFO @ Wed, 28 Jun 2017 00:35:19: 5000000 INFO @ Wed, 28 Jun 2017 00:35:21: 5000000 INFO @ Wed, 28 Jun 2017 00:35:22: 5000000 INFO @ Wed, 28 Jun 2017 00:35:25: 6000000 INFO @ Wed, 28 Jun 2017 00:35:27: 6000000 INFO @ Wed, 28 Jun 2017 00:35:28: 6000000 INFO @ Wed, 28 Jun 2017 00:35:30: 7000000 INFO @ Wed, 28 Jun 2017 00:35:33: 7000000 INFO @ Wed, 28 Jun 2017 00:35:35: 7000000 INFO @ Wed, 28 Jun 2017 00:35:36: 8000000 INFO @ Wed, 28 Jun 2017 00:35:40: 8000000 INFO @ Wed, 28 Jun 2017 00:35:41: 8000000 INFO @ Wed, 28 Jun 2017 00:35:42: 9000000 INFO @ Wed, 28 Jun 2017 00:35:46: 9000000 INFO @ Wed, 28 Jun 2017 00:35:47: 9000000 INFO @ Wed, 28 Jun 2017 00:35:47: 10000000 INFO @ Wed, 28 Jun 2017 00:35:51: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:35:51: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:35:51: #1 total tags in treatment: 5228151 INFO @ Wed, 28 Jun 2017 00:35:51: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:35:51: #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 00:35:51: #1 tags after filtering in treatment: 3782449 INFO @ Wed, 28 Jun 2017 00:35:51: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 28 Jun 2017 00:35:51: #1 finished! INFO @ Wed, 28 Jun 2017 00:35:51: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:35:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:35:52: 10000000 INFO @ Wed, 28 Jun 2017 00:35:52: #2 number of paired peaks: 4338 INFO @ Wed, 28 Jun 2017 00:35:52: start model_add_line... INFO @ Wed, 28 Jun 2017 00:35:52: start X-correlation... INFO @ Wed, 28 Jun 2017 00:35:52: end of X-cor INFO @ Wed, 28 Jun 2017 00:35:52: #2 finished! INFO @ Wed, 28 Jun 2017 00:35:52: #2 predicted fragment length is 135 bps INFO @ Wed, 28 Jun 2017 00:35:52: #2 alternative fragment length(s) may be 135 bps INFO @ Wed, 28 Jun 2017 00:35:52: #2.2 Generate R script for model : SRX749020.10_model.r INFO @ Wed, 28 Jun 2017 00:35:52: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:35:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:35:54: 10000000 INFO @ Wed, 28 Jun 2017 00:35:56: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:35:56: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:35:56: #1 total tags in treatment: 5228151 INFO @ Wed, 28 Jun 2017 00:35:56: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:35:56: #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 00:35:56: #1 tags after filtering in treatment: 3782449 INFO @ Wed, 28 Jun 2017 00:35:56: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 28 Jun 2017 00:35:56: #1 finished! INFO @ Wed, 28 Jun 2017 00:35:56: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:35:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:35:57: #2 number of paired peaks: 4338 INFO @ Wed, 28 Jun 2017 00:35:57: start model_add_line... INFO @ Wed, 28 Jun 2017 00:35:57: start X-correlation... INFO @ Wed, 28 Jun 2017 00:35:57: end of X-cor INFO @ Wed, 28 Jun 2017 00:35:57: #2 finished! INFO @ Wed, 28 Jun 2017 00:35:57: #2 predicted fragment length is 135 bps INFO @ Wed, 28 Jun 2017 00:35:57: #2 alternative fragment length(s) may be 135 bps INFO @ Wed, 28 Jun 2017 00:35:57: #2.2 Generate R script for model : SRX749020.20_model.r INFO @ Wed, 28 Jun 2017 00:35:57: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:35:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:35:58: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:35:58: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:35:58: #1 total tags in treatment: 5228151 INFO @ Wed, 28 Jun 2017 00:35:58: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:35:58: #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 00:35:58: #1 tags after filtering in treatment: 3782449 INFO @ Wed, 28 Jun 2017 00:35:58: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 28 Jun 2017 00:35:58: #1 finished! INFO @ Wed, 28 Jun 2017 00:35:58: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:35:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:35:58: #2 number of paired peaks: 4338 INFO @ Wed, 28 Jun 2017 00:35:58: start model_add_line... INFO @ Wed, 28 Jun 2017 00:35:58: start X-correlation... INFO @ Wed, 28 Jun 2017 00:35:58: end of X-cor INFO @ Wed, 28 Jun 2017 00:35:58: #2 finished! INFO @ Wed, 28 Jun 2017 00:35:58: #2 predicted fragment length is 135 bps INFO @ Wed, 28 Jun 2017 00:35:58: #2 alternative fragment length(s) may be 135 bps INFO @ Wed, 28 Jun 2017 00:35:58: #2.2 Generate R script for model : SRX749020.05_model.r INFO @ Wed, 28 Jun 2017 00:35:58: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:35:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:36:03: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:36:08: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:36:08: #4 Write output xls file... SRX749020.10_peaks.xls INFO @ Wed, 28 Jun 2017 00:36:08: #4 Write peak in narrowPeak format file... SRX749020.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:36:08: #4 Write summits bed file... SRX749020.10_summits.bed INFO @ Wed, 28 Jun 2017 00:36:08: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5076 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:36:09: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:36:14: #4 Write output xls file... SRX749020.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:36:14: #4 Write peak in narrowPeak format file... SRX749020.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:36:14: #4 Write summits bed file... SRX749020.20_summits.bed INFO @ Wed, 28 Jun 2017 00:36:14: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3505 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:36:15: #4 Write output xls file... SRX749020.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:36:15: #4 Write peak in narrowPeak format file... SRX749020.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:36:15: #4 Write summits bed file... SRX749020.05_summits.bed INFO @ Wed, 28 Jun 2017 00:36:15: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7555 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。