Job ID = 9159858 sra ファイルのダウンロード中... Completed: 1006070K bytes transferred in 14 seconds (574100K 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 16257070 spots for /home/okishinya/chipatlas/results/dm3/SRX749059/SRR1636787.sra Written 16257070 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: 00:37:08 16257070 reads; of these: 16257070 (100.00%) were paired; of these: 1769552 (10.88%) aligned concordantly 0 times 10989714 (67.60%) aligned concordantly exactly 1 time 3497804 (21.52%) aligned concordantly >1 times ---- 1769552 pairs aligned concordantly 0 times; of these: 14451 (0.82%) aligned discordantly 1 time ---- 1755101 pairs aligned 0 times concordantly or discordantly; of these: 3510202 mates make up the pairs; of these: 3109846 (88.59%) aligned 0 times 292713 (8.34%) aligned exactly 1 time 107643 (3.07%) aligned >1 times 90.44% overall alignment rate Time searching: 00:37:08 Overall time: 00:37:08 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] 8247541 / 14489428 = 0.5692 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 01:04:40: # Command line: callpeak -t SRX749059.bam -f BAM -g dm -n SRX749059.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749059.10 # format = BAM # ChIP-seq file = ['SRX749059.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 01:04:40: # Command line: callpeak -t SRX749059.bam -f BAM -g dm -n SRX749059.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749059.05 # format = BAM # ChIP-seq file = ['SRX749059.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 01:04:40: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:04:40: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:04:40: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:04:40: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:04:40: # Command line: callpeak -t SRX749059.bam -f BAM -g dm -n SRX749059.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749059.20 # format = BAM # ChIP-seq file = ['SRX749059.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 01:04:40: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:04:40: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:04:46: 1000000 INFO @ Wed, 28 Jun 2017 01:04:46: 1000000 INFO @ Wed, 28 Jun 2017 01:04:46: 1000000 INFO @ Wed, 28 Jun 2017 01:04:51: 2000000 INFO @ Wed, 28 Jun 2017 01:04:52: 2000000 INFO @ Wed, 28 Jun 2017 01:04:52: 2000000 INFO @ Wed, 28 Jun 2017 01:04:57: 3000000 INFO @ Wed, 28 Jun 2017 01:04:57: 3000000 INFO @ Wed, 28 Jun 2017 01:04:57: 3000000 INFO @ Wed, 28 Jun 2017 01:05:02: 4000000 INFO @ Wed, 28 Jun 2017 01:05:03: 4000000 INFO @ Wed, 28 Jun 2017 01:05:03: 4000000 INFO @ Wed, 28 Jun 2017 01:05:07: 5000000 INFO @ Wed, 28 Jun 2017 01:05:09: 5000000 INFO @ Wed, 28 Jun 2017 01:05:09: 5000000 INFO @ Wed, 28 Jun 2017 01:05:13: 6000000 INFO @ Wed, 28 Jun 2017 01:05:14: 6000000 INFO @ Wed, 28 Jun 2017 01:05:14: 6000000 INFO @ Wed, 28 Jun 2017 01:05:18: 7000000 INFO @ Wed, 28 Jun 2017 01:05:20: 7000000 INFO @ Wed, 28 Jun 2017 01:05:20: 7000000 INFO @ Wed, 28 Jun 2017 01:05:24: 8000000 INFO @ Wed, 28 Jun 2017 01:05:26: 8000000 INFO @ Wed, 28 Jun 2017 01:05:26: 8000000 INFO @ Wed, 28 Jun 2017 01:05:29: 9000000 INFO @ Wed, 28 Jun 2017 01:05:31: 9000000 INFO @ Wed, 28 Jun 2017 01:05:31: 9000000 INFO @ Wed, 28 Jun 2017 01:05:34: 10000000 INFO @ Wed, 28 Jun 2017 01:05:37: 10000000 INFO @ Wed, 28 Jun 2017 01:05:37: 10000000 INFO @ Wed, 28 Jun 2017 01:05:40: 11000000 INFO @ Wed, 28 Jun 2017 01:05:43: 11000000 INFO @ Wed, 28 Jun 2017 01:05:43: 11000000 INFO @ Wed, 28 Jun 2017 01:05:45: 12000000 INFO @ Wed, 28 Jun 2017 01:05:49: 12000000 INFO @ Wed, 28 Jun 2017 01:05:49: 12000000 INFO @ Wed, 28 Jun 2017 01:05:51: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:05:51: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:05:51: #1 total tags in treatment: 6245415 INFO @ Wed, 28 Jun 2017 01:05:51: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:05:51: #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 01:05:51: #1 tags after filtering in treatment: 5805597 INFO @ Wed, 28 Jun 2017 01:05:51: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 01:05:51: #1 finished! INFO @ Wed, 28 Jun 2017 01:05:51: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:05:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:05:51: #2 number of paired peaks: 2473 INFO @ Wed, 28 Jun 2017 01:05:51: start model_add_line... INFO @ Wed, 28 Jun 2017 01:05:51: start X-correlation... INFO @ Wed, 28 Jun 2017 01:05:51: end of X-cor INFO @ Wed, 28 Jun 2017 01:05:51: #2 finished! INFO @ Wed, 28 Jun 2017 01:05:51: #2 predicted fragment length is 140 bps INFO @ Wed, 28 Jun 2017 01:05:51: #2 alternative fragment length(s) may be 140 bps INFO @ Wed, 28 Jun 2017 01:05:51: #2.2 Generate R script for model : SRX749059.10_model.r INFO @ Wed, 28 Jun 2017 01:05:51: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:05:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:05:54: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:05:54: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:05:54: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:05:54: #1 total tags in treatment: 6245415 INFO @ Wed, 28 Jun 2017 01:05:54: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:05:54: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:05:54: #1 total tags in treatment: 6245415 INFO @ Wed, 28 Jun 2017 01:05:54: #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 01:05:54: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:05:54: #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 01:05:54: #1 tags after filtering in treatment: 5805597 INFO @ Wed, 28 Jun 2017 01:05:54: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 01:05:54: #1 tags after filtering in treatment: 5805597 INFO @ Wed, 28 Jun 2017 01:05:54: #1 finished! INFO @ Wed, 28 Jun 2017 01:05:54: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:05:54: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 01:05:54: #1 finished! INFO @ Wed, 28 Jun 2017 01:05:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:05:54: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:05:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:05:55: #2 number of paired peaks: 2473 INFO @ Wed, 28 Jun 2017 01:05:55: start model_add_line... INFO @ Wed, 28 Jun 2017 01:05:55: #2 number of paired peaks: 2473 INFO @ Wed, 28 Jun 2017 01:05:55: start model_add_line... INFO @ Wed, 28 Jun 2017 01:05:55: start X-correlation... INFO @ Wed, 28 Jun 2017 01:05:55: end of X-cor INFO @ Wed, 28 Jun 2017 01:05:55: #2 finished! INFO @ Wed, 28 Jun 2017 01:05:55: #2 predicted fragment length is 140 bps INFO @ Wed, 28 Jun 2017 01:05:55: #2 alternative fragment length(s) may be 140 bps INFO @ Wed, 28 Jun 2017 01:05:55: #2.2 Generate R script for model : SRX749059.05_model.r INFO @ Wed, 28 Jun 2017 01:05:55: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:05:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:05:55: start X-correlation... INFO @ Wed, 28 Jun 2017 01:05:55: end of X-cor INFO @ Wed, 28 Jun 2017 01:05:55: #2 finished! INFO @ Wed, 28 Jun 2017 01:05:55: #2 predicted fragment length is 140 bps INFO @ Wed, 28 Jun 2017 01:05:55: #2 alternative fragment length(s) may be 140 bps INFO @ Wed, 28 Jun 2017 01:05:55: #2.2 Generate R script for model : SRX749059.20_model.r INFO @ Wed, 28 Jun 2017 01:05:55: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:05:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:06:06: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:06:09: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:06:10: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:06:14: #4 Write output xls file... SRX749059.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:06:14: #4 Write peak in narrowPeak format file... SRX749059.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:06:14: #4 Write summits bed file... SRX749059.10_summits.bed INFO @ Wed, 28 Jun 2017 01:06:14: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4440 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:06:17: #4 Write output xls file... SRX749059.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:06:17: #4 Write peak in narrowPeak format file... SRX749059.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:06:17: #4 Write summits bed file... SRX749059.20_summits.bed INFO @ Wed, 28 Jun 2017 01:06:17: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1906 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:06:18: #4 Write output xls file... SRX749059.05_peaks.xls INFO @ Wed, 28 Jun 2017 01:06:18: #4 Write peak in narrowPeak format file... SRX749059.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:06:18: #4 Write summits bed file... SRX749059.05_summits.bed INFO @ Wed, 28 Jun 2017 01:06:18: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8324 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。