Job ID = 9158155 sra ファイルのダウンロード中... Completed: 226104K bytes transferred in 4 seconds (372940K 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 5708721 spots for /home/okishinya/chipatlas/results/dm3/SRX1056713/SRR2060647.sra Written 5708721 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: 00:14:07 5708721 reads; of these: 5708721 (100.00%) were paired; of these: 1006758 (17.64%) aligned concordantly 0 times 3334734 (58.41%) aligned concordantly exactly 1 time 1367229 (23.95%) aligned concordantly >1 times ---- 1006758 pairs aligned concordantly 0 times; of these: 91584 (9.10%) aligned discordantly 1 time ---- 915174 pairs aligned 0 times concordantly or discordantly; of these: 1830348 mates make up the pairs; of these: 1460256 (79.78%) aligned 0 times 200156 (10.94%) aligned exactly 1 time 169936 (9.28%) aligned >1 times 87.21% overall alignment rate Time searching: 00:14:07 Overall time: 00:14:07 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_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] 1442826 / 4790555 = 0.3012 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 @ Tue, 27 Jun 2017 15:44:39: # Command line: callpeak -t SRX1056713.bam -f BAM -g dm -n SRX1056713.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1056713.10 # format = BAM # ChIP-seq file = ['SRX1056713.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 @ Tue, 27 Jun 2017 15:44:39: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:44:39: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:44:39: # Command line: callpeak -t SRX1056713.bam -f BAM -g dm -n SRX1056713.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1056713.20 # format = BAM # ChIP-seq file = ['SRX1056713.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 @ Tue, 27 Jun 2017 15:44:39: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:44:39: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:44:39: # Command line: callpeak -t SRX1056713.bam -f BAM -g dm -n SRX1056713.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1056713.05 # format = BAM # ChIP-seq file = ['SRX1056713.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 @ Tue, 27 Jun 2017 15:44:39: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:44:39: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:44:44: 1000000 INFO @ Tue, 27 Jun 2017 15:44:45: 1000000 INFO @ Tue, 27 Jun 2017 15:44:45: 1000000 INFO @ Tue, 27 Jun 2017 15:44:50: 2000000 INFO @ Tue, 27 Jun 2017 15:44:51: 2000000 INFO @ Tue, 27 Jun 2017 15:44:53: 2000000 INFO @ Tue, 27 Jun 2017 15:44:55: 3000000 INFO @ Tue, 27 Jun 2017 15:44:58: 3000000 INFO @ Tue, 27 Jun 2017 15:45:00: 3000000 INFO @ Tue, 27 Jun 2017 15:45:00: 4000000 INFO @ Tue, 27 Jun 2017 15:45:04: 4000000 INFO @ Tue, 27 Jun 2017 15:45:06: 5000000 INFO @ Tue, 27 Jun 2017 15:45:08: 4000000 INFO @ Tue, 27 Jun 2017 15:45:11: 5000000 INFO @ Tue, 27 Jun 2017 15:45:11: 6000000 INFO @ Tue, 27 Jun 2017 15:45:15: 5000000 INFO @ Tue, 27 Jun 2017 15:45:17: 7000000 INFO @ Tue, 27 Jun 2017 15:45:17: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 15:45:17: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 15:45:17: #1 total tags in treatment: 3273775 INFO @ Tue, 27 Jun 2017 15:45:17: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:45:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 15:45:17: #1 tags after filtering in treatment: 3100151 INFO @ Tue, 27 Jun 2017 15:45:17: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 27 Jun 2017 15:45:17: #1 finished! INFO @ Tue, 27 Jun 2017 15:45:17: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:45:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:45:17: 6000000 INFO @ Tue, 27 Jun 2017 15:45:17: #2 number of paired peaks: 2027 INFO @ Tue, 27 Jun 2017 15:45:17: start model_add_line... INFO @ Tue, 27 Jun 2017 15:45:17: start X-correlation... INFO @ Tue, 27 Jun 2017 15:45:17: end of X-cor INFO @ Tue, 27 Jun 2017 15:45:17: #2 finished! INFO @ Tue, 27 Jun 2017 15:45:17: #2 predicted fragment length is 170 bps INFO @ Tue, 27 Jun 2017 15:45:17: #2 alternative fragment length(s) may be 170 bps INFO @ Tue, 27 Jun 2017 15:45:17: #2.2 Generate R script for model : SRX1056713.20_model.r INFO @ Tue, 27 Jun 2017 15:45:17: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:45:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:45:22: 6000000 INFO @ Tue, 27 Jun 2017 15:45:23: 7000000 INFO @ Tue, 27 Jun 2017 15:45:24: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 15:45:24: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 15:45:24: #1 total tags in treatment: 3273775 INFO @ Tue, 27 Jun 2017 15:45:24: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:45:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 15:45:24: #1 tags after filtering in treatment: 3100151 INFO @ Tue, 27 Jun 2017 15:45:24: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 27 Jun 2017 15:45:24: #1 finished! INFO @ Tue, 27 Jun 2017 15:45:24: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:45:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:45:24: #2 number of paired peaks: 2027 INFO @ Tue, 27 Jun 2017 15:45:24: start model_add_line... INFO @ Tue, 27 Jun 2017 15:45:24: start X-correlation... INFO @ Tue, 27 Jun 2017 15:45:24: end of X-cor INFO @ Tue, 27 Jun 2017 15:45:24: #2 finished! INFO @ Tue, 27 Jun 2017 15:45:24: #2 predicted fragment length is 170 bps INFO @ Tue, 27 Jun 2017 15:45:24: #2 alternative fragment length(s) may be 170 bps INFO @ Tue, 27 Jun 2017 15:45:24: #2.2 Generate R script for model : SRX1056713.05_model.r INFO @ Tue, 27 Jun 2017 15:45:24: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:45:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:45:25: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:45:29: 7000000 INFO @ Tue, 27 Jun 2017 15:45:30: #4 Write output xls file... SRX1056713.20_peaks.xls INFO @ Tue, 27 Jun 2017 15:45:30: #4 Write peak in narrowPeak format file... SRX1056713.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:45:30: #4 Write summits bed file... SRX1056713.20_summits.bed INFO @ Tue, 27 Jun 2017 15:45:30: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (602 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:45:30: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 15:45:30: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 15:45:30: #1 total tags in treatment: 3273775 INFO @ Tue, 27 Jun 2017 15:45:30: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:45:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 15:45:30: #1 tags after filtering in treatment: 3100151 INFO @ Tue, 27 Jun 2017 15:45:30: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 27 Jun 2017 15:45:30: #1 finished! INFO @ Tue, 27 Jun 2017 15:45:30: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:45:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:45:30: #2 number of paired peaks: 2027 INFO @ Tue, 27 Jun 2017 15:45:30: start model_add_line... INFO @ Tue, 27 Jun 2017 15:45:30: start X-correlation... INFO @ Tue, 27 Jun 2017 15:45:30: end of X-cor INFO @ Tue, 27 Jun 2017 15:45:30: #2 finished! INFO @ Tue, 27 Jun 2017 15:45:30: #2 predicted fragment length is 170 bps INFO @ Tue, 27 Jun 2017 15:45:30: #2 alternative fragment length(s) may be 170 bps INFO @ Tue, 27 Jun 2017 15:45:30: #2.2 Generate R script for model : SRX1056713.10_model.r INFO @ Tue, 27 Jun 2017 15:45:30: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:45:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:45:32: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:45:37: #4 Write output xls file... SRX1056713.05_peaks.xls INFO @ Tue, 27 Jun 2017 15:45:37: #4 Write peak in narrowPeak format file... SRX1056713.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:45:37: #4 Write summits bed file... SRX1056713.05_summits.bed INFO @ Tue, 27 Jun 2017 15:45:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3605 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:45:38: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:45:42: #4 Write output xls file... SRX1056713.10_peaks.xls INFO @ Tue, 27 Jun 2017 15:45:42: #4 Write peak in narrowPeak format file... SRX1056713.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:45:42: #4 Write summits bed file... SRX1056713.10_summits.bed INFO @ Tue, 27 Jun 2017 15:45:42: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1582 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。