Job ID = 11293718 sra ファイルのダウンロード中... Completed: 307096K bytes transferred in 13 seconds (190464K bits/sec), in 1 file. 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... Read 3826408 spots for /home/okishinya/chipatlas/results/dm3/SRX4940249/SRR8113882.sra Written 3826408 spots for /home/okishinya/chipatlas/results/dm3/SRX4940249/SRR8113882.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:08:07 3826408 reads; of these: 3826408 (100.00%) were paired; of these: 680978 (17.80%) aligned concordantly 0 times 2614143 (68.32%) aligned concordantly exactly 1 time 531287 (13.88%) aligned concordantly >1 times ---- 680978 pairs aligned concordantly 0 times; of these: 143377 (21.05%) aligned discordantly 1 time ---- 537601 pairs aligned 0 times concordantly or discordantly; of these: 1075202 mates make up the pairs; of these: 905768 (84.24%) aligned 0 times 93508 (8.70%) aligned exactly 1 time 75926 (7.06%) aligned >1 times 88.16% overall alignment rate Time searching: 00:08:07 Overall time: 00:08:07 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] 146031 / 3272463 = 0.0446 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, 04 Nov 2018 17:59:18: # Command line: callpeak -t SRX4940249.bam -f BAM -g dm -n SRX4940249.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4940249.10 # format = BAM # ChIP-seq file = ['SRX4940249.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, 04 Nov 2018 17:59:18: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:59:18: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:59:18: # Command line: callpeak -t SRX4940249.bam -f BAM -g dm -n SRX4940249.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4940249.05 # format = BAM # ChIP-seq file = ['SRX4940249.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, 04 Nov 2018 17:59:18: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:59:18: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:59:18: # Command line: callpeak -t SRX4940249.bam -f BAM -g dm -n SRX4940249.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4940249.20 # format = BAM # ChIP-seq file = ['SRX4940249.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, 04 Nov 2018 17:59:18: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:59:18: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:59:26: 1000000 INFO @ Sun, 04 Nov 2018 17:59:26: 1000000 INFO @ Sun, 04 Nov 2018 17:59:26: 1000000 INFO @ Sun, 04 Nov 2018 17:59:35: 2000000 INFO @ Sun, 04 Nov 2018 17:59:35: 2000000 INFO @ Sun, 04 Nov 2018 17:59:35: 2000000 INFO @ Sun, 04 Nov 2018 17:59:44: 3000000 INFO @ Sun, 04 Nov 2018 17:59:44: 3000000 INFO @ Sun, 04 Nov 2018 17:59:44: 3000000 INFO @ Sun, 04 Nov 2018 17:59:52: 4000000 INFO @ Sun, 04 Nov 2018 17:59:52: 4000000 INFO @ Sun, 04 Nov 2018 17:59:52: 4000000 INFO @ Sun, 04 Nov 2018 18:00:01: 5000000 INFO @ Sun, 04 Nov 2018 18:00:01: 5000000 INFO @ Sun, 04 Nov 2018 18:00:01: 5000000 INFO @ Sun, 04 Nov 2018 18:00:10: 6000000 INFO @ Sun, 04 Nov 2018 18:00:10: 6000000 INFO @ Sun, 04 Nov 2018 18:00:10: 6000000 INFO @ Sun, 04 Nov 2018 18:00:13: #1 tag size is determined as 75 bps INFO @ Sun, 04 Nov 2018 18:00:13: #1 tag size = 75 INFO @ Sun, 04 Nov 2018 18:00:13: #1 total tags in treatment: 3001315 INFO @ Sun, 04 Nov 2018 18:00:13: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 18:00:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 18:00:13: #1 tag size is determined as 75 bps INFO @ Sun, 04 Nov 2018 18:00:13: #1 tag size = 75 INFO @ Sun, 04 Nov 2018 18:00:13: #1 total tags in treatment: 3001315 INFO @ Sun, 04 Nov 2018 18:00:13: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 18:00:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 18:00:13: #1 tag size is determined as 75 bps INFO @ Sun, 04 Nov 2018 18:00:13: #1 tag size = 75 INFO @ Sun, 04 Nov 2018 18:00:13: #1 total tags in treatment: 3001315 INFO @ Sun, 04 Nov 2018 18:00:13: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 18:00:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 18:00:14: #1 tags after filtering in treatment: 2911398 INFO @ Sun, 04 Nov 2018 18:00:14: #1 Redundant rate of treatment: 0.03 INFO @ Sun, 04 Nov 2018 18:00:14: #1 finished! INFO @ Sun, 04 Nov 2018 18:00:14: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 18:00:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 18:00:14: #1 tags after filtering in treatment: 2911398 INFO @ Sun, 04 Nov 2018 18:00:14: #1 Redundant rate of treatment: 0.03 INFO @ Sun, 04 Nov 2018 18:00:14: #1 finished! INFO @ Sun, 04 Nov 2018 18:00:14: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 18:00:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 18:00:14: #1 tags after filtering in treatment: 2911398 INFO @ Sun, 04 Nov 2018 18:00:14: #1 Redundant rate of treatment: 0.03 INFO @ Sun, 04 Nov 2018 18:00:14: #1 finished! INFO @ Sun, 04 Nov 2018 18:00:14: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 18:00:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 18:00:14: #2 number of paired peaks: 444 WARNING @ Sun, 04 Nov 2018 18:00:14: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Sun, 04 Nov 2018 18:00:14: start model_add_line... INFO @ Sun, 04 Nov 2018 18:00:14: #2 number of paired peaks: 444 WARNING @ Sun, 04 Nov 2018 18:00:14: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Sun, 04 Nov 2018 18:00:14: start model_add_line... INFO @ Sun, 04 Nov 2018 18:00:14: #2 number of paired peaks: 444 WARNING @ Sun, 04 Nov 2018 18:00:14: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Sun, 04 Nov 2018 18:00:14: start model_add_line... INFO @ Sun, 04 Nov 2018 18:00:14: start X-correlation... INFO @ Sun, 04 Nov 2018 18:00:14: start X-correlation... INFO @ Sun, 04 Nov 2018 18:00:14: start X-correlation... INFO @ Sun, 04 Nov 2018 18:00:14: end of X-cor INFO @ Sun, 04 Nov 2018 18:00:14: end of X-cor INFO @ Sun, 04 Nov 2018 18:00:14: #2 finished! INFO @ Sun, 04 Nov 2018 18:00:14: #2 finished! INFO @ Sun, 04 Nov 2018 18:00:14: end of X-cor INFO @ Sun, 04 Nov 2018 18:00:14: #2 finished! INFO @ Sun, 04 Nov 2018 18:00:14: #2 predicted fragment length is 209 bps INFO @ Sun, 04 Nov 2018 18:00:14: #2 predicted fragment length is 209 bps INFO @ Sun, 04 Nov 2018 18:00:14: #2 alternative fragment length(s) may be 209 bps INFO @ Sun, 04 Nov 2018 18:00:14: #2 alternative fragment length(s) may be 209 bps INFO @ Sun, 04 Nov 2018 18:00:14: #2.2 Generate R script for model : SRX4940249.05_model.r INFO @ Sun, 04 Nov 2018 18:00:14: #2.2 Generate R script for model : SRX4940249.10_model.r INFO @ Sun, 04 Nov 2018 18:00:14: #2 predicted fragment length is 209 bps INFO @ Sun, 04 Nov 2018 18:00:14: #2 alternative fragment length(s) may be 209 bps INFO @ Sun, 04 Nov 2018 18:00:14: #2.2 Generate R script for model : SRX4940249.20_model.r INFO @ Sun, 04 Nov 2018 18:00:14: #3 Call peaks... INFO @ Sun, 04 Nov 2018 18:00:14: #3 Call peaks... INFO @ Sun, 04 Nov 2018 18:00:14: #3 Call peaks... INFO @ Sun, 04 Nov 2018 18:00:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 18:00:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 18:00:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 18:00:21: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:00:21: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:00:21: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:00:25: #4 Write output xls file... SRX4940249.10_peaks.xls INFO @ Sun, 04 Nov 2018 18:00:25: #4 Write peak in narrowPeak format file... SRX4940249.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:00:25: #4 Write summits bed file... SRX4940249.10_summits.bed INFO @ Sun, 04 Nov 2018 18:00:25: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (198 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 18:00:26: #4 Write output xls file... SRX4940249.20_peaks.xls INFO @ Sun, 04 Nov 2018 18:00:26: #4 Write peak in narrowPeak format file... SRX4940249.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:00:26: #4 Write summits bed file... SRX4940249.20_summits.bed INFO @ Sun, 04 Nov 2018 18:00:26: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (42 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 18:00:26: #4 Write output xls file... SRX4940249.05_peaks.xls INFO @ Sun, 04 Nov 2018 18:00:26: #4 Write peak in narrowPeak format file... SRX4940249.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:00:26: #4 Write summits bed file... SRX4940249.05_summits.bed INFO @ Sun, 04 Nov 2018 18:00:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1820 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。