Job ID = 10480682 sra ファイルのダウンロード中... Completed: 402572K bytes transferred in 11 seconds (282421K 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: SINGLE fastq に変換中... Written 13107932 spots for /home/okishinya/chipatlas/results/dm3/SRX3068953/SRR5907429.sra Written 13107932 spots total 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: 00:00:01 Multiseed full-index search: 00:03:21 13107932 reads; of these: 13107932 (100.00%) were unpaired; of these: 4392988 (33.51%) aligned 0 times 7115498 (54.28%) aligned exactly 1 time 1599446 (12.20%) aligned >1 times 66.49% overall alignment rate Time searching: 00:03:22 Overall time: 00:03:22 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_rmdupse_core] 2383482 / 8714944 = 0.2735 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 @ Fri, 16 Mar 2018 07:39:08: # Command line: callpeak -t SRX3068953.bam -f BAM -g dm -n SRX3068953.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3068953.05 # format = BAM # ChIP-seq file = ['SRX3068953.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 @ Fri, 16 Mar 2018 07:39:08: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:39:08: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:39:08: # Command line: callpeak -t SRX3068953.bam -f BAM -g dm -n SRX3068953.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3068953.20 # format = BAM # ChIP-seq file = ['SRX3068953.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 @ Fri, 16 Mar 2018 07:39:08: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:39:08: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:39:08: # Command line: callpeak -t SRX3068953.bam -f BAM -g dm -n SRX3068953.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3068953.10 # format = BAM # ChIP-seq file = ['SRX3068953.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 @ Fri, 16 Mar 2018 07:39:08: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:39:08: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:39:15: 1000000 INFO @ Fri, 16 Mar 2018 07:39:15: 1000000 INFO @ Fri, 16 Mar 2018 07:39:15: 1000000 INFO @ Fri, 16 Mar 2018 07:39:21: 2000000 INFO @ Fri, 16 Mar 2018 07:39:21: 2000000 INFO @ Fri, 16 Mar 2018 07:39:21: 2000000 INFO @ Fri, 16 Mar 2018 07:39:27: 3000000 INFO @ Fri, 16 Mar 2018 07:39:27: 3000000 INFO @ Fri, 16 Mar 2018 07:39:28: 3000000 INFO @ Fri, 16 Mar 2018 07:39:33: 4000000 INFO @ Fri, 16 Mar 2018 07:39:34: 4000000 INFO @ Fri, 16 Mar 2018 07:39:35: 4000000 INFO @ Fri, 16 Mar 2018 07:39:40: 5000000 INFO @ Fri, 16 Mar 2018 07:39:40: 5000000 INFO @ Fri, 16 Mar 2018 07:39:41: 5000000 INFO @ Fri, 16 Mar 2018 07:39:46: 6000000 INFO @ Fri, 16 Mar 2018 07:39:47: 6000000 INFO @ Fri, 16 Mar 2018 07:39:48: 6000000 INFO @ Fri, 16 Mar 2018 07:39:48: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:39:48: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:39:48: #1 total tags in treatment: 6331462 INFO @ Fri, 16 Mar 2018 07:39:48: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:39:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:39:48: #1 tags after filtering in treatment: 6331462 INFO @ Fri, 16 Mar 2018 07:39:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:39:48: #1 finished! INFO @ Fri, 16 Mar 2018 07:39:48: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:39:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:39:49: #2 number of paired peaks: 665 WARNING @ Fri, 16 Mar 2018 07:39:49: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Fri, 16 Mar 2018 07:39:49: start model_add_line... INFO @ Fri, 16 Mar 2018 07:39:49: start X-correlation... INFO @ Fri, 16 Mar 2018 07:39:49: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:39:49: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:39:49: #1 total tags in treatment: 6331462 INFO @ Fri, 16 Mar 2018 07:39:49: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:39:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:39:49: end of X-cor INFO @ Fri, 16 Mar 2018 07:39:49: #2 finished! INFO @ Fri, 16 Mar 2018 07:39:49: #2 predicted fragment length is 136 bps INFO @ Fri, 16 Mar 2018 07:39:49: #2 alternative fragment length(s) may be 136 bps INFO @ Fri, 16 Mar 2018 07:39:49: #2.2 Generate R script for model : SRX3068953.10_model.r INFO @ Fri, 16 Mar 2018 07:39:49: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:39:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:39:49: #1 tags after filtering in treatment: 6331462 INFO @ Fri, 16 Mar 2018 07:39:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:39:49: #1 finished! INFO @ Fri, 16 Mar 2018 07:39:49: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:39:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:39:49: #2 number of paired peaks: 665 WARNING @ Fri, 16 Mar 2018 07:39:49: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Fri, 16 Mar 2018 07:39:49: start model_add_line... INFO @ Fri, 16 Mar 2018 07:39:49: start X-correlation... INFO @ Fri, 16 Mar 2018 07:39:49: end of X-cor INFO @ Fri, 16 Mar 2018 07:39:49: #2 finished! INFO @ Fri, 16 Mar 2018 07:39:49: #2 predicted fragment length is 136 bps INFO @ Fri, 16 Mar 2018 07:39:49: #2 alternative fragment length(s) may be 136 bps INFO @ Fri, 16 Mar 2018 07:39:49: #2.2 Generate R script for model : SRX3068953.05_model.r INFO @ Fri, 16 Mar 2018 07:39:49: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:39:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:39:50: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:39:50: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:39:50: #1 total tags in treatment: 6331462 INFO @ Fri, 16 Mar 2018 07:39:50: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:39:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:39:50: #1 tags after filtering in treatment: 6331462 INFO @ Fri, 16 Mar 2018 07:39:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:39:50: #1 finished! INFO @ Fri, 16 Mar 2018 07:39:50: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:39:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:39:50: #2 number of paired peaks: 665 WARNING @ Fri, 16 Mar 2018 07:39:50: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Fri, 16 Mar 2018 07:39:50: start model_add_line... INFO @ Fri, 16 Mar 2018 07:39:51: start X-correlation... INFO @ Fri, 16 Mar 2018 07:39:51: end of X-cor INFO @ Fri, 16 Mar 2018 07:39:51: #2 finished! INFO @ Fri, 16 Mar 2018 07:39:51: #2 predicted fragment length is 136 bps INFO @ Fri, 16 Mar 2018 07:39:51: #2 alternative fragment length(s) may be 136 bps INFO @ Fri, 16 Mar 2018 07:39:51: #2.2 Generate R script for model : SRX3068953.20_model.r INFO @ Fri, 16 Mar 2018 07:39:51: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:39:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:40:04: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:40:04: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:40:05: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:40:12: #4 Write output xls file... SRX3068953.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:40:12: #4 Write peak in narrowPeak format file... SRX3068953.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:40:12: #4 Write summits bed file... SRX3068953.10_summits.bed INFO @ Fri, 16 Mar 2018 07:40:12: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2402 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:40:13: #4 Write output xls file... SRX3068953.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:40:13: #4 Write peak in narrowPeak format file... SRX3068953.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:40:13: #4 Write summits bed file... SRX3068953.20_summits.bed INFO @ Fri, 16 Mar 2018 07:40:13: Done! INFO @ Fri, 16 Mar 2018 07:40:13: #4 Write output xls file... SRX3068953.05_peaks.xls pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1032 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:40:13: #4 Write peak in narrowPeak format file... SRX3068953.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:40:13: #4 Write summits bed file... SRX3068953.05_summits.bed INFO @ Fri, 16 Mar 2018 07:40:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4533 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。