Job ID = 10480699 sra ファイルのダウンロード中... Completed: 457370K bytes transferred in 17 seconds (214188K 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 14902767 spots for /home/okishinya/chipatlas/results/dm3/SRX3068970/SRR5907446.sra Written 14902767 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: 00:00:00 Multiseed full-index search: 00:04:45 14902767 reads; of these: 14902767 (100.00%) were unpaired; of these: 1052834 (7.06%) aligned 0 times 11185965 (75.06%) aligned exactly 1 time 2663968 (17.88%) aligned >1 times 92.94% overall alignment rate Time searching: 00:04:45 Overall time: 00:04:45 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 8 files... [bam_rmdupse_core] 3168149 / 13849933 = 0.2287 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 07:48:57: # Command line: callpeak -t SRX3068970.bam -f BAM -g dm -n SRX3068970.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3068970.05 # format = BAM # ChIP-seq file = ['SRX3068970.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 07:48:57: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:48:57: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:48:57: # Command line: callpeak -t SRX3068970.bam -f BAM -g dm -n SRX3068970.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3068970.10 # format = BAM # ChIP-seq file = ['SRX3068970.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 07:48:57: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:48:57: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:48:57: # Command line: callpeak -t SRX3068970.bam -f BAM -g dm -n SRX3068970.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3068970.20 # format = BAM # ChIP-seq file = ['SRX3068970.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 07:48:57: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:48:57: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:49:05: 1000000 INFO @ Fri, 16 Mar 2018 07:49:05: 1000000 INFO @ Fri, 16 Mar 2018 07:49:05: 1000000 INFO @ Fri, 16 Mar 2018 07:49:12: 2000000 INFO @ Fri, 16 Mar 2018 07:49:12: 2000000 INFO @ Fri, 16 Mar 2018 07:49:12: 2000000 INFO @ Fri, 16 Mar 2018 07:49:19: 3000000 INFO @ Fri, 16 Mar 2018 07:49:20: 3000000 INFO @ Fri, 16 Mar 2018 07:49:20: 3000000 INFO @ Fri, 16 Mar 2018 07:49:27: 4000000 INFO @ Fri, 16 Mar 2018 07:49:27: 4000000 INFO @ Fri, 16 Mar 2018 07:49:27: 4000000 INFO @ Fri, 16 Mar 2018 07:49:34: 5000000 INFO @ Fri, 16 Mar 2018 07:49:34: 5000000 INFO @ Fri, 16 Mar 2018 07:49:35: 5000000 INFO @ Fri, 16 Mar 2018 07:49:41: 6000000 INFO @ Fri, 16 Mar 2018 07:49:42: 6000000 INFO @ Fri, 16 Mar 2018 07:49:42: 6000000 INFO @ Fri, 16 Mar 2018 07:49:49: 7000000 INFO @ Fri, 16 Mar 2018 07:49:49: 7000000 INFO @ Fri, 16 Mar 2018 07:49:50: 7000000 INFO @ Fri, 16 Mar 2018 07:49:56: 8000000 INFO @ Fri, 16 Mar 2018 07:49:57: 8000000 INFO @ Fri, 16 Mar 2018 07:49:57: 8000000 INFO @ Fri, 16 Mar 2018 07:50:03: 9000000 INFO @ Fri, 16 Mar 2018 07:50:04: 9000000 INFO @ Fri, 16 Mar 2018 07:50:05: 9000000 INFO @ Fri, 16 Mar 2018 07:50:11: 10000000 INFO @ Fri, 16 Mar 2018 07:50:12: 10000000 INFO @ Fri, 16 Mar 2018 07:50:13: 10000000 INFO @ Fri, 16 Mar 2018 07:50:16: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:50:16: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:50:16: #1 total tags in treatment: 10681784 INFO @ Fri, 16 Mar 2018 07:50:16: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:50:16: #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 07:50:16: #1 tags after filtering in treatment: 10681784 INFO @ Fri, 16 Mar 2018 07:50:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:50:16: #1 finished! INFO @ Fri, 16 Mar 2018 07:50:16: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:50:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:50:17: #2 number of paired peaks: 364 WARNING @ Fri, 16 Mar 2018 07:50:17: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Fri, 16 Mar 2018 07:50:17: start model_add_line... INFO @ Fri, 16 Mar 2018 07:50:17: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:50:17: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:50:17: #1 total tags in treatment: 10681784 INFO @ Fri, 16 Mar 2018 07:50:17: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:50:17: #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 07:50:17: start X-correlation... INFO @ Fri, 16 Mar 2018 07:50:17: end of X-cor INFO @ Fri, 16 Mar 2018 07:50:17: #2 finished! INFO @ Fri, 16 Mar 2018 07:50:17: #2 predicted fragment length is 171 bps INFO @ Fri, 16 Mar 2018 07:50:17: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 16 Mar 2018 07:50:17: #2.2 Generate R script for model : SRX3068970.20_model.r INFO @ Fri, 16 Mar 2018 07:50:17: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:50:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:50:17: #1 tags after filtering in treatment: 10681784 INFO @ Fri, 16 Mar 2018 07:50:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:50:17: #1 finished! INFO @ Fri, 16 Mar 2018 07:50:17: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:50:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:50:18: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:50:18: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:50:18: #1 total tags in treatment: 10681784 INFO @ Fri, 16 Mar 2018 07:50:18: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:50:18: #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 07:50:18: #2 number of paired peaks: 364 WARNING @ Fri, 16 Mar 2018 07:50:18: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Fri, 16 Mar 2018 07:50:18: start model_add_line... INFO @ Fri, 16 Mar 2018 07:50:18: #1 tags after filtering in treatment: 10681784 INFO @ Fri, 16 Mar 2018 07:50:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:50:18: #1 finished! INFO @ Fri, 16 Mar 2018 07:50:18: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:50:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:50:18: start X-correlation... INFO @ Fri, 16 Mar 2018 07:50:18: end of X-cor INFO @ Fri, 16 Mar 2018 07:50:18: #2 finished! INFO @ Fri, 16 Mar 2018 07:50:18: #2 predicted fragment length is 171 bps INFO @ Fri, 16 Mar 2018 07:50:18: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 16 Mar 2018 07:50:18: #2.2 Generate R script for model : SRX3068970.10_model.r INFO @ Fri, 16 Mar 2018 07:50:18: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:50:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:50:19: #2 number of paired peaks: 364 WARNING @ Fri, 16 Mar 2018 07:50:19: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Fri, 16 Mar 2018 07:50:19: start model_add_line... INFO @ Fri, 16 Mar 2018 07:50:19: start X-correlation... INFO @ Fri, 16 Mar 2018 07:50:19: end of X-cor INFO @ Fri, 16 Mar 2018 07:50:19: #2 finished! INFO @ Fri, 16 Mar 2018 07:50:19: #2 predicted fragment length is 171 bps INFO @ Fri, 16 Mar 2018 07:50:19: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 16 Mar 2018 07:50:19: #2.2 Generate R script for model : SRX3068970.05_model.r INFO @ Fri, 16 Mar 2018 07:50:19: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:50:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:50:41: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:50:42: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:50:43: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:50:55: #4 Write output xls file... SRX3068970.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:50:55: #4 Write peak in narrowPeak format file... SRX3068970.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:50:55: #4 Write summits bed file... SRX3068970.20_summits.bed INFO @ Fri, 16 Mar 2018 07:50:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (300 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:50:57: #4 Write output xls file... SRX3068970.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:50:57: #4 Write peak in narrowPeak format file... SRX3068970.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:50:57: #4 Write summits bed file... SRX3068970.05_summits.bed INFO @ Fri, 16 Mar 2018 07:50:57: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (866 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:50:58: #4 Write output xls file... SRX3068970.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:50:58: #4 Write peak in narrowPeak format file... SRX3068970.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:50:58: #4 Write summits bed file... SRX3068970.10_summits.bed INFO @ Fri, 16 Mar 2018 07:50:58: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (529 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。