Job ID = 10609602 sra ファイルのダウンロード中... Completed: 387725K bytes transferred in 24 seconds (130538K 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... Read 30534205 spots for /home/okishinya/chipatlas/results/dm3/SRX3011235/SRR5834712.sra Written 30534205 spots for /home/okishinya/chipatlas/results/dm3/SRX3011235/SRR5834712.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: 00:08:56 30534205 reads; of these: 30534205 (100.00%) were unpaired; of these: 16280192 (53.32%) aligned 0 times 9265473 (30.34%) aligned exactly 1 time 4988540 (16.34%) aligned >1 times 46.68% overall alignment rate Time searching: 00:08:56 Overall time: 00:08:56 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] 8595668 / 14254013 = 0.6030 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 @ Mon, 07 May 2018 13:00:03: # Command line: callpeak -t SRX3011235.bam -f BAM -g dm -n SRX3011235.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011235.20 # format = BAM # ChIP-seq file = ['SRX3011235.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 @ Mon, 07 May 2018 13:00:03: #1 read tag files... INFO @ Mon, 07 May 2018 13:00:03: #1 read treatment tags... INFO @ Mon, 07 May 2018 13:00:03: # Command line: callpeak -t SRX3011235.bam -f BAM -g dm -n SRX3011235.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011235.10 # format = BAM # ChIP-seq file = ['SRX3011235.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 @ Mon, 07 May 2018 13:00:03: #1 read tag files... INFO @ Mon, 07 May 2018 13:00:03: #1 read treatment tags... INFO @ Mon, 07 May 2018 13:00:03: # Command line: callpeak -t SRX3011235.bam -f BAM -g dm -n SRX3011235.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011235.05 # format = BAM # ChIP-seq file = ['SRX3011235.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 @ Mon, 07 May 2018 13:00:03: #1 read tag files... INFO @ Mon, 07 May 2018 13:00:03: #1 read treatment tags... INFO @ Mon, 07 May 2018 13:00:10: 1000000 INFO @ Mon, 07 May 2018 13:00:10: 1000000 INFO @ Mon, 07 May 2018 13:00:10: 1000000 INFO @ Mon, 07 May 2018 13:00:16: 2000000 INFO @ Mon, 07 May 2018 13:00:17: 2000000 INFO @ Mon, 07 May 2018 13:00:17: 2000000 INFO @ Mon, 07 May 2018 13:00:23: 3000000 INFO @ Mon, 07 May 2018 13:00:24: 3000000 INFO @ Mon, 07 May 2018 13:00:24: 3000000 INFO @ Mon, 07 May 2018 13:00:29: 4000000 INFO @ Mon, 07 May 2018 13:00:31: 4000000 INFO @ Mon, 07 May 2018 13:00:31: 4000000 INFO @ Mon, 07 May 2018 13:00:36: 5000000 INFO @ Mon, 07 May 2018 13:00:38: 5000000 INFO @ Mon, 07 May 2018 13:00:38: 5000000 INFO @ Mon, 07 May 2018 13:00:40: #1 tag size is determined as 50 bps INFO @ Mon, 07 May 2018 13:00:40: #1 tag size = 50 INFO @ Mon, 07 May 2018 13:00:40: #1 total tags in treatment: 5658345 INFO @ Mon, 07 May 2018 13:00:40: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 13:00:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 13:00:40: #1 tags after filtering in treatment: 5658345 INFO @ Mon, 07 May 2018 13:00:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 13:00:40: #1 finished! INFO @ Mon, 07 May 2018 13:00:40: #2 Build Peak Model... INFO @ Mon, 07 May 2018 13:00:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 13:00:41: #2 number of paired peaks: 4186 INFO @ Mon, 07 May 2018 13:00:41: start model_add_line... INFO @ Mon, 07 May 2018 13:00:41: start X-correlation... INFO @ Mon, 07 May 2018 13:00:41: end of X-cor INFO @ Mon, 07 May 2018 13:00:41: #2 finished! INFO @ Mon, 07 May 2018 13:00:41: #2 predicted fragment length is 82 bps INFO @ Mon, 07 May 2018 13:00:41: #2 alternative fragment length(s) may be 82 bps INFO @ Mon, 07 May 2018 13:00:41: #2.2 Generate R script for model : SRX3011235.10_model.r WARNING @ Mon, 07 May 2018 13:00:41: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 May 2018 13:00:41: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Mon, 07 May 2018 13:00:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 May 2018 13:00:41: #3 Call peaks... INFO @ Mon, 07 May 2018 13:00:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 13:00:43: #1 tag size is determined as 50 bps INFO @ Mon, 07 May 2018 13:00:43: #1 tag size = 50 INFO @ Mon, 07 May 2018 13:00:43: #1 total tags in treatment: 5658345 INFO @ Mon, 07 May 2018 13:00:43: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 13:00:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 13:00:43: #1 tag size is determined as 50 bps INFO @ Mon, 07 May 2018 13:00:43: #1 tag size = 50 INFO @ Mon, 07 May 2018 13:00:43: #1 total tags in treatment: 5658345 INFO @ Mon, 07 May 2018 13:00:43: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 13:00:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 13:00:43: #1 tags after filtering in treatment: 5658345 INFO @ Mon, 07 May 2018 13:00:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 13:00:43: #1 finished! INFO @ Mon, 07 May 2018 13:00:43: #2 Build Peak Model... INFO @ Mon, 07 May 2018 13:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 13:00:43: #1 tags after filtering in treatment: 5658345 INFO @ Mon, 07 May 2018 13:00:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 13:00:43: #1 finished! INFO @ Mon, 07 May 2018 13:00:43: #2 Build Peak Model... INFO @ Mon, 07 May 2018 13:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 13:00:44: #2 number of paired peaks: 4186 INFO @ Mon, 07 May 2018 13:00:44: start model_add_line... INFO @ Mon, 07 May 2018 13:00:44: #2 number of paired peaks: 4186 INFO @ Mon, 07 May 2018 13:00:44: start model_add_line... INFO @ Mon, 07 May 2018 13:00:44: start X-correlation... INFO @ Mon, 07 May 2018 13:00:44: end of X-cor INFO @ Mon, 07 May 2018 13:00:44: #2 finished! INFO @ Mon, 07 May 2018 13:00:44: #2 predicted fragment length is 82 bps INFO @ Mon, 07 May 2018 13:00:44: #2 alternative fragment length(s) may be 82 bps INFO @ Mon, 07 May 2018 13:00:44: #2.2 Generate R script for model : SRX3011235.05_model.r WARNING @ Mon, 07 May 2018 13:00:44: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 May 2018 13:00:44: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Mon, 07 May 2018 13:00:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 May 2018 13:00:44: #3 Call peaks... INFO @ Mon, 07 May 2018 13:00:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 13:00:44: start X-correlation... INFO @ Mon, 07 May 2018 13:00:44: end of X-cor INFO @ Mon, 07 May 2018 13:00:44: #2 finished! INFO @ Mon, 07 May 2018 13:00:44: #2 predicted fragment length is 82 bps INFO @ Mon, 07 May 2018 13:00:44: #2 alternative fragment length(s) may be 82 bps INFO @ Mon, 07 May 2018 13:00:44: #2.2 Generate R script for model : SRX3011235.20_model.r WARNING @ Mon, 07 May 2018 13:00:44: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 May 2018 13:00:44: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Mon, 07 May 2018 13:00:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 May 2018 13:00:44: #3 Call peaks... INFO @ Mon, 07 May 2018 13:00:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 13:00:56: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 13:00:59: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 13:00:59: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 13:01:03: #4 Write output xls file... SRX3011235.10_peaks.xls INFO @ Mon, 07 May 2018 13:01:03: #4 Write peak in narrowPeak format file... SRX3011235.10_peaks.narrowPeak INFO @ Mon, 07 May 2018 13:01:03: #4 Write summits bed file... SRX3011235.10_summits.bed INFO @ Mon, 07 May 2018 13:01:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4246 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 07 May 2018 13:01:06: #4 Write output xls file... SRX3011235.05_peaks.xls INFO @ Mon, 07 May 2018 13:01:06: #4 Write peak in narrowPeak format file... SRX3011235.05_peaks.narrowPeak INFO @ Mon, 07 May 2018 13:01:06: #4 Write summits bed file... SRX3011235.05_summits.bed INFO @ Mon, 07 May 2018 13:01:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7092 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 07 May 2018 13:01:07: #4 Write output xls file... SRX3011235.20_peaks.xls INFO @ Mon, 07 May 2018 13:01:07: #4 Write peak in narrowPeak format file... SRX3011235.20_peaks.narrowPeak INFO @ Mon, 07 May 2018 13:01:07: #4 Write summits bed file... SRX3011235.20_summits.bed INFO @ Mon, 07 May 2018 13:01:07: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2251 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。