Job ID = 10175309 sra ファイルのダウンロード中... Completed: 4484727K bytes transferred in 256 seconds (143173K 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 105103288 spots for /home/okishinya/chipatlas/results/dm3/SRX3176344/SRR6025852.sra Written 105103288 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: 00:36:06 105103288 reads; of these: 105103288 (100.00%) were unpaired; of these: 67495355 (64.22%) aligned 0 times 30414708 (28.94%) aligned exactly 1 time 7193225 (6.84%) aligned >1 times 35.78% overall alignment rate Time searching: 00:36:06 Overall time: 00:36:06 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 16 files... [bam_rmdupse_core] 29091912 / 37607933 = 0.7736 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, 06 Nov 2017 13:22:10: # Command line: callpeak -t SRX3176344.bam -f BAM -g dm -n SRX3176344.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3176344.10 # format = BAM # ChIP-seq file = ['SRX3176344.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, 06 Nov 2017 13:22:10: # Command line: callpeak -t SRX3176344.bam -f BAM -g dm -n SRX3176344.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3176344.05 # format = BAM # ChIP-seq file = ['SRX3176344.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, 06 Nov 2017 13:22:10: # Command line: callpeak -t SRX3176344.bam -f BAM -g dm -n SRX3176344.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3176344.20 # format = BAM # ChIP-seq file = ['SRX3176344.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, 06 Nov 2017 13:22:10: #1 read tag files... INFO @ Mon, 06 Nov 2017 13:22:10: #1 read tag files... INFO @ Mon, 06 Nov 2017 13:22:10: #1 read tag files... INFO @ Mon, 06 Nov 2017 13:22:10: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 13:22:10: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 13:22:10: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 13:22:19: 1000000 INFO @ Mon, 06 Nov 2017 13:22:19: 1000000 INFO @ Mon, 06 Nov 2017 13:22:19: 1000000 INFO @ Mon, 06 Nov 2017 13:22:27: 2000000 INFO @ Mon, 06 Nov 2017 13:22:27: 2000000 INFO @ Mon, 06 Nov 2017 13:22:27: 2000000 INFO @ Mon, 06 Nov 2017 13:22:35: 3000000 INFO @ Mon, 06 Nov 2017 13:22:35: 3000000 INFO @ Mon, 06 Nov 2017 13:22:36: 3000000 INFO @ Mon, 06 Nov 2017 13:22:43: 4000000 INFO @ Mon, 06 Nov 2017 13:22:44: 4000000 INFO @ Mon, 06 Nov 2017 13:22:44: 4000000 INFO @ Mon, 06 Nov 2017 13:22:51: 5000000 INFO @ Mon, 06 Nov 2017 13:22:52: 5000000 INFO @ Mon, 06 Nov 2017 13:22:53: 5000000 INFO @ Mon, 06 Nov 2017 13:22:59: 6000000 INFO @ Mon, 06 Nov 2017 13:23:01: 6000000 INFO @ Mon, 06 Nov 2017 13:23:02: 6000000 INFO @ Mon, 06 Nov 2017 13:23:08: 7000000 INFO @ Mon, 06 Nov 2017 13:23:10: 7000000 INFO @ Mon, 06 Nov 2017 13:23:11: 7000000 INFO @ Mon, 06 Nov 2017 13:23:16: 8000000 INFO @ Mon, 06 Nov 2017 13:23:19: 8000000 INFO @ Mon, 06 Nov 2017 13:23:20: 8000000 INFO @ Mon, 06 Nov 2017 13:23:20: #1 tag size is determined as 101 bps INFO @ Mon, 06 Nov 2017 13:23:20: #1 tag size = 101 INFO @ Mon, 06 Nov 2017 13:23:20: #1 total tags in treatment: 8516021 INFO @ Mon, 06 Nov 2017 13:23:20: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 13:23:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 13:23:20: #1 tags after filtering in treatment: 8516021 INFO @ Mon, 06 Nov 2017 13:23:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 13:23:20: #1 finished! INFO @ Mon, 06 Nov 2017 13:23:20: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 13:23:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 13:23:21: #2 number of paired peaks: 1382 INFO @ Mon, 06 Nov 2017 13:23:21: start model_add_line... INFO @ Mon, 06 Nov 2017 13:23:21: start X-correlation... INFO @ Mon, 06 Nov 2017 13:23:21: end of X-cor INFO @ Mon, 06 Nov 2017 13:23:21: #2 finished! INFO @ Mon, 06 Nov 2017 13:23:21: #2 predicted fragment length is 124 bps INFO @ Mon, 06 Nov 2017 13:23:21: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 06 Nov 2017 13:23:21: #2.2 Generate R script for model : SRX3176344.20_model.r WARNING @ Mon, 06 Nov 2017 13:23:21: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 13:23:21: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Mon, 06 Nov 2017 13:23:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 13:23:21: #3 Call peaks... INFO @ Mon, 06 Nov 2017 13:23:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 13:23:23: #1 tag size is determined as 101 bps INFO @ Mon, 06 Nov 2017 13:23:23: #1 tag size = 101 INFO @ Mon, 06 Nov 2017 13:23:23: #1 total tags in treatment: 8516021 INFO @ Mon, 06 Nov 2017 13:23:23: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 13:23:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 13:23:23: #1 tags after filtering in treatment: 8516021 INFO @ Mon, 06 Nov 2017 13:23:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 13:23:23: #1 finished! INFO @ Mon, 06 Nov 2017 13:23:23: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 13:23:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 13:23:24: #2 number of paired peaks: 1382 INFO @ Mon, 06 Nov 2017 13:23:24: start model_add_line... INFO @ Mon, 06 Nov 2017 13:23:24: #1 tag size is determined as 101 bps INFO @ Mon, 06 Nov 2017 13:23:24: #1 tag size = 101 INFO @ Mon, 06 Nov 2017 13:23:24: #1 total tags in treatment: 8516021 INFO @ Mon, 06 Nov 2017 13:23:24: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 13:23:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 13:23:24: start X-correlation... INFO @ Mon, 06 Nov 2017 13:23:24: end of X-cor INFO @ Mon, 06 Nov 2017 13:23:24: #2 finished! INFO @ Mon, 06 Nov 2017 13:23:24: #2 predicted fragment length is 124 bps INFO @ Mon, 06 Nov 2017 13:23:24: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 06 Nov 2017 13:23:24: #2.2 Generate R script for model : SRX3176344.10_model.r WARNING @ Mon, 06 Nov 2017 13:23:24: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 13:23:24: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Mon, 06 Nov 2017 13:23:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 13:23:24: #3 Call peaks... INFO @ Mon, 06 Nov 2017 13:23:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 13:23:24: #1 tags after filtering in treatment: 8516021 INFO @ Mon, 06 Nov 2017 13:23:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 13:23:24: #1 finished! INFO @ Mon, 06 Nov 2017 13:23:24: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 13:23:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 13:23:25: #2 number of paired peaks: 1382 INFO @ Mon, 06 Nov 2017 13:23:25: start model_add_line... INFO @ Mon, 06 Nov 2017 13:23:25: start X-correlation... INFO @ Mon, 06 Nov 2017 13:23:25: end of X-cor INFO @ Mon, 06 Nov 2017 13:23:25: #2 finished! INFO @ Mon, 06 Nov 2017 13:23:25: #2 predicted fragment length is 124 bps INFO @ Mon, 06 Nov 2017 13:23:25: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 06 Nov 2017 13:23:25: #2.2 Generate R script for model : SRX3176344.05_model.r WARNING @ Mon, 06 Nov 2017 13:23:25: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 13:23:25: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Mon, 06 Nov 2017 13:23:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 13:23:25: #3 Call peaks... INFO @ Mon, 06 Nov 2017 13:23:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 13:23:41: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 13:23:45: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 13:23:45: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 13:23:53: #4 Write output xls file... SRX3176344.20_peaks.xls INFO @ Mon, 06 Nov 2017 13:23:53: #4 Write peak in narrowPeak format file... SRX3176344.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 13:23:53: #4 Write summits bed file... SRX3176344.20_summits.bed INFO @ Mon, 06 Nov 2017 13:23:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2464 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 13:23:56: #4 Write output xls file... SRX3176344.10_peaks.xls INFO @ Mon, 06 Nov 2017 13:23:56: #4 Write peak in narrowPeak format file... SRX3176344.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 13:23:56: #4 Write summits bed file... SRX3176344.10_summits.bed INFO @ Mon, 06 Nov 2017 13:23:56: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5903 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 13:23:57: #4 Write output xls file... SRX3176344.05_peaks.xls INFO @ Mon, 06 Nov 2017 13:23:58: #4 Write peak in narrowPeak format file... SRX3176344.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 13:23:58: #4 Write summits bed file... SRX3176344.05_summits.bed INFO @ Mon, 06 Nov 2017 13:23:58: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11011 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。