Job ID = 10175304 sra ファイルのダウンロード中... Completed: 168879K bytes transferred in 5 seconds (230672K 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 10349415 spots for /home/okishinya/chipatlas/results/dm3/SRX3170977/SRR6019824.sra Written 10349415 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: 00:03:08 10349415 reads; of these: 10349415 (100.00%) were unpaired; of these: 442555 (4.28%) aligned 0 times 8131255 (78.57%) aligned exactly 1 time 1775605 (17.16%) aligned >1 times 95.72% overall alignment rate Time searching: 00:03:08 Overall time: 00:03:08 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] 2988871 / 9906860 = 0.3017 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 12:27:41: # Command line: callpeak -t SRX3170977.bam -f BAM -g dm -n SRX3170977.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3170977.05 # format = BAM # ChIP-seq file = ['SRX3170977.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 12:27:41: # Command line: callpeak -t SRX3170977.bam -f BAM -g dm -n SRX3170977.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3170977.20 # format = BAM # ChIP-seq file = ['SRX3170977.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 12:27:41: # Command line: callpeak -t SRX3170977.bam -f BAM -g dm -n SRX3170977.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3170977.10 # format = BAM # ChIP-seq file = ['SRX3170977.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 12:27:41: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:27:41: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:27:41: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:27:41: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:27:41: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:27:41: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:27:47: 1000000 INFO @ Mon, 06 Nov 2017 12:27:47: 1000000 INFO @ Mon, 06 Nov 2017 12:27:47: 1000000 INFO @ Mon, 06 Nov 2017 12:27:53: 2000000 INFO @ Mon, 06 Nov 2017 12:27:53: 2000000 INFO @ Mon, 06 Nov 2017 12:27:53: 2000000 INFO @ Mon, 06 Nov 2017 12:27:59: 3000000 INFO @ Mon, 06 Nov 2017 12:28:00: 3000000 INFO @ Mon, 06 Nov 2017 12:28:00: 3000000 INFO @ Mon, 06 Nov 2017 12:28:06: 4000000 INFO @ Mon, 06 Nov 2017 12:28:06: 4000000 INFO @ Mon, 06 Nov 2017 12:28:06: 4000000 INFO @ Mon, 06 Nov 2017 12:28:12: 5000000 INFO @ Mon, 06 Nov 2017 12:28:12: 5000000 INFO @ Mon, 06 Nov 2017 12:28:12: 5000000 INFO @ Mon, 06 Nov 2017 12:28:18: 6000000 INFO @ Mon, 06 Nov 2017 12:28:19: 6000000 INFO @ Mon, 06 Nov 2017 12:28:19: 6000000 INFO @ Mon, 06 Nov 2017 12:28:24: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 12:28:24: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 12:28:24: #1 total tags in treatment: 6917989 INFO @ Mon, 06 Nov 2017 12:28:24: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:28:24: #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 12:28:24: #1 tags after filtering in treatment: 6917989 INFO @ Mon, 06 Nov 2017 12:28:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:28:24: #1 finished! INFO @ Mon, 06 Nov 2017 12:28:24: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:28:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:28:25: #2 number of paired peaks: 1378 INFO @ Mon, 06 Nov 2017 12:28:25: start model_add_line... INFO @ Mon, 06 Nov 2017 12:28:25: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 12:28:25: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 12:28:25: #1 total tags in treatment: 6917989 INFO @ Mon, 06 Nov 2017 12:28:25: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:28:25: #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 12:28:25: start X-correlation... INFO @ Mon, 06 Nov 2017 12:28:25: #1 tags after filtering in treatment: 6917989 INFO @ Mon, 06 Nov 2017 12:28:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:28:25: #1 finished! INFO @ Mon, 06 Nov 2017 12:28:25: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:28:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:28:25: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 12:28:25: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 12:28:25: #1 total tags in treatment: 6917989 INFO @ Mon, 06 Nov 2017 12:28:25: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:28:25: #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 12:28:25: #1 tags after filtering in treatment: 6917989 INFO @ Mon, 06 Nov 2017 12:28:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:28:25: #1 finished! INFO @ Mon, 06 Nov 2017 12:28:25: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:28:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:28:25: end of X-cor INFO @ Mon, 06 Nov 2017 12:28:25: #2 finished! INFO @ Mon, 06 Nov 2017 12:28:25: #2 predicted fragment length is 176 bps INFO @ Mon, 06 Nov 2017 12:28:25: #2 alternative fragment length(s) may be 176 bps INFO @ Mon, 06 Nov 2017 12:28:25: #2.2 Generate R script for model : SRX3170977.20_model.r INFO @ Mon, 06 Nov 2017 12:28:25: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:28:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:28:25: #2 number of paired peaks: 1378 INFO @ Mon, 06 Nov 2017 12:28:25: start model_add_line... INFO @ Mon, 06 Nov 2017 12:28:25: start X-correlation... INFO @ Mon, 06 Nov 2017 12:28:25: end of X-cor INFO @ Mon, 06 Nov 2017 12:28:25: #2 finished! INFO @ Mon, 06 Nov 2017 12:28:25: #2 predicted fragment length is 176 bps INFO @ Mon, 06 Nov 2017 12:28:25: #2 alternative fragment length(s) may be 176 bps INFO @ Mon, 06 Nov 2017 12:28:25: #2.2 Generate R script for model : SRX3170977.05_model.r INFO @ Mon, 06 Nov 2017 12:28:25: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:28:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:28:25: #2 number of paired peaks: 1378 INFO @ Mon, 06 Nov 2017 12:28:25: start model_add_line... INFO @ Mon, 06 Nov 2017 12:28:26: start X-correlation... INFO @ Mon, 06 Nov 2017 12:28:26: end of X-cor INFO @ Mon, 06 Nov 2017 12:28:26: #2 finished! INFO @ Mon, 06 Nov 2017 12:28:26: #2 predicted fragment length is 176 bps INFO @ Mon, 06 Nov 2017 12:28:26: #2 alternative fragment length(s) may be 176 bps INFO @ Mon, 06 Nov 2017 12:28:26: #2.2 Generate R script for model : SRX3170977.10_model.r INFO @ Mon, 06 Nov 2017 12:28:26: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:28:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:28:43: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:28:43: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:28:44: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:28:52: #4 Write output xls file... SRX3170977.20_peaks.xls INFO @ Mon, 06 Nov 2017 12:28:52: #4 Write peak in narrowPeak format file... SRX3170977.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:28:52: #4 Write summits bed file... SRX3170977.20_summits.bed INFO @ Mon, 06 Nov 2017 12:28:52: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (243 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:28:52: #4 Write output xls file... SRX3170977.05_peaks.xls INFO @ Mon, 06 Nov 2017 12:28:52: #4 Write peak in narrowPeak format file... SRX3170977.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:28:52: #4 Write summits bed file... SRX3170977.05_summits.bed INFO @ Mon, 06 Nov 2017 12:28:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1572 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:28:53: #4 Write output xls file... SRX3170977.10_peaks.xls INFO @ Mon, 06 Nov 2017 12:28:53: #4 Write peak in narrowPeak format file... SRX3170977.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:28:53: #4 Write summits bed file... SRX3170977.10_summits.bed INFO @ Mon, 06 Nov 2017 12:28:53: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (545 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。