Job ID = 10480738 sra ファイルのダウンロード中... Completed: 309003K bytes transferred in 31 seconds (80535K 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 10507971 spots for /home/okishinya/chipatlas/results/dm3/SRX3380797/SRR6278160.sra Written 10507971 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: 00:03:49 10507971 reads; of these: 10507971 (100.00%) were unpaired; of these: 740949 (7.05%) aligned 0 times 7115492 (67.72%) aligned exactly 1 time 2651530 (25.23%) aligned >1 times 92.95% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 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] 1419547 / 9767022 = 0.1453 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 07:52:30: # Command line: callpeak -t SRX3380797.bam -f BAM -g dm -n SRX3380797.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3380797.20 # format = BAM # ChIP-seq file = ['SRX3380797.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 07:52:30: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:52:30: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:52:30: # Command line: callpeak -t SRX3380797.bam -f BAM -g dm -n SRX3380797.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3380797.05 # format = BAM # ChIP-seq file = ['SRX3380797.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 07:52:30: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:52:30: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:52:30: # Command line: callpeak -t SRX3380797.bam -f BAM -g dm -n SRX3380797.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3380797.10 # format = BAM # ChIP-seq file = ['SRX3380797.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 07:52:30: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:52:30: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:52:36: 1000000 INFO @ Fri, 16 Mar 2018 07:52:37: 1000000 INFO @ Fri, 16 Mar 2018 07:52:37: 1000000 INFO @ Fri, 16 Mar 2018 07:52:43: 2000000 INFO @ Fri, 16 Mar 2018 07:52:43: 2000000 INFO @ Fri, 16 Mar 2018 07:52:43: 2000000 INFO @ Fri, 16 Mar 2018 07:52:49: 3000000 INFO @ Fri, 16 Mar 2018 07:52:49: 3000000 INFO @ Fri, 16 Mar 2018 07:52:50: 3000000 INFO @ Fri, 16 Mar 2018 07:52:56: 4000000 INFO @ Fri, 16 Mar 2018 07:52:56: 4000000 INFO @ Fri, 16 Mar 2018 07:52:56: 4000000 INFO @ Fri, 16 Mar 2018 07:53:02: 5000000 INFO @ Fri, 16 Mar 2018 07:53:02: 5000000 INFO @ Fri, 16 Mar 2018 07:53:03: 5000000 INFO @ Fri, 16 Mar 2018 07:53:09: 6000000 INFO @ Fri, 16 Mar 2018 07:53:09: 6000000 INFO @ Fri, 16 Mar 2018 07:53:09: 6000000 INFO @ Fri, 16 Mar 2018 07:53:15: 7000000 INFO @ Fri, 16 Mar 2018 07:53:16: 7000000 INFO @ Fri, 16 Mar 2018 07:53:16: 7000000 INFO @ Fri, 16 Mar 2018 07:53:22: 8000000 INFO @ Fri, 16 Mar 2018 07:53:22: 8000000 INFO @ Fri, 16 Mar 2018 07:53:22: 8000000 INFO @ Fri, 16 Mar 2018 07:53:24: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:53:24: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:53:24: #1 total tags in treatment: 8347475 INFO @ Fri, 16 Mar 2018 07:53:24: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:53:24: #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 07:53:24: #1 tags after filtering in treatment: 8347475 INFO @ Fri, 16 Mar 2018 07:53:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:53:24: #1 finished! INFO @ Fri, 16 Mar 2018 07:53:24: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:53:24: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:53:24: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:53:24: #1 total tags in treatment: 8347475 INFO @ Fri, 16 Mar 2018 07:53:24: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:53:24: #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 07:53:24: #1 tags after filtering in treatment: 8347475 INFO @ Fri, 16 Mar 2018 07:53:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:53:24: #1 finished! INFO @ Fri, 16 Mar 2018 07:53:24: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:53:25: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:53:25: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:53:25: #1 total tags in treatment: 8347475 INFO @ Fri, 16 Mar 2018 07:53:25: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:53:25: #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 07:53:25: #1 tags after filtering in treatment: 8347475 INFO @ Fri, 16 Mar 2018 07:53:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:53:25: #1 finished! INFO @ Fri, 16 Mar 2018 07:53:25: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:53:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:53:25: #2 number of paired peaks: 5256 INFO @ Fri, 16 Mar 2018 07:53:25: start model_add_line... INFO @ Fri, 16 Mar 2018 07:53:25: start X-correlation... INFO @ Fri, 16 Mar 2018 07:53:25: end of X-cor INFO @ Fri, 16 Mar 2018 07:53:25: #2 finished! INFO @ Fri, 16 Mar 2018 07:53:25: #2 predicted fragment length is 128 bps INFO @ Fri, 16 Mar 2018 07:53:25: #2 alternative fragment length(s) may be 4,128,597 bps INFO @ Fri, 16 Mar 2018 07:53:25: #2.2 Generate R script for model : SRX3380797.20_model.r INFO @ Fri, 16 Mar 2018 07:53:25: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:53:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:53:26: #2 number of paired peaks: 5256 INFO @ Fri, 16 Mar 2018 07:53:26: start model_add_line... INFO @ Fri, 16 Mar 2018 07:53:26: start X-correlation... INFO @ Fri, 16 Mar 2018 07:53:26: end of X-cor INFO @ Fri, 16 Mar 2018 07:53:26: #2 finished! INFO @ Fri, 16 Mar 2018 07:53:26: #2 predicted fragment length is 128 bps INFO @ Fri, 16 Mar 2018 07:53:26: #2 alternative fragment length(s) may be 4,128,597 bps INFO @ Fri, 16 Mar 2018 07:53:26: #2.2 Generate R script for model : SRX3380797.10_model.r INFO @ Fri, 16 Mar 2018 07:53:26: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:53:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:53:26: #2 number of paired peaks: 5256 INFO @ Fri, 16 Mar 2018 07:53:26: start model_add_line... INFO @ Fri, 16 Mar 2018 07:53:26: start X-correlation... INFO @ Fri, 16 Mar 2018 07:53:26: end of X-cor INFO @ Fri, 16 Mar 2018 07:53:26: #2 finished! INFO @ Fri, 16 Mar 2018 07:53:26: #2 predicted fragment length is 128 bps INFO @ Fri, 16 Mar 2018 07:53:26: #2 alternative fragment length(s) may be 4,128,597 bps INFO @ Fri, 16 Mar 2018 07:53:26: #2.2 Generate R script for model : SRX3380797.05_model.r INFO @ Fri, 16 Mar 2018 07:53:26: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:53:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:53:50: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:53:50: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:53:51: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:54:02: #4 Write output xls file... SRX3380797.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:54:02: #4 Write output xls file... SRX3380797.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:54:02: #4 Write peak in narrowPeak format file... SRX3380797.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:54:02: #4 Write peak in narrowPeak format file... SRX3380797.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:54:02: #4 Write summits bed file... SRX3380797.20_summits.bed INFO @ Fri, 16 Mar 2018 07:54:02: Done! INFO @ Fri, 16 Mar 2018 07:54:02: #4 Write summits bed file... SRX3380797.10_summits.bed INFO @ Fri, 16 Mar 2018 07:54:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1908 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4454 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:54:03: #4 Write output xls file... SRX3380797.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:54:03: #4 Write peak in narrowPeak format file... SRX3380797.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:54:03: #4 Write summits bed file... SRX3380797.05_summits.bed INFO @ Fri, 16 Mar 2018 07:54:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8272 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。