Job ID = 11170897 sra ファイルのダウンロード中... Completed: 288855K bytes transferred in 4 seconds (473765K 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 13296061 spots for /home/okishinya/chipatlas/results/dm3/SRX1490788/SRR3031655.sra Written 13296061 spots for /home/okishinya/chipatlas/results/dm3/SRX1490788/SRR3031655.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: 00:05:59 13296061 reads; of these: 13296061 (100.00%) were unpaired; of these: 2538395 (19.09%) aligned 0 times 6008783 (45.19%) aligned exactly 1 time 4748883 (35.72%) aligned >1 times 80.91% overall alignment rate Time searching: 00:05:59 Overall time: 00:05:59 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] 8679165 / 10757666 = 0.8068 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 @ Sat, 08 Sep 2018 11:49:36: # Command line: callpeak -t SRX1490788.bam -f BAM -g dm -n SRX1490788.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1490788.10 # format = BAM # ChIP-seq file = ['SRX1490788.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 @ Sat, 08 Sep 2018 11:49:36: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:49:36: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:49:36: # Command line: callpeak -t SRX1490788.bam -f BAM -g dm -n SRX1490788.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1490788.05 # format = BAM # ChIP-seq file = ['SRX1490788.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 @ Sat, 08 Sep 2018 11:49:36: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:49:36: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:49:36: # Command line: callpeak -t SRX1490788.bam -f BAM -g dm -n SRX1490788.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1490788.20 # format = BAM # ChIP-seq file = ['SRX1490788.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 @ Sat, 08 Sep 2018 11:49:36: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:49:36: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:49:43: 1000000 INFO @ Sat, 08 Sep 2018 11:49:43: 1000000 INFO @ Sat, 08 Sep 2018 11:49:43: 1000000 INFO @ Sat, 08 Sep 2018 11:49:50: 2000000 INFO @ Sat, 08 Sep 2018 11:49:50: 2000000 INFO @ Sat, 08 Sep 2018 11:49:50: 2000000 INFO @ Sat, 08 Sep 2018 11:49:51: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 11:49:51: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 11:49:51: #1 total tags in treatment: 2078501 INFO @ Sat, 08 Sep 2018 11:49:51: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:49:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:49:51: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 11:49:51: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 11:49:51: #1 total tags in treatment: 2078501 INFO @ Sat, 08 Sep 2018 11:49:51: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:49:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:49:51: #1 tags after filtering in treatment: 2078501 INFO @ Sat, 08 Sep 2018 11:49:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:49:51: #1 finished! INFO @ Sat, 08 Sep 2018 11:49:51: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:49:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:49:51: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 11:49:51: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 11:49:51: #1 total tags in treatment: 2078501 INFO @ Sat, 08 Sep 2018 11:49:51: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:49:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:49:51: #1 tags after filtering in treatment: 2078501 INFO @ Sat, 08 Sep 2018 11:49:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:49:51: #1 finished! INFO @ Sat, 08 Sep 2018 11:49:51: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:49:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:49:51: #1 tags after filtering in treatment: 2078501 INFO @ Sat, 08 Sep 2018 11:49:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:49:51: #1 finished! INFO @ Sat, 08 Sep 2018 11:49:51: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:49:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:49:51: #2 number of paired peaks: 1948 INFO @ Sat, 08 Sep 2018 11:49:51: start model_add_line... INFO @ Sat, 08 Sep 2018 11:49:51: #2 number of paired peaks: 1948 INFO @ Sat, 08 Sep 2018 11:49:51: start model_add_line... INFO @ Sat, 08 Sep 2018 11:49:51: start X-correlation... INFO @ Sat, 08 Sep 2018 11:49:51: end of X-cor INFO @ Sat, 08 Sep 2018 11:49:51: #2 finished! INFO @ Sat, 08 Sep 2018 11:49:51: #2 predicted fragment length is 126 bps INFO @ Sat, 08 Sep 2018 11:49:51: #2 alternative fragment length(s) may be 126 bps INFO @ Sat, 08 Sep 2018 11:49:51: #2.2 Generate R script for model : SRX1490788.10_model.r INFO @ Sat, 08 Sep 2018 11:49:51: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:49:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:49:51: #2 number of paired peaks: 1948 INFO @ Sat, 08 Sep 2018 11:49:51: start model_add_line... INFO @ Sat, 08 Sep 2018 11:49:51: start X-correlation... INFO @ Sat, 08 Sep 2018 11:49:51: end of X-cor INFO @ Sat, 08 Sep 2018 11:49:51: #2 finished! INFO @ Sat, 08 Sep 2018 11:49:51: #2 predicted fragment length is 126 bps INFO @ Sat, 08 Sep 2018 11:49:51: #2 alternative fragment length(s) may be 126 bps INFO @ Sat, 08 Sep 2018 11:49:51: #2.2 Generate R script for model : SRX1490788.20_model.r INFO @ Sat, 08 Sep 2018 11:49:51: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:49:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:49:51: start X-correlation... INFO @ Sat, 08 Sep 2018 11:49:51: end of X-cor INFO @ Sat, 08 Sep 2018 11:49:51: #2 finished! INFO @ Sat, 08 Sep 2018 11:49:51: #2 predicted fragment length is 126 bps INFO @ Sat, 08 Sep 2018 11:49:51: #2 alternative fragment length(s) may be 126 bps INFO @ Sat, 08 Sep 2018 11:49:51: #2.2 Generate R script for model : SRX1490788.05_model.r INFO @ Sat, 08 Sep 2018 11:49:51: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:49:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:49:57: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:49:57: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:49:57: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:49:59: #4 Write output xls file... SRX1490788.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:49:59: #4 Write output xls file... SRX1490788.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:49:59: #4 Write peak in narrowPeak format file... SRX1490788.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:49:59: #4 Write peak in narrowPeak format file... SRX1490788.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:49:59: #4 Write summits bed file... SRX1490788.10_summits.bed INFO @ Sat, 08 Sep 2018 11:49:59: #4 Write summits bed file... SRX1490788.20_summits.bed INFO @ Sat, 08 Sep 2018 11:50:00: Done! INFO @ Sat, 08 Sep 2018 11:50:00: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1263 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2042 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:50:00: #4 Write output xls file... SRX1490788.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:50:00: #4 Write peak in narrowPeak format file... SRX1490788.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:50:00: #4 Write summits bed file... SRX1490788.05_summits.bed INFO @ Sat, 08 Sep 2018 11:50:00: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3501 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。