Job ID = 10714576 sra ファイルのダウンロード中... Completed: 69946K bytes transferred in 3 seconds (159722K 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 4367034 spots for /home/okishinya/chipatlas/results/dm3/SRX4053330/SRR7132383.sra Written 4367034 spots for /home/okishinya/chipatlas/results/dm3/SRX4053330/SRR7132383.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:12 4367034 reads; of these: 4367034 (100.00%) were unpaired; of these: 1362321 (31.20%) aligned 0 times 2412248 (55.24%) aligned exactly 1 time 592465 (13.57%) aligned >1 times 68.80% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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] 387284 / 3004713 = 0.1289 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 @ Sun, 03 Jun 2018 13:34:40: # Command line: callpeak -t SRX4053330.bam -f BAM -g dm -n SRX4053330.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4053330.05 # format = BAM # ChIP-seq file = ['SRX4053330.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 @ Sun, 03 Jun 2018 13:34:40: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:34:40: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:34:40: # Command line: callpeak -t SRX4053330.bam -f BAM -g dm -n SRX4053330.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4053330.20 # format = BAM # ChIP-seq file = ['SRX4053330.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 @ Sun, 03 Jun 2018 13:34:40: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:34:40: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:34:40: # Command line: callpeak -t SRX4053330.bam -f BAM -g dm -n SRX4053330.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4053330.10 # format = BAM # ChIP-seq file = ['SRX4053330.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 @ Sun, 03 Jun 2018 13:34:40: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:34:40: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:34:47: 1000000 INFO @ Sun, 03 Jun 2018 13:34:47: 1000000 INFO @ Sun, 03 Jun 2018 13:34:47: 1000000 INFO @ Sun, 03 Jun 2018 13:34:54: 2000000 INFO @ Sun, 03 Jun 2018 13:34:54: 2000000 INFO @ Sun, 03 Jun 2018 13:34:54: 2000000 INFO @ Sun, 03 Jun 2018 13:34:58: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:34:58: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:34:58: #1 total tags in treatment: 2617429 INFO @ Sun, 03 Jun 2018 13:34:58: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:34:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:34:58: #1 tags after filtering in treatment: 2617429 INFO @ Sun, 03 Jun 2018 13:34:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:34:58: #1 finished! INFO @ Sun, 03 Jun 2018 13:34:58: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:34:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:34:58: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:34:58: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:34:58: #1 total tags in treatment: 2617429 INFO @ Sun, 03 Jun 2018 13:34:58: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:34:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:34:58: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:34:58: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:34:58: #1 total tags in treatment: 2617429 INFO @ Sun, 03 Jun 2018 13:34:58: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:34:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:34:58: #1 tags after filtering in treatment: 2617429 INFO @ Sun, 03 Jun 2018 13:34:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:34:58: #1 finished! INFO @ Sun, 03 Jun 2018 13:34:58: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:34:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:34:58: #1 tags after filtering in treatment: 2617429 INFO @ Sun, 03 Jun 2018 13:34:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:34:58: #1 finished! INFO @ Sun, 03 Jun 2018 13:34:58: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:34:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:34:58: #2 number of paired peaks: 5844 INFO @ Sun, 03 Jun 2018 13:34:58: start model_add_line... INFO @ Sun, 03 Jun 2018 13:34:58: start X-correlation... INFO @ Sun, 03 Jun 2018 13:34:58: end of X-cor INFO @ Sun, 03 Jun 2018 13:34:58: #2 finished! INFO @ Sun, 03 Jun 2018 13:34:58: #2 predicted fragment length is 232 bps INFO @ Sun, 03 Jun 2018 13:34:58: #2 alternative fragment length(s) may be 4,217,232 bps INFO @ Sun, 03 Jun 2018 13:34:58: #2.2 Generate R script for model : SRX4053330.10_model.r INFO @ Sun, 03 Jun 2018 13:34:58: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:34:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:34:59: #2 number of paired peaks: 5844 INFO @ Sun, 03 Jun 2018 13:34:59: start model_add_line... INFO @ Sun, 03 Jun 2018 13:34:59: #2 number of paired peaks: 5844 INFO @ Sun, 03 Jun 2018 13:34:59: start model_add_line... INFO @ Sun, 03 Jun 2018 13:34:59: start X-correlation... INFO @ Sun, 03 Jun 2018 13:34:59: end of X-cor INFO @ Sun, 03 Jun 2018 13:34:59: #2 finished! INFO @ Sun, 03 Jun 2018 13:34:59: #2 predicted fragment length is 232 bps INFO @ Sun, 03 Jun 2018 13:34:59: #2 alternative fragment length(s) may be 4,217,232 bps INFO @ Sun, 03 Jun 2018 13:34:59: #2.2 Generate R script for model : SRX4053330.20_model.r INFO @ Sun, 03 Jun 2018 13:34:59: start X-correlation... INFO @ Sun, 03 Jun 2018 13:34:59: end of X-cor INFO @ Sun, 03 Jun 2018 13:34:59: #2 finished! INFO @ Sun, 03 Jun 2018 13:34:59: #2 predicted fragment length is 232 bps INFO @ Sun, 03 Jun 2018 13:34:59: #2 alternative fragment length(s) may be 4,217,232 bps INFO @ Sun, 03 Jun 2018 13:34:59: #2.2 Generate R script for model : SRX4053330.05_model.r INFO @ Sun, 03 Jun 2018 13:34:59: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:34:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:34:59: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:34:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:35:07: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:35:07: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:35:07: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:35:10: #4 Write output xls file... SRX4053330.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:35:10: #4 Write output xls file... SRX4053330.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:35:10: #4 Write peak in narrowPeak format file... SRX4053330.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:35:10: #4 Write peak in narrowPeak format file... SRX4053330.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:35:10: #4 Write summits bed file... SRX4053330.20_summits.bed INFO @ Sun, 03 Jun 2018 13:35:10: #4 Write summits bed file... SRX4053330.10_summits.bed INFO @ Sun, 03 Jun 2018 13:35:10: Done! INFO @ Sun, 03 Jun 2018 13:35:10: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (303 records, 4 fields): 2 millis pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (130 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:35:11: #4 Write output xls file... SRX4053330.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:35:11: #4 Write peak in narrowPeak format file... SRX4053330.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:35:11: #4 Write summits bed file... SRX4053330.05_summits.bed INFO @ Sun, 03 Jun 2018 13:35:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (727 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。