Job ID = 10714579 sra ファイルのダウンロード中... Completed: 80396K bytes transferred in 3 seconds (173505K 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 5387630 spots for /home/okishinya/chipatlas/results/dm3/SRX4053333/SRR7132380.sra Written 5387630 spots for /home/okishinya/chipatlas/results/dm3/SRX4053333/SRR7132380.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: 00:01:23 5387630 reads; of these: 5387630 (100.00%) were unpaired; of these: 640543 (11.89%) aligned 0 times 4376540 (81.23%) aligned exactly 1 time 370547 (6.88%) aligned >1 times 88.11% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 1171453 / 4747087 = 0.2468 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 13:37:06: # Command line: callpeak -t SRX4053333.bam -f BAM -g dm -n SRX4053333.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4053333.10 # format = BAM # ChIP-seq file = ['SRX4053333.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 13:37:06: # Command line: callpeak -t SRX4053333.bam -f BAM -g dm -n SRX4053333.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4053333.20 # format = BAM # ChIP-seq file = ['SRX4053333.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 13:37:06: # Command line: callpeak -t SRX4053333.bam -f BAM -g dm -n SRX4053333.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4053333.05 # format = BAM # ChIP-seq file = ['SRX4053333.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 13:37:06: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:37:06: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:37:06: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:37:06: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:37:06: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:37:06: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:37:13: 1000000 INFO @ Sun, 03 Jun 2018 13:37:13: 1000000 INFO @ Sun, 03 Jun 2018 13:37:14: 1000000 INFO @ Sun, 03 Jun 2018 13:37:20: 2000000 INFO @ Sun, 03 Jun 2018 13:37:20: 2000000 INFO @ Sun, 03 Jun 2018 13:37:22: 2000000 INFO @ Sun, 03 Jun 2018 13:37:28: 3000000 INFO @ Sun, 03 Jun 2018 13:37:28: 3000000 INFO @ Sun, 03 Jun 2018 13:37:29: 3000000 INFO @ Sun, 03 Jun 2018 13:37:32: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:37:32: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:37:32: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:37:32: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:37:32: #1 total tags in treatment: 3575634 INFO @ Sun, 03 Jun 2018 13:37:32: #1 total tags in treatment: 3575634 INFO @ Sun, 03 Jun 2018 13:37:32: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:37:32: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:37:32: #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 13:37:32: #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 13:37:32: #1 tags after filtering in treatment: 3575634 INFO @ Sun, 03 Jun 2018 13:37:32: #1 tags after filtering in treatment: 3575634 INFO @ Sun, 03 Jun 2018 13:37:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:37:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:37:32: #1 finished! INFO @ Sun, 03 Jun 2018 13:37:32: #1 finished! INFO @ Sun, 03 Jun 2018 13:37:32: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:37:32: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:37:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:37:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:37:33: #2 number of paired peaks: 9572 INFO @ Sun, 03 Jun 2018 13:37:33: start model_add_line... INFO @ Sun, 03 Jun 2018 13:37:33: #2 number of paired peaks: 9572 INFO @ Sun, 03 Jun 2018 13:37:33: start model_add_line... INFO @ Sun, 03 Jun 2018 13:37:33: start X-correlation... INFO @ Sun, 03 Jun 2018 13:37:33: end of X-cor INFO @ Sun, 03 Jun 2018 13:37:33: #2 finished! INFO @ Sun, 03 Jun 2018 13:37:33: #2 predicted fragment length is 171 bps INFO @ Sun, 03 Jun 2018 13:37:33: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 03 Jun 2018 13:37:33: #2.2 Generate R script for model : SRX4053333.20_model.r INFO @ Sun, 03 Jun 2018 13:37:33: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:37:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:37:33: start X-correlation... INFO @ Sun, 03 Jun 2018 13:37:33: end of X-cor INFO @ Sun, 03 Jun 2018 13:37:33: #2 finished! INFO @ Sun, 03 Jun 2018 13:37:33: #2 predicted fragment length is 171 bps INFO @ Sun, 03 Jun 2018 13:37:33: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 03 Jun 2018 13:37:33: #2.2 Generate R script for model : SRX4053333.05_model.r INFO @ Sun, 03 Jun 2018 13:37:33: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:37:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:37:33: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:37:33: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:37:33: #1 total tags in treatment: 3575634 INFO @ Sun, 03 Jun 2018 13:37:33: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:37:33: #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 13:37:34: #1 tags after filtering in treatment: 3575634 INFO @ Sun, 03 Jun 2018 13:37:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:37:34: #1 finished! INFO @ Sun, 03 Jun 2018 13:37:34: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:37:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:37:34: #2 number of paired peaks: 9572 INFO @ Sun, 03 Jun 2018 13:37:34: start model_add_line... INFO @ Sun, 03 Jun 2018 13:37:35: start X-correlation... INFO @ Sun, 03 Jun 2018 13:37:35: end of X-cor INFO @ Sun, 03 Jun 2018 13:37:35: #2 finished! INFO @ Sun, 03 Jun 2018 13:37:35: #2 predicted fragment length is 171 bps INFO @ Sun, 03 Jun 2018 13:37:35: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 03 Jun 2018 13:37:35: #2.2 Generate R script for model : SRX4053333.10_model.r INFO @ Sun, 03 Jun 2018 13:37:35: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:37:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:37:44: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:37:44: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:37:45: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:37:49: #4 Write output xls file... SRX4053333.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:37:49: #4 Write peak in narrowPeak format file... SRX4053333.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:37:49: #4 Write summits bed file... SRX4053333.20_summits.bed INFO @ Sun, 03 Jun 2018 13:37:49: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4883 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:37:49: #4 Write output xls file... SRX4053333.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:37:49: #4 Write peak in narrowPeak format file... SRX4053333.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:37:50: #4 Write summits bed file... SRX4053333.05_summits.bed INFO @ Sun, 03 Jun 2018 13:37:50: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5953 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:37:51: #4 Write output xls file... SRX4053333.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:37:51: #4 Write peak in narrowPeak format file... SRX4053333.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:37:51: #4 Write summits bed file... SRX4053333.10_summits.bed INFO @ Sun, 03 Jun 2018 13:37:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5618 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。