Job ID = 11293647 sra ファイルのダウンロード中... Completed: 178688K bytes transferred in 9 seconds (149575K 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 6890646 spots for /home/okishinya/chipatlas/results/ce10/SRX4344456/SRR7474923.sra Written 6890646 spots for /home/okishinya/chipatlas/results/ce10/SRX4344456/SRR7474923.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:26 6890646 reads; of these: 6890646 (100.00%) were unpaired; of these: 2321152 (33.69%) aligned 0 times 3919004 (56.87%) aligned exactly 1 time 650490 (9.44%) aligned >1 times 66.31% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1473818 / 4569494 = 0.3225 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, 04 Nov 2018 17:49:38: # Command line: callpeak -t SRX4344456.bam -f BAM -g ce -n SRX4344456.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4344456.05 # format = BAM # ChIP-seq file = ['SRX4344456.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 04 Nov 2018 17:49:38: # Command line: callpeak -t SRX4344456.bam -f BAM -g ce -n SRX4344456.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4344456.10 # format = BAM # ChIP-seq file = ['SRX4344456.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 04 Nov 2018 17:49:38: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:49:38: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:49:38: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:49:38: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:49:38: # Command line: callpeak -t SRX4344456.bam -f BAM -g ce -n SRX4344456.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4344456.20 # format = BAM # ChIP-seq file = ['SRX4344456.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 04 Nov 2018 17:49:38: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:49:38: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:49:46: 1000000 INFO @ Sun, 04 Nov 2018 17:49:47: 1000000 INFO @ Sun, 04 Nov 2018 17:49:47: 1000000 INFO @ Sun, 04 Nov 2018 17:49:54: 2000000 INFO @ Sun, 04 Nov 2018 17:49:56: 2000000 INFO @ Sun, 04 Nov 2018 17:49:56: 2000000 INFO @ Sun, 04 Nov 2018 17:50:01: 3000000 INFO @ Sun, 04 Nov 2018 17:50:02: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:50:02: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:50:02: #1 total tags in treatment: 3095676 INFO @ Sun, 04 Nov 2018 17:50:02: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:50:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:50:02: #1 tags after filtering in treatment: 3095676 INFO @ Sun, 04 Nov 2018 17:50:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:50:02: #1 finished! INFO @ Sun, 04 Nov 2018 17:50:02: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:50:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:50:02: #2 number of paired peaks: 1168 INFO @ Sun, 04 Nov 2018 17:50:02: start model_add_line... INFO @ Sun, 04 Nov 2018 17:50:03: start X-correlation... INFO @ Sun, 04 Nov 2018 17:50:03: end of X-cor INFO @ Sun, 04 Nov 2018 17:50:03: #2 finished! INFO @ Sun, 04 Nov 2018 17:50:03: #2 predicted fragment length is 155 bps INFO @ Sun, 04 Nov 2018 17:50:03: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 04 Nov 2018 17:50:03: #2.2 Generate R script for model : SRX4344456.20_model.r INFO @ Sun, 04 Nov 2018 17:50:03: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:50:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:50:05: 3000000 INFO @ Sun, 04 Nov 2018 17:50:05: 3000000 INFO @ Sun, 04 Nov 2018 17:50:05: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:50:05: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:50:05: #1 total tags in treatment: 3095676 INFO @ Sun, 04 Nov 2018 17:50:05: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:50:05: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:50:05: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:50:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:50:05: #1 total tags in treatment: 3095676 INFO @ Sun, 04 Nov 2018 17:50:05: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:50:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:50:05: #1 tags after filtering in treatment: 3095676 INFO @ Sun, 04 Nov 2018 17:50:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:50:05: #1 finished! INFO @ Sun, 04 Nov 2018 17:50:05: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:50:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:50:05: #1 tags after filtering in treatment: 3095676 INFO @ Sun, 04 Nov 2018 17:50:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:50:05: #1 finished! INFO @ Sun, 04 Nov 2018 17:50:05: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:50:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:50:06: #2 number of paired peaks: 1168 INFO @ Sun, 04 Nov 2018 17:50:06: start model_add_line... INFO @ Sun, 04 Nov 2018 17:50:06: #2 number of paired peaks: 1168 INFO @ Sun, 04 Nov 2018 17:50:06: start model_add_line... INFO @ Sun, 04 Nov 2018 17:50:06: start X-correlation... INFO @ Sun, 04 Nov 2018 17:50:06: start X-correlation... INFO @ Sun, 04 Nov 2018 17:50:06: end of X-cor INFO @ Sun, 04 Nov 2018 17:50:06: end of X-cor INFO @ Sun, 04 Nov 2018 17:50:06: #2 finished! INFO @ Sun, 04 Nov 2018 17:50:06: #2 finished! INFO @ Sun, 04 Nov 2018 17:50:06: #2 predicted fragment length is 155 bps INFO @ Sun, 04 Nov 2018 17:50:06: #2 predicted fragment length is 155 bps INFO @ Sun, 04 Nov 2018 17:50:06: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 04 Nov 2018 17:50:06: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 04 Nov 2018 17:50:06: #2.2 Generate R script for model : SRX4344456.10_model.r INFO @ Sun, 04 Nov 2018 17:50:06: #2.2 Generate R script for model : SRX4344456.05_model.r INFO @ Sun, 04 Nov 2018 17:50:06: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:50:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:50:06: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:50:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:50:11: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:50:14: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:50:15: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:50:16: #4 Write output xls file... SRX4344456.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:50:16: #4 Write peak in narrowPeak format file... SRX4344456.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:50:16: #4 Write summits bed file... SRX4344456.20_summits.bed INFO @ Sun, 04 Nov 2018 17:50:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (769 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:50:19: #4 Write output xls file... SRX4344456.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:50:19: #4 Write peak in narrowPeak format file... SRX4344456.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:50:19: #4 Write summits bed file... SRX4344456.10_summits.bed INFO @ Sun, 04 Nov 2018 17:50:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1499 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:50:19: #4 Write output xls file... SRX4344456.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:50:19: #4 Write peak in narrowPeak format file... SRX4344456.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:50:19: #4 Write summits bed file... SRX4344456.05_summits.bed INFO @ Sun, 04 Nov 2018 17:50:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2571 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。