Job ID = 11240700 sra ファイルのダウンロード中... Completed: 317414K bytes transferred in 7 seconds (338087K 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 10540793 spots for /home/okishinya/chipatlas/results/ce10/SRX4456923/SRR7591864.sra Written 10540793 spots for /home/okishinya/chipatlas/results/ce10/SRX4456923/SRR7591864.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: 00:02:09 10540793 reads; of these: 10540793 (100.00%) were unpaired; of these: 3474709 (32.96%) aligned 0 times 6094245 (57.82%) aligned exactly 1 time 971839 (9.22%) aligned >1 times 67.04% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 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] 1256937 / 7066084 = 0.1779 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, 07 Oct 2018 20:32:24: # Command line: callpeak -t SRX4456923.bam -f BAM -g ce -n SRX4456923.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4456923.10 # format = BAM # ChIP-seq file = ['SRX4456923.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, 07 Oct 2018 20:32:24: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:32:24: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:32:24: # Command line: callpeak -t SRX4456923.bam -f BAM -g ce -n SRX4456923.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4456923.20 # format = BAM # ChIP-seq file = ['SRX4456923.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, 07 Oct 2018 20:32:24: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:32:24: # Command line: callpeak -t SRX4456923.bam -f BAM -g ce -n SRX4456923.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4456923.05 # format = BAM # ChIP-seq file = ['SRX4456923.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, 07 Oct 2018 20:32:24: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:32:24: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:32:24: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:32:30: 1000000 INFO @ Sun, 07 Oct 2018 20:32:31: 1000000 INFO @ Sun, 07 Oct 2018 20:32:31: 1000000 INFO @ Sun, 07 Oct 2018 20:32:37: 2000000 INFO @ Sun, 07 Oct 2018 20:32:37: 2000000 INFO @ Sun, 07 Oct 2018 20:32:38: 2000000 INFO @ Sun, 07 Oct 2018 20:32:44: 3000000 INFO @ Sun, 07 Oct 2018 20:32:44: 3000000 INFO @ Sun, 07 Oct 2018 20:32:45: 3000000 INFO @ Sun, 07 Oct 2018 20:32:51: 4000000 INFO @ Sun, 07 Oct 2018 20:32:51: 4000000 INFO @ Sun, 07 Oct 2018 20:32:52: 4000000 INFO @ Sun, 07 Oct 2018 20:32:58: 5000000 INFO @ Sun, 07 Oct 2018 20:32:58: 5000000 INFO @ Sun, 07 Oct 2018 20:32:59: 5000000 INFO @ Sun, 07 Oct 2018 20:33:03: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:33:03: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:33:03: #1 total tags in treatment: 5809147 INFO @ Sun, 07 Oct 2018 20:33:03: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:33:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:33:03: #1 tags after filtering in treatment: 5809147 INFO @ Sun, 07 Oct 2018 20:33:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:33:03: #1 finished! INFO @ Sun, 07 Oct 2018 20:33:03: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:33:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:33:04: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:33:04: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:33:04: #1 total tags in treatment: 5809147 INFO @ Sun, 07 Oct 2018 20:33:04: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:33:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:33:04: #1 tags after filtering in treatment: 5809147 INFO @ Sun, 07 Oct 2018 20:33:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:33:04: #1 finished! INFO @ Sun, 07 Oct 2018 20:33:04: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:33:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:33:04: #2 number of paired peaks: 2651 INFO @ Sun, 07 Oct 2018 20:33:04: start model_add_line... INFO @ Sun, 07 Oct 2018 20:33:04: start X-correlation... INFO @ Sun, 07 Oct 2018 20:33:04: end of X-cor INFO @ Sun, 07 Oct 2018 20:33:04: #2 finished! INFO @ Sun, 07 Oct 2018 20:33:04: #2 predicted fragment length is 148 bps INFO @ Sun, 07 Oct 2018 20:33:04: #2 alternative fragment length(s) may be 145,148 bps INFO @ Sun, 07 Oct 2018 20:33:04: #2.2 Generate R script for model : SRX4456923.20_model.r INFO @ Sun, 07 Oct 2018 20:33:04: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:33:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:33:04: #2 number of paired peaks: 2651 INFO @ Sun, 07 Oct 2018 20:33:04: start model_add_line... INFO @ Sun, 07 Oct 2018 20:33:04: start X-correlation... INFO @ Sun, 07 Oct 2018 20:33:04: end of X-cor INFO @ Sun, 07 Oct 2018 20:33:04: #2 finished! INFO @ Sun, 07 Oct 2018 20:33:04: #2 predicted fragment length is 148 bps INFO @ Sun, 07 Oct 2018 20:33:04: #2 alternative fragment length(s) may be 145,148 bps INFO @ Sun, 07 Oct 2018 20:33:04: #2.2 Generate R script for model : SRX4456923.10_model.r INFO @ Sun, 07 Oct 2018 20:33:04: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:33:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:33:05: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:33:05: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:33:05: #1 total tags in treatment: 5809147 INFO @ Sun, 07 Oct 2018 20:33:05: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:33:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:33:05: #1 tags after filtering in treatment: 5809147 INFO @ Sun, 07 Oct 2018 20:33:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:33:05: #1 finished! INFO @ Sun, 07 Oct 2018 20:33:05: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:33:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:33:05: #2 number of paired peaks: 2651 INFO @ Sun, 07 Oct 2018 20:33:05: start model_add_line... INFO @ Sun, 07 Oct 2018 20:33:05: start X-correlation... INFO @ Sun, 07 Oct 2018 20:33:05: end of X-cor INFO @ Sun, 07 Oct 2018 20:33:05: #2 finished! INFO @ Sun, 07 Oct 2018 20:33:05: #2 predicted fragment length is 148 bps INFO @ Sun, 07 Oct 2018 20:33:05: #2 alternative fragment length(s) may be 145,148 bps INFO @ Sun, 07 Oct 2018 20:33:05: #2.2 Generate R script for model : SRX4456923.05_model.r INFO @ Sun, 07 Oct 2018 20:33:05: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:33:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:33:19: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:33:21: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:33:22: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:33:27: #4 Write output xls file... SRX4456923.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:33:27: #4 Write peak in narrowPeak format file... SRX4456923.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:33:27: #4 Write summits bed file... SRX4456923.10_summits.bed INFO @ Sun, 07 Oct 2018 20:33:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1991 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:33:29: #4 Write output xls file... SRX4456923.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:33:29: #4 Write peak in narrowPeak format file... SRX4456923.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:33:29: #4 Write summits bed file... SRX4456923.20_summits.bed INFO @ Sun, 07 Oct 2018 20:33:29: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (748 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:33:31: #4 Write output xls file... SRX4456923.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:33:31: #4 Write peak in narrowPeak format file... SRX4456923.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:33:31: #4 Write summits bed file... SRX4456923.05_summits.bed INFO @ Sun, 07 Oct 2018 20:33:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3850 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。