Job ID = 10609052 sra ファイルのダウンロード中... Completed: 398171K bytes transferred in 29 seconds (111693K 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 20981917 spots for /home/okishinya/chipatlas/results/ce10/SRX2202779/SRR4319285.sra Written 20981917 spots for /home/okishinya/chipatlas/results/ce10/SRX2202779/SRR4319285.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: 00:04:34 20981917 reads; of these: 20981917 (100.00%) were unpaired; of these: 6106381 (29.10%) aligned 0 times 9569837 (45.61%) aligned exactly 1 time 5305699 (25.29%) aligned >1 times 70.90% overall alignment rate Time searching: 00:04:34 Overall time: 00:04:34 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] 6565056 / 14875536 = 0.4413 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 @ Fri, 04 May 2018 07:10:43: # Command line: callpeak -t SRX2202779.bam -f BAM -g ce -n SRX2202779.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202779.10 # format = BAM # ChIP-seq file = ['SRX2202779.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 @ Fri, 04 May 2018 07:10:43: #1 read tag files... INFO @ Fri, 04 May 2018 07:10:43: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:10:43: # Command line: callpeak -t SRX2202779.bam -f BAM -g ce -n SRX2202779.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202779.05 # format = BAM # ChIP-seq file = ['SRX2202779.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 @ Fri, 04 May 2018 07:10:43: #1 read tag files... INFO @ Fri, 04 May 2018 07:10:43: # Command line: callpeak -t SRX2202779.bam -f BAM -g ce -n SRX2202779.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202779.20 # format = BAM # ChIP-seq file = ['SRX2202779.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 @ Fri, 04 May 2018 07:10:43: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:10:43: #1 read tag files... INFO @ Fri, 04 May 2018 07:10:43: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:10:51: 1000000 INFO @ Fri, 04 May 2018 07:10:51: 1000000 INFO @ Fri, 04 May 2018 07:10:52: 1000000 INFO @ Fri, 04 May 2018 07:10:59: 2000000 INFO @ Fri, 04 May 2018 07:11:00: 2000000 INFO @ Fri, 04 May 2018 07:11:01: 2000000 INFO @ Fri, 04 May 2018 07:11:07: 3000000 INFO @ Fri, 04 May 2018 07:11:08: 3000000 INFO @ Fri, 04 May 2018 07:11:10: 3000000 INFO @ Fri, 04 May 2018 07:11:15: 4000000 INFO @ Fri, 04 May 2018 07:11:16: 4000000 INFO @ Fri, 04 May 2018 07:11:19: 4000000 INFO @ Fri, 04 May 2018 07:11:23: 5000000 INFO @ Fri, 04 May 2018 07:11:24: 5000000 INFO @ Fri, 04 May 2018 07:11:27: 5000000 INFO @ Fri, 04 May 2018 07:11:31: 6000000 INFO @ Fri, 04 May 2018 07:11:32: 6000000 INFO @ Fri, 04 May 2018 07:11:36: 6000000 INFO @ Fri, 04 May 2018 07:11:38: 7000000 INFO @ Fri, 04 May 2018 07:11:40: 7000000 INFO @ Fri, 04 May 2018 07:11:44: 7000000 INFO @ Fri, 04 May 2018 07:11:46: 8000000 INFO @ Fri, 04 May 2018 07:11:48: 8000000 INFO @ Fri, 04 May 2018 07:11:49: #1 tag size is determined as 36 bps INFO @ Fri, 04 May 2018 07:11:49: #1 tag size = 36 INFO @ Fri, 04 May 2018 07:11:49: #1 total tags in treatment: 8310480 INFO @ Fri, 04 May 2018 07:11:49: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:11:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:11:49: #1 tags after filtering in treatment: 8310480 INFO @ Fri, 04 May 2018 07:11:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:11:49: #1 finished! INFO @ Fri, 04 May 2018 07:11:49: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:11:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:11:50: #2 number of paired peaks: 1543 INFO @ Fri, 04 May 2018 07:11:50: start model_add_line... INFO @ Fri, 04 May 2018 07:11:50: start X-correlation... INFO @ Fri, 04 May 2018 07:11:50: end of X-cor INFO @ Fri, 04 May 2018 07:11:50: #2 finished! INFO @ Fri, 04 May 2018 07:11:50: #2 predicted fragment length is 133 bps INFO @ Fri, 04 May 2018 07:11:50: #2 alternative fragment length(s) may be 133 bps INFO @ Fri, 04 May 2018 07:11:50: #2.2 Generate R script for model : SRX2202779.10_model.r INFO @ Fri, 04 May 2018 07:11:50: #3 Call peaks... INFO @ Fri, 04 May 2018 07:11:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:11:50: #1 tag size is determined as 36 bps INFO @ Fri, 04 May 2018 07:11:50: #1 tag size = 36 INFO @ Fri, 04 May 2018 07:11:50: #1 total tags in treatment: 8310480 INFO @ Fri, 04 May 2018 07:11:50: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:11:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:11:51: #1 tags after filtering in treatment: 8310480 INFO @ Fri, 04 May 2018 07:11:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:11:51: #1 finished! INFO @ Fri, 04 May 2018 07:11:51: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:11:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:11:51: #2 number of paired peaks: 1543 INFO @ Fri, 04 May 2018 07:11:51: start model_add_line... INFO @ Fri, 04 May 2018 07:11:51: start X-correlation... INFO @ Fri, 04 May 2018 07:11:51: end of X-cor INFO @ Fri, 04 May 2018 07:11:51: #2 finished! INFO @ Fri, 04 May 2018 07:11:51: #2 predicted fragment length is 133 bps INFO @ Fri, 04 May 2018 07:11:51: #2 alternative fragment length(s) may be 133 bps INFO @ Fri, 04 May 2018 07:11:51: #2.2 Generate R script for model : SRX2202779.20_model.r INFO @ Fri, 04 May 2018 07:11:51: #3 Call peaks... INFO @ Fri, 04 May 2018 07:11:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:11:53: 8000000 INFO @ Fri, 04 May 2018 07:11:55: #1 tag size is determined as 36 bps INFO @ Fri, 04 May 2018 07:11:55: #1 tag size = 36 INFO @ Fri, 04 May 2018 07:11:55: #1 total tags in treatment: 8310480 INFO @ Fri, 04 May 2018 07:11:55: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:11:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:11:55: #1 tags after filtering in treatment: 8310480 INFO @ Fri, 04 May 2018 07:11:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:11:55: #1 finished! INFO @ Fri, 04 May 2018 07:11:55: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:11:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:11:56: #2 number of paired peaks: 1543 INFO @ Fri, 04 May 2018 07:11:56: start model_add_line... INFO @ Fri, 04 May 2018 07:11:56: start X-correlation... INFO @ Fri, 04 May 2018 07:11:56: end of X-cor INFO @ Fri, 04 May 2018 07:11:56: #2 finished! INFO @ Fri, 04 May 2018 07:11:56: #2 predicted fragment length is 133 bps INFO @ Fri, 04 May 2018 07:11:56: #2 alternative fragment length(s) may be 133 bps INFO @ Fri, 04 May 2018 07:11:56: #2.2 Generate R script for model : SRX2202779.05_model.r INFO @ Fri, 04 May 2018 07:11:56: #3 Call peaks... INFO @ Fri, 04 May 2018 07:11:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:12:15: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:12:15: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:12:21: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:12:26: #4 Write output xls file... SRX2202779.20_peaks.xls INFO @ Fri, 04 May 2018 07:12:26: #4 Write peak in narrowPeak format file... SRX2202779.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:12:26: #4 Write summits bed file... SRX2202779.20_summits.bed INFO @ Fri, 04 May 2018 07:12:26: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1255 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:12:27: #4 Write output xls file... SRX2202779.10_peaks.xls INFO @ Fri, 04 May 2018 07:12:27: #4 Write peak in narrowPeak format file... SRX2202779.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:12:27: #4 Write summits bed file... SRX2202779.10_summits.bed INFO @ Fri, 04 May 2018 07:12:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2917 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:12:33: #4 Write output xls file... SRX2202779.05_peaks.xls INFO @ Fri, 04 May 2018 07:12:33: #4 Write peak in narrowPeak format file... SRX2202779.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:12:33: #4 Write summits bed file... SRX2202779.05_summits.bed INFO @ Fri, 04 May 2018 07:12:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5727 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。