Job ID = 10609051 sra ファイルのダウンロード中... Completed: 196644K bytes transferred in 24 seconds (66636K 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 16007623 spots for /home/okishinya/chipatlas/results/ce10/SRX2202776/SRR4319282.sra Written 16007623 spots for /home/okishinya/chipatlas/results/ce10/SRX2202776/SRR4319282.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: 00:04:00 16007623 reads; of these: 16007623 (100.00%) were unpaired; of these: 3804064 (23.76%) aligned 0 times 7469016 (46.66%) aligned exactly 1 time 4734543 (29.58%) aligned >1 times 76.24% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3395762 / 12203559 = 0.2783 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 07:10:05: # Command line: callpeak -t SRX2202776.bam -f BAM -g ce -n SRX2202776.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202776.10 # format = BAM # ChIP-seq file = ['SRX2202776.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 07:10:05: #1 read tag files... INFO @ Fri, 04 May 2018 07:10:05: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:10:05: # Command line: callpeak -t SRX2202776.bam -f BAM -g ce -n SRX2202776.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202776.05 # format = BAM # ChIP-seq file = ['SRX2202776.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 07:10:05: #1 read tag files... INFO @ Fri, 04 May 2018 07:10:05: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:10:05: # Command line: callpeak -t SRX2202776.bam -f BAM -g ce -n SRX2202776.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202776.20 # format = BAM # ChIP-seq file = ['SRX2202776.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 07:10:05: #1 read tag files... INFO @ Fri, 04 May 2018 07:10:05: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:10:13: 1000000 INFO @ Fri, 04 May 2018 07:10:13: 1000000 INFO @ Fri, 04 May 2018 07:10:13: 1000000 INFO @ Fri, 04 May 2018 07:10:20: 2000000 INFO @ Fri, 04 May 2018 07:10:21: 2000000 INFO @ Fri, 04 May 2018 07:10:21: 2000000 INFO @ Fri, 04 May 2018 07:10:28: 3000000 INFO @ Fri, 04 May 2018 07:10:29: 3000000 INFO @ Fri, 04 May 2018 07:10:29: 3000000 INFO @ Fri, 04 May 2018 07:10:36: 4000000 INFO @ Fri, 04 May 2018 07:10:37: 4000000 INFO @ Fri, 04 May 2018 07:10:37: 4000000 INFO @ Fri, 04 May 2018 07:10:44: 5000000 INFO @ Fri, 04 May 2018 07:10:45: 5000000 INFO @ Fri, 04 May 2018 07:10:45: 5000000 INFO @ Fri, 04 May 2018 07:10:53: 6000000 INFO @ Fri, 04 May 2018 07:10:53: 6000000 INFO @ Fri, 04 May 2018 07:10:53: 6000000 INFO @ Fri, 04 May 2018 07:11:01: 7000000 INFO @ Fri, 04 May 2018 07:11:02: 7000000 INFO @ Fri, 04 May 2018 07:11:02: 7000000 INFO @ Fri, 04 May 2018 07:11:10: 8000000 INFO @ Fri, 04 May 2018 07:11:10: 8000000 INFO @ Fri, 04 May 2018 07:11:10: 8000000 INFO @ Fri, 04 May 2018 07:11:17: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:11:17: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:11:17: #1 total tags in treatment: 8807797 INFO @ Fri, 04 May 2018 07:11:17: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:11:17: #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 07:11:17: #1 tags after filtering in treatment: 8807797 INFO @ Fri, 04 May 2018 07:11:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:11:17: #1 finished! INFO @ Fri, 04 May 2018 07:11:17: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:11:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:11:17: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:11:17: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:11:17: #1 total tags in treatment: 8807797 INFO @ Fri, 04 May 2018 07:11:17: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:11:17: #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 07:11:17: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:11:17: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:11:17: #1 total tags in treatment: 8807797 INFO @ Fri, 04 May 2018 07:11:17: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:11:17: #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 07:11:17: #1 tags after filtering in treatment: 8807797 INFO @ Fri, 04 May 2018 07:11:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:11:17: #1 finished! INFO @ Fri, 04 May 2018 07:11:17: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:11:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:11:17: #1 tags after filtering in treatment: 8807797 INFO @ Fri, 04 May 2018 07:11:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:11:17: #1 finished! INFO @ Fri, 04 May 2018 07:11:17: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:11:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:11:18: #2 number of paired peaks: 2325 INFO @ Fri, 04 May 2018 07:11:18: start model_add_line... INFO @ Fri, 04 May 2018 07:11:18: start X-correlation... INFO @ Fri, 04 May 2018 07:11:18: end of X-cor INFO @ Fri, 04 May 2018 07:11:18: #2 finished! INFO @ Fri, 04 May 2018 07:11:18: #2 predicted fragment length is 114 bps INFO @ Fri, 04 May 2018 07:11:18: #2 alternative fragment length(s) may be 3,114 bps INFO @ Fri, 04 May 2018 07:11:18: #2.2 Generate R script for model : SRX2202776.10_model.r INFO @ Fri, 04 May 2018 07:11:18: #3 Call peaks... INFO @ Fri, 04 May 2018 07:11:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:11:18: #2 number of paired peaks: 2325 INFO @ Fri, 04 May 2018 07:11:18: start model_add_line... INFO @ Fri, 04 May 2018 07:11:18: #2 number of paired peaks: 2325 INFO @ Fri, 04 May 2018 07:11:18: start model_add_line... INFO @ Fri, 04 May 2018 07:11:18: start X-correlation... INFO @ Fri, 04 May 2018 07:11:18: end of X-cor INFO @ Fri, 04 May 2018 07:11:18: #2 finished! INFO @ Fri, 04 May 2018 07:11:18: #2 predicted fragment length is 114 bps INFO @ Fri, 04 May 2018 07:11:18: #2 alternative fragment length(s) may be 3,114 bps INFO @ Fri, 04 May 2018 07:11:18: #2.2 Generate R script for model : SRX2202776.20_model.r INFO @ Fri, 04 May 2018 07:11:18: #3 Call peaks... INFO @ Fri, 04 May 2018 07:11:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:11:18: start X-correlation... INFO @ Fri, 04 May 2018 07:11:18: end of X-cor INFO @ Fri, 04 May 2018 07:11:18: #2 finished! INFO @ Fri, 04 May 2018 07:11:18: #2 predicted fragment length is 114 bps INFO @ Fri, 04 May 2018 07:11:18: #2 alternative fragment length(s) may be 3,114 bps INFO @ Fri, 04 May 2018 07:11:18: #2.2 Generate R script for model : SRX2202776.05_model.r INFO @ Fri, 04 May 2018 07:11:18: #3 Call peaks... INFO @ Fri, 04 May 2018 07:11:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:11:43: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:11:43: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:11:44: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:11:55: #4 Write output xls file... SRX2202776.10_peaks.xls INFO @ Fri, 04 May 2018 07:11:55: #4 Write peak in narrowPeak format file... SRX2202776.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:11:55: #4 Write summits bed file... SRX2202776.10_summits.bed INFO @ Fri, 04 May 2018 07:11:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1949 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:11:55: #4 Write output xls file... SRX2202776.05_peaks.xls INFO @ Fri, 04 May 2018 07:11:55: #4 Write peak in narrowPeak format file... SRX2202776.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:11:55: #4 Write summits bed file... SRX2202776.05_summits.bed INFO @ Fri, 04 May 2018 07:11:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4152 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:11:55: #4 Write output xls file... SRX2202776.20_peaks.xls INFO @ Fri, 04 May 2018 07:11:55: #4 Write peak in narrowPeak format file... SRX2202776.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:11:55: #4 Write summits bed file... SRX2202776.20_summits.bed INFO @ Fri, 04 May 2018 07:11:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (735 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。