Job ID = 11634705 sra ファイルのダウンロード中... Completed: 700098K bytes transferred in 11 seconds (508508K 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 37600702 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4957441/SRR8136455.sra Written 37600702 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4957441/SRR8136455.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: 00:06:14 37600702 reads; of these: 37600702 (100.00%) were unpaired; of these: 7421735 (19.74%) aligned 0 times 20211861 (53.75%) aligned exactly 1 time 9967106 (26.51%) aligned >1 times 80.26% overall alignment rate Time searching: 00:06:14 Overall time: 00:06:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 26918393 / 30178967 = 0.8920 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, 15 Feb 2019 10:40:36: # Command line: callpeak -t SRX4957441.bam -f BAM -g 12100000 -n SRX4957441.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4957441.10 # format = BAM # ChIP-seq file = ['SRX4957441.bam'] # control file = None # effective genome size = 1.21e+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, 15 Feb 2019 10:40:36: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:40:36: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:40:36: # Command line: callpeak -t SRX4957441.bam -f BAM -g 12100000 -n SRX4957441.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4957441.20 # format = BAM # ChIP-seq file = ['SRX4957441.bam'] # control file = None # effective genome size = 1.21e+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, 15 Feb 2019 10:40:36: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:40:36: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:40:36: # Command line: callpeak -t SRX4957441.bam -f BAM -g 12100000 -n SRX4957441.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4957441.05 # format = BAM # ChIP-seq file = ['SRX4957441.bam'] # control file = None # effective genome size = 1.21e+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, 15 Feb 2019 10:40:36: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:40:36: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:40:43: 1000000 INFO @ Fri, 15 Feb 2019 10:40:43: 1000000 INFO @ Fri, 15 Feb 2019 10:40:43: 1000000 INFO @ Fri, 15 Feb 2019 10:40:49: 2000000 INFO @ Fri, 15 Feb 2019 10:40:49: 2000000 INFO @ Fri, 15 Feb 2019 10:40:49: 2000000 INFO @ Fri, 15 Feb 2019 10:40:55: 3000000 INFO @ Fri, 15 Feb 2019 10:40:56: 3000000 INFO @ Fri, 15 Feb 2019 10:40:56: 3000000 INFO @ Fri, 15 Feb 2019 10:40:57: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:40:57: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:40:57: #1 total tags in treatment: 3260574 INFO @ Fri, 15 Feb 2019 10:40:57: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:40:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:40:57: #1 tags after filtering in treatment: 3260574 INFO @ Fri, 15 Feb 2019 10:40:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:40:57: #1 finished! INFO @ Fri, 15 Feb 2019 10:40:57: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:40:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:40:57: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:40:57: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:40:57: #1 total tags in treatment: 3260574 INFO @ Fri, 15 Feb 2019 10:40:57: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:40:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:40:57: #2 number of paired peaks: 159 WARNING @ Fri, 15 Feb 2019 10:40:57: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Fri, 15 Feb 2019 10:40:57: start model_add_line... INFO @ Fri, 15 Feb 2019 10:40:57: #1 tags after filtering in treatment: 3260574 INFO @ Fri, 15 Feb 2019 10:40:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:40:57: #1 finished! INFO @ Fri, 15 Feb 2019 10:40:57: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:40:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:40:57: start X-correlation... INFO @ Fri, 15 Feb 2019 10:40:57: end of X-cor INFO @ Fri, 15 Feb 2019 10:40:57: #2 finished! INFO @ Fri, 15 Feb 2019 10:40:57: #2 predicted fragment length is 374 bps INFO @ Fri, 15 Feb 2019 10:40:57: #2 alternative fragment length(s) may be 374 bps INFO @ Fri, 15 Feb 2019 10:40:57: #2.2 Generate R script for model : SRX4957441.05_model.r INFO @ Fri, 15 Feb 2019 10:40:57: #3 Call peaks... INFO @ Fri, 15 Feb 2019 10:40:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 10:40:57: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:40:57: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:40:57: #1 total tags in treatment: 3260574 INFO @ Fri, 15 Feb 2019 10:40:57: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:40:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:40:57: #1 tags after filtering in treatment: 3260574 INFO @ Fri, 15 Feb 2019 10:40:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:40:57: #1 finished! INFO @ Fri, 15 Feb 2019 10:40:57: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:40:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:40:57: #2 number of paired peaks: 159 WARNING @ Fri, 15 Feb 2019 10:40:57: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Fri, 15 Feb 2019 10:40:57: start model_add_line... INFO @ Fri, 15 Feb 2019 10:40:57: start X-correlation... INFO @ Fri, 15 Feb 2019 10:40:57: end of X-cor INFO @ Fri, 15 Feb 2019 10:40:57: #2 finished! INFO @ Fri, 15 Feb 2019 10:40:57: #2 predicted fragment length is 374 bps INFO @ Fri, 15 Feb 2019 10:40:57: #2 alternative fragment length(s) may be 374 bps INFO @ Fri, 15 Feb 2019 10:40:57: #2.2 Generate R script for model : SRX4957441.20_model.r INFO @ Fri, 15 Feb 2019 10:40:57: #3 Call peaks... INFO @ Fri, 15 Feb 2019 10:40:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 10:40:58: #2 number of paired peaks: 159 WARNING @ Fri, 15 Feb 2019 10:40:58: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Fri, 15 Feb 2019 10:40:58: start model_add_line... INFO @ Fri, 15 Feb 2019 10:40:58: start X-correlation... INFO @ Fri, 15 Feb 2019 10:40:58: end of X-cor INFO @ Fri, 15 Feb 2019 10:40:58: #2 finished! INFO @ Fri, 15 Feb 2019 10:40:58: #2 predicted fragment length is 374 bps INFO @ Fri, 15 Feb 2019 10:40:58: #2 alternative fragment length(s) may be 374 bps INFO @ Fri, 15 Feb 2019 10:40:58: #2.2 Generate R script for model : SRX4957441.10_model.r INFO @ Fri, 15 Feb 2019 10:40:58: #3 Call peaks... INFO @ Fri, 15 Feb 2019 10:40:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 10:41:19: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 10:41:19: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 10:41:19: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 10:41:22: #4 Write output xls file... SRX4957441.05_peaks.xls INFO @ Fri, 15 Feb 2019 10:41:22: #4 Write peak in narrowPeak format file... SRX4957441.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 10:41:22: #4 Write summits bed file... SRX4957441.05_summits.bed INFO @ Fri, 15 Feb 2019 10:41:22: Done! pass1 - making usageList (16 chroms): 5 millis pass2 - checking and writing primary data (1117 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 10:41:22: #4 Write output xls file... SRX4957441.10_peaks.xls INFO @ Fri, 15 Feb 2019 10:41:22: #4 Write peak in narrowPeak format file... SRX4957441.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 10:41:22: #4 Write summits bed file... SRX4957441.10_summits.bed INFO @ Fri, 15 Feb 2019 10:41:22: Done! pass1 - making usageList (16 chroms): 5 millis pass2 - checking and writing primary data (872 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 10:41:22: #4 Write output xls file... SRX4957441.20_peaks.xls INFO @ Fri, 15 Feb 2019 10:41:22: #4 Write peak in narrowPeak format file... SRX4957441.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 10:41:22: #4 Write summits bed file... SRX4957441.20_summits.bed INFO @ Fri, 15 Feb 2019 10:41:23: Done! pass1 - making usageList (16 chroms): 5 millis pass2 - checking and writing primary data (687 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。