Job ID = 9160146 sra ファイルのダウンロード中... Completed: 195598K bytes transferred in 12 seconds (131078K bits/sec), in 1 file, 2 directories. 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... Written 5649982 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2737260/SRR5448393.sra Written 5649982 spots total 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: 00:00:38 5649982 reads; of these: 5649982 (100.00%) were unpaired; of these: 3686044 (65.24%) aligned 0 times 1197894 (21.20%) aligned exactly 1 time 766044 (13.56%) aligned >1 times 34.76% overall alignment rate Time searching: 00:00:38 Overall time: 00:00:38 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_rmdupse_core] 824311 / 1963938 = 0.4197 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 @ Wed, 28 Jun 2017 01:57:41: # Command line: callpeak -t SRX2737260.bam -f BAM -g 12100000 -n SRX2737260.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2737260.05 # format = BAM # ChIP-seq file = ['SRX2737260.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 @ Wed, 28 Jun 2017 01:57:41: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:57:41: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:57:41: # Command line: callpeak -t SRX2737260.bam -f BAM -g 12100000 -n SRX2737260.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2737260.20 # format = BAM # ChIP-seq file = ['SRX2737260.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 @ Wed, 28 Jun 2017 01:57:41: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:57:41: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:57:41: # Command line: callpeak -t SRX2737260.bam -f BAM -g 12100000 -n SRX2737260.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2737260.10 # format = BAM # ChIP-seq file = ['SRX2737260.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 @ Wed, 28 Jun 2017 01:57:41: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:57:41: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:57:48: 1000000 INFO @ Wed, 28 Jun 2017 01:57:48: 1000000 INFO @ Wed, 28 Jun 2017 01:57:48: 1000000 INFO @ Wed, 28 Jun 2017 01:57:49: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:57:49: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:57:49: #1 total tags in treatment: 1139627 INFO @ Wed, 28 Jun 2017 01:57:49: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:57:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:57:49: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:57:49: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:57:49: #1 total tags in treatment: 1139627 INFO @ Wed, 28 Jun 2017 01:57:49: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:57:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:57:49: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:57:49: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:57:49: #1 total tags in treatment: 1139627 INFO @ Wed, 28 Jun 2017 01:57:49: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:57:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:57:49: #1 tags after filtering in treatment: 1139627 INFO @ Wed, 28 Jun 2017 01:57:49: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 01:57:49: #1 finished! INFO @ Wed, 28 Jun 2017 01:57:49: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:57:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:57:49: #1 tags after filtering in treatment: 1139627 INFO @ Wed, 28 Jun 2017 01:57:49: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 01:57:49: #1 finished! INFO @ Wed, 28 Jun 2017 01:57:49: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:57:49: #1 tags after filtering in treatment: 1139627 INFO @ Wed, 28 Jun 2017 01:57:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:57:49: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 01:57:49: #1 finished! INFO @ Wed, 28 Jun 2017 01:57:49: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:57:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:57:49: #2 number of paired peaks: 132 WARNING @ Wed, 28 Jun 2017 01:57:49: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Wed, 28 Jun 2017 01:57:49: start model_add_line... INFO @ Wed, 28 Jun 2017 01:57:49: start X-correlation... INFO @ Wed, 28 Jun 2017 01:57:49: end of X-cor INFO @ Wed, 28 Jun 2017 01:57:49: #2 finished! INFO @ Wed, 28 Jun 2017 01:57:49: #2 predicted fragment length is 247 bps INFO @ Wed, 28 Jun 2017 01:57:49: #2 alternative fragment length(s) may be 2,23,50,70,92,154,205,247,281,285,369,491,577 bps INFO @ Wed, 28 Jun 2017 01:57:49: #2.2 Generate R script for model : SRX2737260.05_model.r INFO @ Wed, 28 Jun 2017 01:57:49: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:57:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:57:49: #2 number of paired peaks: 132 WARNING @ Wed, 28 Jun 2017 01:57:49: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Wed, 28 Jun 2017 01:57:49: start model_add_line... INFO @ Wed, 28 Jun 2017 01:57:49: #2 number of paired peaks: 132 WARNING @ Wed, 28 Jun 2017 01:57:49: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Wed, 28 Jun 2017 01:57:49: start model_add_line... INFO @ Wed, 28 Jun 2017 01:57:49: start X-correlation... INFO @ Wed, 28 Jun 2017 01:57:49: start X-correlation... INFO @ Wed, 28 Jun 2017 01:57:49: end of X-cor INFO @ Wed, 28 Jun 2017 01:57:49: #2 finished! INFO @ Wed, 28 Jun 2017 01:57:49: #2 predicted fragment length is 247 bps INFO @ Wed, 28 Jun 2017 01:57:49: #2 alternative fragment length(s) may be 2,23,50,70,92,154,205,247,281,285,369,491,577 bps INFO @ Wed, 28 Jun 2017 01:57:49: #2.2 Generate R script for model : SRX2737260.20_model.r INFO @ Wed, 28 Jun 2017 01:57:49: end of X-cor INFO @ Wed, 28 Jun 2017 01:57:49: #2 finished! INFO @ Wed, 28 Jun 2017 01:57:49: #2 predicted fragment length is 247 bps INFO @ Wed, 28 Jun 2017 01:57:49: #2 alternative fragment length(s) may be 2,23,50,70,92,154,205,247,281,285,369,491,577 bps INFO @ Wed, 28 Jun 2017 01:57:49: #2.2 Generate R script for model : SRX2737260.10_model.r INFO @ Wed, 28 Jun 2017 01:57:49: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:57:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:57:49: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:57:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:57:53: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:57:53: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:57:53: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:57:54: #4 Write output xls file... SRX2737260.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:57:54: #4 Write peak in narrowPeak format file... SRX2737260.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:57:54: #4 Write summits bed file... SRX2737260.10_summits.bed INFO @ Wed, 28 Jun 2017 01:57:54: Done! INFO @ Wed, 28 Jun 2017 01:57:54: #4 Write output xls file... SRX2737260.05_peaks.xls INFO @ Wed, 28 Jun 2017 01:57:54: #4 Write peak in narrowPeak format file... SRX2737260.05_peaks.narrowPeak pass1 - making usageList (17 chroms): 1 millis INFO @ Wed, 28 Jun 2017 01:57:54: #4 Write summits bed file... SRX2737260.05_summits.bed pass2 - checking and writing primary data (81 records, 4 fields): 2 millis INFO @ Wed, 28 Jun 2017 01:57:54: Done! CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (240 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:57:54: #4 Write output xls file... SRX2737260.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:57:54: #4 Write peak in narrowPeak format file... SRX2737260.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:57:54: #4 Write summits bed file... SRX2737260.20_summits.bed INFO @ Wed, 28 Jun 2017 01:57:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (38 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。