Job ID = 4178426 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 990,577 reads read : 1,981,154 reads written : 1,981,154 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:45 990577 reads; of these: 990577 (100.00%) were paired; of these: 536222 (54.13%) aligned concordantly 0 times 405964 (40.98%) aligned concordantly exactly 1 time 48391 (4.89%) aligned concordantly >1 times ---- 536222 pairs aligned concordantly 0 times; of these: 41690 (7.77%) aligned discordantly 1 time ---- 494532 pairs aligned 0 times concordantly or discordantly; of these: 989064 mates make up the pairs; of these: 948098 (95.86%) aligned 0 times 28787 (2.91%) aligned exactly 1 time 12179 (1.23%) aligned >1 times 52.14% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 4234 / 327466 = 0.0129 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:21:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 12:21:25: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:21:25: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:21:33: 1000000 INFO @ Thu, 05 Dec 2019 12:21:33: #1 tag size is determined as 68 bps INFO @ Thu, 05 Dec 2019 12:21:33: #1 tag size = 68 INFO @ Thu, 05 Dec 2019 12:21:33: #1 total tags in treatment: 450178 INFO @ Thu, 05 Dec 2019 12:21:33: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:21:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:21:33: #1 tags after filtering in treatment: 446309 INFO @ Thu, 05 Dec 2019 12:21:33: #1 Redundant rate of treatment: 0.01 INFO @ Thu, 05 Dec 2019 12:21:33: #1 finished! INFO @ Thu, 05 Dec 2019 12:21:33: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:21:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:21:33: #2 number of paired peaks: 800 WARNING @ Thu, 05 Dec 2019 12:21:33: Fewer paired peaks (800) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 800 pairs to build model! INFO @ Thu, 05 Dec 2019 12:21:33: start model_add_line... INFO @ Thu, 05 Dec 2019 12:21:34: start X-correlation... INFO @ Thu, 05 Dec 2019 12:21:34: end of X-cor INFO @ Thu, 05 Dec 2019 12:21:34: #2 finished! INFO @ Thu, 05 Dec 2019 12:21:34: #2 predicted fragment length is 260 bps INFO @ Thu, 05 Dec 2019 12:21:34: #2 alternative fragment length(s) may be 93,129,234,260 bps INFO @ Thu, 05 Dec 2019 12:21:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.05_model.r INFO @ Thu, 05 Dec 2019 12:21:34: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:21:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:21:35: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:21:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:21:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:21:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.05_summits.bed INFO @ Thu, 05 Dec 2019 12:21:35: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:21:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 12:21:55: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:21:55: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:22:03: 1000000 INFO @ Thu, 05 Dec 2019 12:22:03: #1 tag size is determined as 68 bps INFO @ Thu, 05 Dec 2019 12:22:03: #1 tag size = 68 INFO @ Thu, 05 Dec 2019 12:22:03: #1 total tags in treatment: 450178 INFO @ Thu, 05 Dec 2019 12:22:03: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:22:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:22:03: #1 tags after filtering in treatment: 446309 INFO @ Thu, 05 Dec 2019 12:22:03: #1 Redundant rate of treatment: 0.01 INFO @ Thu, 05 Dec 2019 12:22:03: #1 finished! INFO @ Thu, 05 Dec 2019 12:22:03: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:22:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:22:03: #2 number of paired peaks: 800 WARNING @ Thu, 05 Dec 2019 12:22:03: Fewer paired peaks (800) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 800 pairs to build model! INFO @ Thu, 05 Dec 2019 12:22:03: start model_add_line... INFO @ Thu, 05 Dec 2019 12:22:03: start X-correlation... INFO @ Thu, 05 Dec 2019 12:22:03: end of X-cor INFO @ Thu, 05 Dec 2019 12:22:03: #2 finished! INFO @ Thu, 05 Dec 2019 12:22:03: #2 predicted fragment length is 260 bps INFO @ Thu, 05 Dec 2019 12:22:03: #2 alternative fragment length(s) may be 93,129,234,260 bps INFO @ Thu, 05 Dec 2019 12:22:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.10_model.r INFO @ Thu, 05 Dec 2019 12:22:03: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:22:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:22:04: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:22:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:22:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:22:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.10_summits.bed INFO @ Thu, 05 Dec 2019 12:22:04: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 0 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:22:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 12:22:25: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:22:25: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:22:33: 1000000 INFO @ Thu, 05 Dec 2019 12:22:33: #1 tag size is determined as 68 bps INFO @ Thu, 05 Dec 2019 12:22:33: #1 tag size = 68 INFO @ Thu, 05 Dec 2019 12:22:33: #1 total tags in treatment: 450178 INFO @ Thu, 05 Dec 2019 12:22:33: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:22:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:22:33: #1 tags after filtering in treatment: 446309 INFO @ Thu, 05 Dec 2019 12:22:33: #1 Redundant rate of treatment: 0.01 INFO @ Thu, 05 Dec 2019 12:22:33: #1 finished! INFO @ Thu, 05 Dec 2019 12:22:33: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:22:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:22:33: #2 number of paired peaks: 800 WARNING @ Thu, 05 Dec 2019 12:22:33: Fewer paired peaks (800) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 800 pairs to build model! INFO @ Thu, 05 Dec 2019 12:22:33: start model_add_line... INFO @ Thu, 05 Dec 2019 12:22:33: start X-correlation... INFO @ Thu, 05 Dec 2019 12:22:33: end of X-cor INFO @ Thu, 05 Dec 2019 12:22:33: #2 finished! INFO @ Thu, 05 Dec 2019 12:22:33: #2 predicted fragment length is 260 bps INFO @ Thu, 05 Dec 2019 12:22:33: #2 alternative fragment length(s) may be 93,129,234,260 bps INFO @ Thu, 05 Dec 2019 12:22:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.20_model.r INFO @ Thu, 05 Dec 2019 12:22:33: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:22:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:22:34: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:22:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:22:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:22:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3434307/SRX3434307.20_summits.bed INFO @ Thu, 05 Dec 2019 12:22:35: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。