Job ID = 4178420 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,683,074 reads read : 3,366,148 reads written : 3,366,148 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: 00:00:01 Multiseed full-index search: 00:03:30 1683074 reads; of these: 1683074 (100.00%) were paired; of these: 398276 (23.66%) aligned concordantly 0 times 1075335 (63.89%) aligned concordantly exactly 1 time 209463 (12.45%) aligned concordantly >1 times ---- 398276 pairs aligned concordantly 0 times; of these: 253653 (63.69%) aligned discordantly 1 time ---- 144623 pairs aligned 0 times concordantly or discordantly; of these: 289246 mates make up the pairs; of these: 150485 (52.03%) aligned 0 times 65452 (22.63%) aligned exactly 1 time 73309 (25.34%) aligned >1 times 95.53% overall alignment rate Time searching: 00:03:31 Overall time: 00:03:31 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] 201869 / 1536852 = 0.1314 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:24:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.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 12:24:58: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:24:58: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:25:05: 1000000 INFO @ Thu, 05 Dec 2019 12:25:12: 2000000 INFO @ Thu, 05 Dec 2019 12:25:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.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 12:25:16: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:25:16: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:25:18: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:25:18: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:25:18: #1 total tags in treatment: 1110446 INFO @ Thu, 05 Dec 2019 12:25:18: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:25:18: #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 12:25:18: #1 tags after filtering in treatment: 1101370 INFO @ Thu, 05 Dec 2019 12:25:18: #1 Redundant rate of treatment: 0.01 INFO @ Thu, 05 Dec 2019 12:25:18: #1 finished! INFO @ Thu, 05 Dec 2019 12:25:18: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:25:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:25:18: #2 number of paired peaks: 244 WARNING @ Thu, 05 Dec 2019 12:25:18: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Thu, 05 Dec 2019 12:25:18: start model_add_line... INFO @ Thu, 05 Dec 2019 12:25:18: start X-correlation... INFO @ Thu, 05 Dec 2019 12:25:18: end of X-cor INFO @ Thu, 05 Dec 2019 12:25:18: #2 finished! INFO @ Thu, 05 Dec 2019 12:25:18: #2 predicted fragment length is 283 bps INFO @ Thu, 05 Dec 2019 12:25:18: #2 alternative fragment length(s) may be 250,283 bps INFO @ Thu, 05 Dec 2019 12:25:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.05_model.r INFO @ Thu, 05 Dec 2019 12:25:21: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:25:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:25:23: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:25:23: 1000000 INFO @ Thu, 05 Dec 2019 12:25:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:25:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:25:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.05_summits.bed INFO @ Thu, 05 Dec 2019 12:25:24: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (148 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:25:30: 2000000 INFO @ Thu, 05 Dec 2019 12:25:35: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:25:35: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:25:35: #1 total tags in treatment: 1110446 INFO @ Thu, 05 Dec 2019 12:25:35: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:25:35: #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 12:25:35: #1 tags after filtering in treatment: 1101370 INFO @ Thu, 05 Dec 2019 12:25:35: #1 Redundant rate of treatment: 0.01 INFO @ Thu, 05 Dec 2019 12:25:35: #1 finished! INFO @ Thu, 05 Dec 2019 12:25:35: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:25:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:25:36: #2 number of paired peaks: 244 WARNING @ Thu, 05 Dec 2019 12:25:36: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Thu, 05 Dec 2019 12:25:36: start model_add_line... INFO @ Thu, 05 Dec 2019 12:25:36: start X-correlation... INFO @ Thu, 05 Dec 2019 12:25:36: end of X-cor INFO @ Thu, 05 Dec 2019 12:25:36: #2 finished! INFO @ Thu, 05 Dec 2019 12:25:36: #2 predicted fragment length is 283 bps INFO @ Thu, 05 Dec 2019 12:25:36: #2 alternative fragment length(s) may be 250,283 bps INFO @ Thu, 05 Dec 2019 12:25:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.10_model.r INFO @ Thu, 05 Dec 2019 12:25:36: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:25:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:25:38: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:25:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:25:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:25:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.10_summits.bed INFO @ Thu, 05 Dec 2019 12:25:39: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (108 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:25:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.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 12:25:46: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:25:46: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:25:53: 1000000 INFO @ Thu, 05 Dec 2019 12:25:59: 2000000 INFO @ Thu, 05 Dec 2019 12:26:04: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:26:04: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:26:04: #1 total tags in treatment: 1110446 INFO @ Thu, 05 Dec 2019 12:26:04: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:26:04: #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 12:26:04: #1 tags after filtering in treatment: 1101370 INFO @ Thu, 05 Dec 2019 12:26:04: #1 Redundant rate of treatment: 0.01 INFO @ Thu, 05 Dec 2019 12:26:04: #1 finished! INFO @ Thu, 05 Dec 2019 12:26:04: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:26:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:26:04: #2 number of paired peaks: 244 WARNING @ Thu, 05 Dec 2019 12:26:04: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Thu, 05 Dec 2019 12:26:04: start model_add_line... INFO @ Thu, 05 Dec 2019 12:26:04: start X-correlation... INFO @ Thu, 05 Dec 2019 12:26:04: end of X-cor INFO @ Thu, 05 Dec 2019 12:26:04: #2 finished! INFO @ Thu, 05 Dec 2019 12:26:04: #2 predicted fragment length is 283 bps INFO @ Thu, 05 Dec 2019 12:26:04: #2 alternative fragment length(s) may be 250,283 bps INFO @ Thu, 05 Dec 2019 12:26:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.20_model.r INFO @ Thu, 05 Dec 2019 12:26:04: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:26:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:26:07: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:26:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:26:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:26:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2095158/SRX2095158.20_summits.bed INFO @ Thu, 05 Dec 2019 12:26:08: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (76 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。