Job ID = 1296450 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,240,256 reads read : 20,480,512 reads written : 20,480,512 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:02:46 10240256 reads; of these: 10240256 (100.00%) were paired; of these: 9944890 (97.12%) aligned concordantly 0 times 203837 (1.99%) aligned concordantly exactly 1 time 91529 (0.89%) aligned concordantly >1 times ---- 9944890 pairs aligned concordantly 0 times; of these: 1743 (0.02%) aligned discordantly 1 time ---- 9943147 pairs aligned 0 times concordantly or discordantly; of these: 19886294 mates make up the pairs; of these: 19573891 (98.43%) aligned 0 times 121874 (0.61%) aligned exactly 1 time 190529 (0.96%) aligned >1 times 4.43% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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] 6441 / 295781 = 0.0218 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 @ Mon, 03 Jun 2019 16:26:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.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 @ Mon, 03 Jun 2019 16:26:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:26:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:26:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.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 @ Mon, 03 Jun 2019 16:26:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:26:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:26:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.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 @ Mon, 03 Jun 2019 16:26:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:26:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:27:03: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 16:27:03: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 16:27:03: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 16:27:03: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 16:27:03: #1 total tags in treatment: 288938 INFO @ Mon, 03 Jun 2019 16:27:03: #1 total tags in treatment: 288938 INFO @ Mon, 03 Jun 2019 16:27:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:27:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:27:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 16:27:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 16:27:03: #1 tags after filtering in treatment: 284920 INFO @ Mon, 03 Jun 2019 16:27:03: #1 tags after filtering in treatment: 284920 INFO @ Mon, 03 Jun 2019 16:27:03: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 03 Jun 2019 16:27:03: #1 finished! INFO @ Mon, 03 Jun 2019 16:27:03: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 03 Jun 2019 16:27:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:27:03: #1 finished! INFO @ Mon, 03 Jun 2019 16:27:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:27:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:27:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:27:03: #2 number of paired peaks: 662 WARNING @ Mon, 03 Jun 2019 16:27:03: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Mon, 03 Jun 2019 16:27:03: start model_add_line... INFO @ Mon, 03 Jun 2019 16:27:03: #2 number of paired peaks: 662 WARNING @ Mon, 03 Jun 2019 16:27:03: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Mon, 03 Jun 2019 16:27:03: start model_add_line... INFO @ Mon, 03 Jun 2019 16:27:03: start X-correlation... INFO @ Mon, 03 Jun 2019 16:27:03: start X-correlation... INFO @ Mon, 03 Jun 2019 16:27:03: end of X-cor INFO @ Mon, 03 Jun 2019 16:27:03: end of X-cor INFO @ Mon, 03 Jun 2019 16:27:03: #2 finished! INFO @ Mon, 03 Jun 2019 16:27:03: #2 finished! INFO @ Mon, 03 Jun 2019 16:27:03: #2 predicted fragment length is 89 bps INFO @ Mon, 03 Jun 2019 16:27:03: #2 alternative fragment length(s) may be 89 bps INFO @ Mon, 03 Jun 2019 16:27:03: #2 predicted fragment length is 89 bps INFO @ Mon, 03 Jun 2019 16:27:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.10_model.r INFO @ Mon, 03 Jun 2019 16:27:03: #2 alternative fragment length(s) may be 89 bps INFO @ Mon, 03 Jun 2019 16:27:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.20_model.r INFO @ Mon, 03 Jun 2019 16:27:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:27:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:27:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:27:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:27:03: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 16:27:03: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 16:27:03: #1 total tags in treatment: 288938 INFO @ Mon, 03 Jun 2019 16:27:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:27:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 16:27:03: #1 tags after filtering in treatment: 284920 INFO @ Mon, 03 Jun 2019 16:27:03: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 03 Jun 2019 16:27:03: #1 finished! INFO @ Mon, 03 Jun 2019 16:27:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:27:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:27:04: #2 number of paired peaks: 662 WARNING @ Mon, 03 Jun 2019 16:27:04: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Mon, 03 Jun 2019 16:27:04: start model_add_line... INFO @ Mon, 03 Jun 2019 16:27:04: start X-correlation... INFO @ Mon, 03 Jun 2019 16:27:04: end of X-cor INFO @ Mon, 03 Jun 2019 16:27:04: #2 finished! INFO @ Mon, 03 Jun 2019 16:27:04: #2 predicted fragment length is 89 bps INFO @ Mon, 03 Jun 2019 16:27:04: #2 alternative fragment length(s) may be 89 bps INFO @ Mon, 03 Jun 2019 16:27:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.05_model.r INFO @ Mon, 03 Jun 2019 16:27:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:27:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:27:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:27:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:27:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:27:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:27:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:27:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.10_summits.bed INFO @ Mon, 03 Jun 2019 16:27:05: Done! INFO @ Mon, 03 Jun 2019 16:27:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:27:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:27:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.20_summits.bed INFO @ Mon, 03 Jun 2019 16:27:05: Done! pass1 - making usageList (4 chroms): 1 millis pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (28 records, 4 fields): 1 millis pass2 - checking and writing primary data (47 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:27:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:27:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:27:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650777/SRX4650777.05_summits.bed INFO @ Mon, 03 Jun 2019 16:27:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (86 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。