Job ID = 1299396 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,375,300 reads read : 22,750,600 reads written : 22,750,600 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: 00:15:13 11375300 reads; of these: 11375300 (100.00%) were paired; of these: 6163175 (54.18%) aligned concordantly 0 times 3864448 (33.97%) aligned concordantly exactly 1 time 1347677 (11.85%) aligned concordantly >1 times ---- 6163175 pairs aligned concordantly 0 times; of these: 80184 (1.30%) aligned discordantly 1 time ---- 6082991 pairs aligned 0 times concordantly or discordantly; of these: 12165982 mates make up the pairs; of these: 11942613 (98.16%) aligned 0 times 140573 (1.16%) aligned exactly 1 time 82796 (0.68%) aligned >1 times 47.51% overall alignment rate Time searching: 00:15:13 Overall time: 00:15:13 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_sort_core] merging from 8 files... [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] 1743072 / 5289207 = 0.3296 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 18:34:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.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 18:34:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:34:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:34:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.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 18:34:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:34:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:34:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.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 18:34:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:34:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:35:07: 1000000 INFO @ Mon, 03 Jun 2019 18:35:07: 1000000 INFO @ Mon, 03 Jun 2019 18:35:08: 1000000 INFO @ Mon, 03 Jun 2019 18:35:14: 2000000 INFO @ Mon, 03 Jun 2019 18:35:15: 2000000 INFO @ Mon, 03 Jun 2019 18:35:16: 2000000 INFO @ Mon, 03 Jun 2019 18:35:22: 3000000 INFO @ Mon, 03 Jun 2019 18:35:23: 3000000 INFO @ Mon, 03 Jun 2019 18:35:24: 3000000 INFO @ Mon, 03 Jun 2019 18:35:29: 4000000 INFO @ Mon, 03 Jun 2019 18:35:30: 4000000 INFO @ Mon, 03 Jun 2019 18:35:33: 4000000 INFO @ Mon, 03 Jun 2019 18:35:36: 5000000 INFO @ Mon, 03 Jun 2019 18:35:38: 5000000 INFO @ Mon, 03 Jun 2019 18:35:41: 5000000 INFO @ Mon, 03 Jun 2019 18:35:44: 6000000 INFO @ Mon, 03 Jun 2019 18:35:45: 6000000 INFO @ Mon, 03 Jun 2019 18:35:49: 6000000 INFO @ Mon, 03 Jun 2019 18:35:51: 7000000 INFO @ Mon, 03 Jun 2019 18:35:52: 7000000 INFO @ Mon, 03 Jun 2019 18:35:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:35:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:35:53: #1 total tags in treatment: 3481801 INFO @ Mon, 03 Jun 2019 18:35:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:35:53: #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 18:35:53: #1 tags after filtering in treatment: 3413671 INFO @ Mon, 03 Jun 2019 18:35:53: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 18:35:53: #1 finished! INFO @ Mon, 03 Jun 2019 18:35:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:35:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:35:54: #2 number of paired peaks: 472 WARNING @ Mon, 03 Jun 2019 18:35:54: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Mon, 03 Jun 2019 18:35:54: start model_add_line... INFO @ Mon, 03 Jun 2019 18:35:54: start X-correlation... INFO @ Mon, 03 Jun 2019 18:35:54: end of X-cor INFO @ Mon, 03 Jun 2019 18:35:54: #2 finished! INFO @ Mon, 03 Jun 2019 18:35:54: #2 predicted fragment length is 142 bps INFO @ Mon, 03 Jun 2019 18:35:54: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 03 Jun 2019 18:35:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.05_model.r INFO @ Mon, 03 Jun 2019 18:35:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:35:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:35:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:35:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:35:55: #1 total tags in treatment: 3481801 INFO @ Mon, 03 Jun 2019 18:35:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:35:55: #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 18:35:55: #1 tags after filtering in treatment: 3413671 INFO @ Mon, 03 Jun 2019 18:35:55: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 18:35:55: #1 finished! INFO @ Mon, 03 Jun 2019 18:35:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:35:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:35:55: #2 number of paired peaks: 472 WARNING @ Mon, 03 Jun 2019 18:35:55: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Mon, 03 Jun 2019 18:35:55: start model_add_line... INFO @ Mon, 03 Jun 2019 18:35:55: start X-correlation... INFO @ Mon, 03 Jun 2019 18:35:55: end of X-cor INFO @ Mon, 03 Jun 2019 18:35:55: #2 finished! INFO @ Mon, 03 Jun 2019 18:35:55: #2 predicted fragment length is 142 bps INFO @ Mon, 03 Jun 2019 18:35:55: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 03 Jun 2019 18:35:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.10_model.r INFO @ Mon, 03 Jun 2019 18:35:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:35:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:35:57: 7000000 INFO @ Mon, 03 Jun 2019 18:36:00: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:36:00: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:36:00: #1 total tags in treatment: 3481801 INFO @ Mon, 03 Jun 2019 18:36:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:36:00: #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 18:36:00: #1 tags after filtering in treatment: 3413671 INFO @ Mon, 03 Jun 2019 18:36:00: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 18:36:00: #1 finished! INFO @ Mon, 03 Jun 2019 18:36:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:36:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:36:00: #2 number of paired peaks: 472 WARNING @ Mon, 03 Jun 2019 18:36:00: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Mon, 03 Jun 2019 18:36:00: start model_add_line... INFO @ Mon, 03 Jun 2019 18:36:00: start X-correlation... INFO @ Mon, 03 Jun 2019 18:36:00: end of X-cor INFO @ Mon, 03 Jun 2019 18:36:00: #2 finished! INFO @ Mon, 03 Jun 2019 18:36:00: #2 predicted fragment length is 142 bps INFO @ Mon, 03 Jun 2019 18:36:00: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 03 Jun 2019 18:36:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.20_model.r INFO @ Mon, 03 Jun 2019 18:36:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:36:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:36:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:36:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:36:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.05_peaks.xls INFO @ Mon, 03 Jun 2019 18:36:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:36:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.05_summits.bed INFO @ Mon, 03 Jun 2019 18:36:10: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (941 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:36:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:36:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.10_peaks.xls INFO @ Mon, 03 Jun 2019 18:36:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:36:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.10_summits.bed INFO @ Mon, 03 Jun 2019 18:36:11: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (608 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:36:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.20_peaks.xls INFO @ Mon, 03 Jun 2019 18:36:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:36:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474576/SRX474576.20_summits.bed INFO @ Mon, 03 Jun 2019 18:36:16: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (392 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。