Job ID = 1299483 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,056,558 reads read : 26,113,116 reads written : 26,113,116 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: 00:30:36 13056558 reads; of these: 13056558 (100.00%) were paired; of these: 5088226 (38.97%) aligned concordantly 0 times 6076937 (46.54%) aligned concordantly exactly 1 time 1891395 (14.49%) aligned concordantly >1 times ---- 5088226 pairs aligned concordantly 0 times; of these: 72036 (1.42%) aligned discordantly 1 time ---- 5016190 pairs aligned 0 times concordantly or discordantly; of these: 10032380 mates make up the pairs; of these: 9718993 (96.88%) aligned 0 times 185310 (1.85%) aligned exactly 1 time 128077 (1.28%) aligned >1 times 62.78% overall alignment rate Time searching: 00:30:36 Overall time: 00:30:36 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] 1836437 / 8033202 = 0.2286 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 18:58:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.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 18:58:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:58:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:58:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.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 18:58:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:58:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:58:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.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 18:58:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:58:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:58:38: 1000000 INFO @ Mon, 03 Jun 2019 18:58:38: 1000000 INFO @ Mon, 03 Jun 2019 18:58:38: 1000000 INFO @ Mon, 03 Jun 2019 18:58:49: 2000000 INFO @ Mon, 03 Jun 2019 18:58:49: 2000000 INFO @ Mon, 03 Jun 2019 18:58:50: 2000000 INFO @ Mon, 03 Jun 2019 18:58:59: 3000000 INFO @ Mon, 03 Jun 2019 18:59:00: 3000000 INFO @ Mon, 03 Jun 2019 18:59:01: 3000000 INFO @ Mon, 03 Jun 2019 18:59:11: 4000000 INFO @ Mon, 03 Jun 2019 18:59:12: 4000000 INFO @ Mon, 03 Jun 2019 18:59:13: 4000000 INFO @ Mon, 03 Jun 2019 18:59:21: 5000000 INFO @ Mon, 03 Jun 2019 18:59:23: 5000000 INFO @ Mon, 03 Jun 2019 18:59:25: 5000000 INFO @ Mon, 03 Jun 2019 18:59:32: 6000000 INFO @ Mon, 03 Jun 2019 18:59:34: 6000000 INFO @ Mon, 03 Jun 2019 18:59:36: 6000000 INFO @ Mon, 03 Jun 2019 18:59:44: 7000000 INFO @ Mon, 03 Jun 2019 18:59:46: 7000000 INFO @ Mon, 03 Jun 2019 18:59:48: 7000000 INFO @ Mon, 03 Jun 2019 18:59:55: 8000000 INFO @ Mon, 03 Jun 2019 18:59:58: 8000000 INFO @ Mon, 03 Jun 2019 18:59:59: 8000000 INFO @ Mon, 03 Jun 2019 19:00:06: 9000000 INFO @ Mon, 03 Jun 2019 19:00:09: 9000000 INFO @ Mon, 03 Jun 2019 19:00:11: 9000000 INFO @ Mon, 03 Jun 2019 19:00:18: 10000000 INFO @ Mon, 03 Jun 2019 19:00:21: 10000000 INFO @ Mon, 03 Jun 2019 19:00:23: 10000000 INFO @ Mon, 03 Jun 2019 19:00:30: 11000000 INFO @ Mon, 03 Jun 2019 19:00:32: 11000000 INFO @ Mon, 03 Jun 2019 19:00:35: 11000000 INFO @ Mon, 03 Jun 2019 19:00:41: 12000000 INFO @ Mon, 03 Jun 2019 19:00:44: 12000000 INFO @ Mon, 03 Jun 2019 19:00:47: 12000000 INFO @ Mon, 03 Jun 2019 19:00:49: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:00:49: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:00:49: #1 total tags in treatment: 6141577 INFO @ Mon, 03 Jun 2019 19:00:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:00:49: #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 19:00:49: #1 tags after filtering in treatment: 5477855 INFO @ Mon, 03 Jun 2019 19:00:49: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 19:00:49: #1 finished! INFO @ Mon, 03 Jun 2019 19:00:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:00:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:00:50: #2 number of paired peaks: 483 WARNING @ Mon, 03 Jun 2019 19:00:50: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Mon, 03 Jun 2019 19:00:50: start model_add_line... INFO @ Mon, 03 Jun 2019 19:00:50: start X-correlation... INFO @ Mon, 03 Jun 2019 19:00:50: end of X-cor INFO @ Mon, 03 Jun 2019 19:00:50: #2 finished! INFO @ Mon, 03 Jun 2019 19:00:50: #2 predicted fragment length is 143 bps INFO @ Mon, 03 Jun 2019 19:00:50: #2 alternative fragment length(s) may be 143 bps INFO @ Mon, 03 Jun 2019 19:00:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.20_model.r INFO @ Mon, 03 Jun 2019 19:00:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:00:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:00:52: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:00:52: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:00:52: #1 total tags in treatment: 6141577 INFO @ Mon, 03 Jun 2019 19:00:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:00:52: #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 19:00:52: #1 tags after filtering in treatment: 5477855 INFO @ Mon, 03 Jun 2019 19:00:52: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 19:00:52: #1 finished! INFO @ Mon, 03 Jun 2019 19:00:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:00:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:00:54: #2 number of paired peaks: 483 WARNING @ Mon, 03 Jun 2019 19:00:54: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Mon, 03 Jun 2019 19:00:54: start model_add_line... INFO @ Mon, 03 Jun 2019 19:00:54: start X-correlation... INFO @ Mon, 03 Jun 2019 19:00:54: end of X-cor INFO @ Mon, 03 Jun 2019 19:00:54: #2 finished! INFO @ Mon, 03 Jun 2019 19:00:54: #2 predicted fragment length is 143 bps INFO @ Mon, 03 Jun 2019 19:00:54: #2 alternative fragment length(s) may be 143 bps INFO @ Mon, 03 Jun 2019 19:00:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.05_model.r INFO @ Mon, 03 Jun 2019 19:00:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:00:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:00:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:00:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:00:55: #1 total tags in treatment: 6141577 INFO @ Mon, 03 Jun 2019 19:00:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:00:55: #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 19:00:55: #1 tags after filtering in treatment: 5477855 INFO @ Mon, 03 Jun 2019 19:00:55: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 19:00:55: #1 finished! INFO @ Mon, 03 Jun 2019 19:00:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:00:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:00:56: #2 number of paired peaks: 483 WARNING @ Mon, 03 Jun 2019 19:00:56: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Mon, 03 Jun 2019 19:00:56: start model_add_line... INFO @ Mon, 03 Jun 2019 19:00:56: start X-correlation... INFO @ Mon, 03 Jun 2019 19:00:56: end of X-cor INFO @ Mon, 03 Jun 2019 19:00:56: #2 finished! INFO @ Mon, 03 Jun 2019 19:00:56: #2 predicted fragment length is 143 bps INFO @ Mon, 03 Jun 2019 19:00:56: #2 alternative fragment length(s) may be 143 bps INFO @ Mon, 03 Jun 2019 19:00:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.10_model.r INFO @ Mon, 03 Jun 2019 19:00:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:00:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:01:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:01:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:01:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:01:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:01:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:01:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.20_summits.bed INFO @ Mon, 03 Jun 2019 19:01:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (432 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:01:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:01:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:01:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.05_summits.bed INFO @ Mon, 03 Jun 2019 19:01:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4630 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:01:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:01:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:01:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474583/SRX474583.10_summits.bed INFO @ Mon, 03 Jun 2019 19:01:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1985 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。