Job ID = 1293891 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 19,495,013 reads read : 38,990,026 reads written : 38,990,026 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: 00:07:20 19495013 reads; of these: 19495013 (100.00%) were paired; of these: 16743105 (85.88%) aligned concordantly 0 times 2193657 (11.25%) aligned concordantly exactly 1 time 558251 (2.86%) aligned concordantly >1 times ---- 16743105 pairs aligned concordantly 0 times; of these: 4694 (0.03%) aligned discordantly 1 time ---- 16738411 pairs aligned 0 times concordantly or discordantly; of these: 33476822 mates make up the pairs; of these: 33356218 (99.64%) aligned 0 times 93780 (0.28%) aligned exactly 1 time 26824 (0.08%) aligned >1 times 14.45% overall alignment rate Time searching: 00:07:20 Overall time: 00:07:20 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] 357398 / 2754040 = 0.1298 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 03:11:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.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 03:11:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:11:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:11:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.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 03:11:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:11:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:11:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.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 03:11:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:11:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:11:13: 1000000 INFO @ Mon, 03 Jun 2019 03:11:15: 1000000 INFO @ Mon, 03 Jun 2019 03:11:15: 1000000 INFO @ Mon, 03 Jun 2019 03:11:19: 2000000 INFO @ Mon, 03 Jun 2019 03:11:25: 2000000 INFO @ Mon, 03 Jun 2019 03:11:25: 2000000 INFO @ Mon, 03 Jun 2019 03:11:26: 3000000 INFO @ Mon, 03 Jun 2019 03:11:33: 4000000 INFO @ Mon, 03 Jun 2019 03:11:35: 3000000 INFO @ Mon, 03 Jun 2019 03:11:35: 3000000 INFO @ Mon, 03 Jun 2019 03:11:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:11:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:11:39: #1 total tags in treatment: 2395027 INFO @ Mon, 03 Jun 2019 03:11:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:11:39: #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 03:11:39: #1 tags after filtering in treatment: 2357069 INFO @ Mon, 03 Jun 2019 03:11:39: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 03:11:39: #1 finished! INFO @ Mon, 03 Jun 2019 03:11:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:11:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:11:39: #2 number of paired peaks: 623 WARNING @ Mon, 03 Jun 2019 03:11:39: Fewer paired peaks (623) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 623 pairs to build model! INFO @ Mon, 03 Jun 2019 03:11:39: start model_add_line... INFO @ Mon, 03 Jun 2019 03:11:39: start X-correlation... INFO @ Mon, 03 Jun 2019 03:11:39: end of X-cor INFO @ Mon, 03 Jun 2019 03:11:39: #2 finished! INFO @ Mon, 03 Jun 2019 03:11:39: #2 predicted fragment length is 109 bps INFO @ Mon, 03 Jun 2019 03:11:39: #2 alternative fragment length(s) may be 109 bps INFO @ Mon, 03 Jun 2019 03:11:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.20_model.r INFO @ Mon, 03 Jun 2019 03:11:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:11:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:11:44: 4000000 INFO @ Mon, 03 Jun 2019 03:11:44: 4000000 INFO @ Mon, 03 Jun 2019 03:11:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:11:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:11:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:11:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.20_summits.bed INFO @ Mon, 03 Jun 2019 03:11:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (121 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:11:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:11:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:11:53: #1 total tags in treatment: 2395027 INFO @ Mon, 03 Jun 2019 03:11:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:11:53: #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 03:11:53: #1 tags after filtering in treatment: 2357069 INFO @ Mon, 03 Jun 2019 03:11:53: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 03:11:53: #1 finished! INFO @ Mon, 03 Jun 2019 03:11:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:11:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:11:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:11:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:11:53: #1 total tags in treatment: 2395027 INFO @ Mon, 03 Jun 2019 03:11:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:11:53: #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 03:11:53: #1 tags after filtering in treatment: 2357069 INFO @ Mon, 03 Jun 2019 03:11:53: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 03:11:53: #1 finished! INFO @ Mon, 03 Jun 2019 03:11:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:11:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:11:53: #2 number of paired peaks: 623 WARNING @ Mon, 03 Jun 2019 03:11:53: Fewer paired peaks (623) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 623 pairs to build model! INFO @ Mon, 03 Jun 2019 03:11:53: start model_add_line... INFO @ Mon, 03 Jun 2019 03:11:53: start X-correlation... INFO @ Mon, 03 Jun 2019 03:11:53: end of X-cor INFO @ Mon, 03 Jun 2019 03:11:53: #2 finished! INFO @ Mon, 03 Jun 2019 03:11:53: #2 predicted fragment length is 109 bps INFO @ Mon, 03 Jun 2019 03:11:53: #2 alternative fragment length(s) may be 109 bps INFO @ Mon, 03 Jun 2019 03:11:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.10_model.r INFO @ Mon, 03 Jun 2019 03:11:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:11:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:11:54: #2 number of paired peaks: 623 WARNING @ Mon, 03 Jun 2019 03:11:54: Fewer paired peaks (623) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 623 pairs to build model! INFO @ Mon, 03 Jun 2019 03:11:54: start model_add_line... INFO @ Mon, 03 Jun 2019 03:11:54: start X-correlation... INFO @ Mon, 03 Jun 2019 03:11:54: end of X-cor INFO @ Mon, 03 Jun 2019 03:11:54: #2 finished! INFO @ Mon, 03 Jun 2019 03:11:54: #2 predicted fragment length is 109 bps INFO @ Mon, 03 Jun 2019 03:11:54: #2 alternative fragment length(s) may be 109 bps INFO @ Mon, 03 Jun 2019 03:11:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.05_model.r INFO @ Mon, 03 Jun 2019 03:11:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:11:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:12:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:12:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:12:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:12:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:12:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.10_summits.bed INFO @ Mon, 03 Jun 2019 03:12:04: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (264 records, 4 fields): 2 millis INFO @ Mon, 03 Jun 2019 03:12:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.05_peaks.xls CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:12:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:12:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX143462/SRX143462.05_summits.bed INFO @ Mon, 03 Jun 2019 03:12:04: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (658 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。