Job ID = 2590988 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 957,780 reads read : 1,915,560 reads written : 1,915,560 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: 00:00:00 Multiseed full-index search: 00:03:12 957780 reads; of these: 957780 (100.00%) were paired; of these: 313653 (32.75%) aligned concordantly 0 times 282240 (29.47%) aligned concordantly exactly 1 time 361887 (37.78%) aligned concordantly >1 times ---- 313653 pairs aligned concordantly 0 times; of these: 18792 (5.99%) aligned discordantly 1 time ---- 294861 pairs aligned 0 times concordantly or discordantly; of these: 589722 mates make up the pairs; of these: 299143 (50.73%) aligned 0 times 90562 (15.36%) aligned exactly 1 time 200017 (33.92%) aligned >1 times 84.38% overall alignment rate Time searching: 00:03:12 Overall time: 00:03:12 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] 534143 / 661253 = 0.8078 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 @ Tue, 13 Aug 2019 00:21:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.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 @ Tue, 13 Aug 2019 00:21:03: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:21:03: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:21:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.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 @ Tue, 13 Aug 2019 00:21:04: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:21:04: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:21:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.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 @ Tue, 13 Aug 2019 00:21:05: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:21:05: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:21:07: #1 tag size is determined as 75 bps INFO @ Tue, 13 Aug 2019 00:21:07: #1 tag size = 75 INFO @ Tue, 13 Aug 2019 00:21:07: #1 total tags in treatment: 121506 INFO @ Tue, 13 Aug 2019 00:21:07: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:21:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:21:07: #1 tags after filtering in treatment: 94177 INFO @ Tue, 13 Aug 2019 00:21:07: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 13 Aug 2019 00:21:07: #1 finished! INFO @ Tue, 13 Aug 2019 00:21:07: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:21:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:21:08: #2 number of paired peaks: 6388 INFO @ Tue, 13 Aug 2019 00:21:08: start model_add_line... INFO @ Tue, 13 Aug 2019 00:21:08: start X-correlation... INFO @ Tue, 13 Aug 2019 00:21:08: end of X-cor INFO @ Tue, 13 Aug 2019 00:21:08: #2 finished! INFO @ Tue, 13 Aug 2019 00:21:08: #2 predicted fragment length is 295 bps INFO @ Tue, 13 Aug 2019 00:21:08: #2 alternative fragment length(s) may be 6,124,246,295 bps INFO @ Tue, 13 Aug 2019 00:21:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.05_model.r INFO @ Tue, 13 Aug 2019 00:21:08: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:21:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:21:08: #1 tag size is determined as 75 bps INFO @ Tue, 13 Aug 2019 00:21:08: #1 tag size = 75 INFO @ Tue, 13 Aug 2019 00:21:08: #1 total tags in treatment: 121506 INFO @ Tue, 13 Aug 2019 00:21:08: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:21:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:21:08: #1 tags after filtering in treatment: 94177 INFO @ Tue, 13 Aug 2019 00:21:08: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 13 Aug 2019 00:21:08: #1 finished! INFO @ Tue, 13 Aug 2019 00:21:08: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:21:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:21:08: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:21:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:21:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:21:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.05_summits.bed INFO @ Tue, 13 Aug 2019 00:21:08: Done! INFO @ Tue, 13 Aug 2019 00:21:08: #2 number of paired peaks: 6388 INFO @ Tue, 13 Aug 2019 00:21:08: start model_add_line... INFO @ Tue, 13 Aug 2019 00:21:08: start X-correlation... INFO @ Tue, 13 Aug 2019 00:21:08: end of X-cor INFO @ Tue, 13 Aug 2019 00:21:08: #2 finished! INFO @ Tue, 13 Aug 2019 00:21:08: #2 predicted fragment length is 295 bps INFO @ Tue, 13 Aug 2019 00:21:08: #2 alternative fragment length(s) may be 6,124,246,295 bps INFO @ Tue, 13 Aug 2019 00:21:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.10_model.r INFO @ Tue, 13 Aug 2019 00:21:08: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:21:08: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (30 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:21:08: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:21:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:21:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:21:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.10_summits.bed INFO @ Tue, 13 Aug 2019 00:21:09: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (1 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 INFO @ Tue, 13 Aug 2019 00:21:09: #1 tag size is determined as 75 bps INFO @ Tue, 13 Aug 2019 00:21:09: #1 tag size = 75 INFO @ Tue, 13 Aug 2019 00:21:09: #1 total tags in treatment: 121506 INFO @ Tue, 13 Aug 2019 00:21:09: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:21:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換中... INFO @ Tue, 13 Aug 2019 00:21:09: #1 tags after filtering in treatment: 94177 INFO @ Tue, 13 Aug 2019 00:21:09: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 13 Aug 2019 00:21:09: #1 finished! INFO @ Tue, 13 Aug 2019 00:21:09: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:21:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:21:10: #2 number of paired peaks: 6388 INFO @ Tue, 13 Aug 2019 00:21:10: start model_add_line... INFO @ Tue, 13 Aug 2019 00:21:10: start X-correlation... INFO @ Tue, 13 Aug 2019 00:21:10: end of X-cor INFO @ Tue, 13 Aug 2019 00:21:10: #2 finished! INFO @ Tue, 13 Aug 2019 00:21:10: #2 predicted fragment length is 295 bps INFO @ Tue, 13 Aug 2019 00:21:10: #2 alternative fragment length(s) may be 6,124,246,295 bps INFO @ Tue, 13 Aug 2019 00:21:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.20_model.r INFO @ Tue, 13 Aug 2019 00:21:10: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:21:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:21:10: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:21:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:21:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:21:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441118/SRX6441118.20_summits.bed INFO @ Tue, 13 Aug 2019 00:21:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。