Job ID = 2590984 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,211,908 reads read : 4,423,816 reads written : 4,423,816 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: 00:12:04 2211908 reads; of these: 2211908 (100.00%) were paired; of these: 363050 (16.41%) aligned concordantly 0 times 451949 (20.43%) aligned concordantly exactly 1 time 1396909 (63.15%) aligned concordantly >1 times ---- 363050 pairs aligned concordantly 0 times; of these: 19692 (5.42%) aligned discordantly 1 time ---- 343358 pairs aligned 0 times concordantly or discordantly; of these: 686716 mates make up the pairs; of these: 268935 (39.16%) aligned 0 times 60464 (8.80%) aligned exactly 1 time 357317 (52.03%) aligned >1 times 93.92% overall alignment rate Time searching: 00:12:04 Overall time: 00:12:04 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] 1536699 / 1867347 = 0.8229 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 00:31:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.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 00:31:52: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:31:52: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:31:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.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 00:31:53: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:31:53: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:31:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.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 00:31:54: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:31:54: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:32:00: 1000000 INFO @ Tue, 13 Aug 2019 00:32:01: #1 tag size is determined as 81 bps INFO @ Tue, 13 Aug 2019 00:32:01: #1 tag size = 81 INFO @ Tue, 13 Aug 2019 00:32:01: #1 total tags in treatment: 324365 INFO @ Tue, 13 Aug 2019 00:32:01: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:32:01: #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 00:32:01: #1 tags after filtering in treatment: 235933 INFO @ Tue, 13 Aug 2019 00:32:01: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 13 Aug 2019 00:32:01: #1 finished! INFO @ Tue, 13 Aug 2019 00:32:01: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:32:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:32:01: #2 number of paired peaks: 8962 INFO @ Tue, 13 Aug 2019 00:32:01: start model_add_line... INFO @ Tue, 13 Aug 2019 00:32:01: start X-correlation... INFO @ Tue, 13 Aug 2019 00:32:01: end of X-cor INFO @ Tue, 13 Aug 2019 00:32:01: #2 finished! INFO @ Tue, 13 Aug 2019 00:32:01: #2 predicted fragment length is 294 bps INFO @ Tue, 13 Aug 2019 00:32:01: #2 alternative fragment length(s) may be 5,113,294 bps INFO @ Tue, 13 Aug 2019 00:32:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.05_model.r INFO @ Tue, 13 Aug 2019 00:32:01: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:32:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:32:02: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:32:02: 1000000 INFO @ Tue, 13 Aug 2019 00:32:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:32:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:32:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.05_summits.bed INFO @ Tue, 13 Aug 2019 00:32:02: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (277 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:32:03: #1 tag size is determined as 81 bps INFO @ Tue, 13 Aug 2019 00:32:03: #1 tag size = 81 INFO @ Tue, 13 Aug 2019 00:32:03: #1 total tags in treatment: 324365 INFO @ Tue, 13 Aug 2019 00:32:03: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:32:03: #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 00:32:03: #1 tags after filtering in treatment: 235933 INFO @ Tue, 13 Aug 2019 00:32:03: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 13 Aug 2019 00:32:03: #1 finished! INFO @ Tue, 13 Aug 2019 00:32:03: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:32:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:32:03: #2 number of paired peaks: 8962 INFO @ Tue, 13 Aug 2019 00:32:03: start model_add_line... INFO @ Tue, 13 Aug 2019 00:32:03: start X-correlation... INFO @ Tue, 13 Aug 2019 00:32:03: end of X-cor INFO @ Tue, 13 Aug 2019 00:32:03: #2 finished! INFO @ Tue, 13 Aug 2019 00:32:03: #2 predicted fragment length is 294 bps INFO @ Tue, 13 Aug 2019 00:32:03: #2 alternative fragment length(s) may be 5,113,294 bps INFO @ Tue, 13 Aug 2019 00:32:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.20_model.r INFO @ Tue, 13 Aug 2019 00:32:03: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:32:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:32:03: 1000000 INFO @ Tue, 13 Aug 2019 00:32:04: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:32:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:32:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:32:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.20_summits.bed INFO @ Tue, 13 Aug 2019 00:32:04: Done! INFO @ Tue, 13 Aug 2019 00:32:04: #1 tag size is determined as 81 bps INFO @ Tue, 13 Aug 2019 00:32:04: #1 tag size = 81 INFO @ Tue, 13 Aug 2019 00:32:04: #1 total tags in treatment: 324365 INFO @ Tue, 13 Aug 2019 00:32:04: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:32:04: #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 00:32:04: #1 tags after filtering in treatment: 235933 INFO @ Tue, 13 Aug 2019 00:32:04: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 13 Aug 2019 00:32:04: #1 finished! INFO @ Tue, 13 Aug 2019 00:32:04: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:32:04: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:32:04: #2 number of paired peaks: 8962 INFO @ Tue, 13 Aug 2019 00:32:04: start model_add_line... INFO @ Tue, 13 Aug 2019 00:32:04: start X-correlation... INFO @ Tue, 13 Aug 2019 00:32:04: end of X-cor INFO @ Tue, 13 Aug 2019 00:32:04: #2 finished! INFO @ Tue, 13 Aug 2019 00:32:04: #2 predicted fragment length is 294 bps INFO @ Tue, 13 Aug 2019 00:32:04: #2 alternative fragment length(s) may be 5,113,294 bps INFO @ Tue, 13 Aug 2019 00:32:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.10_model.r INFO @ Tue, 13 Aug 2019 00:32:04: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:32:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:32:05: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:32:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:32:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:32:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441114/SRX6441114.10_summits.bed INFO @ Tue, 13 Aug 2019 00:32:05: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (26 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。