Job ID = 1294043 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,585,248 reads read : 11,170,496 reads written : 11,170,496 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: 00:11:46 5585248 reads; of these: 5585248 (100.00%) were paired; of these: 1553355 (27.81%) aligned concordantly 0 times 3367215 (60.29%) aligned concordantly exactly 1 time 664678 (11.90%) aligned concordantly >1 times ---- 1553355 pairs aligned concordantly 0 times; of these: 416822 (26.83%) aligned discordantly 1 time ---- 1136533 pairs aligned 0 times concordantly or discordantly; of these: 2273066 mates make up the pairs; of these: 1910378 (84.04%) aligned 0 times 154380 (6.79%) aligned exactly 1 time 208308 (9.16%) aligned >1 times 82.90% overall alignment rate Time searching: 00:11:46 Overall time: 00:11:46 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] 191314 / 4444180 = 0.0430 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 04:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.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 04:42:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:42:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.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 04:42:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:42:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.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 04:42:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:42:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:42:26: 1000000 INFO @ Mon, 03 Jun 2019 04:42:26: 1000000 INFO @ Mon, 03 Jun 2019 04:42:26: 1000000 INFO @ Mon, 03 Jun 2019 04:42:34: 2000000 INFO @ Mon, 03 Jun 2019 04:42:35: 2000000 INFO @ Mon, 03 Jun 2019 04:42:35: 2000000 INFO @ Mon, 03 Jun 2019 04:42:43: 3000000 INFO @ Mon, 03 Jun 2019 04:42:44: 3000000 INFO @ Mon, 03 Jun 2019 04:42:44: 3000000 INFO @ Mon, 03 Jun 2019 04:42:52: 4000000 INFO @ Mon, 03 Jun 2019 04:42:53: 4000000 INFO @ Mon, 03 Jun 2019 04:42:53: 4000000 INFO @ Mon, 03 Jun 2019 04:43:00: 5000000 INFO @ Mon, 03 Jun 2019 04:43:02: 5000000 INFO @ Mon, 03 Jun 2019 04:43:02: 5000000 INFO @ Mon, 03 Jun 2019 04:43:09: 6000000 INFO @ Mon, 03 Jun 2019 04:43:11: 6000000 INFO @ Mon, 03 Jun 2019 04:43:11: 6000000 INFO @ Mon, 03 Jun 2019 04:43:17: 7000000 INFO @ Mon, 03 Jun 2019 04:43:20: 7000000 INFO @ Mon, 03 Jun 2019 04:43:20: 7000000 INFO @ Mon, 03 Jun 2019 04:43:26: 8000000 INFO @ Mon, 03 Jun 2019 04:43:29: 8000000 INFO @ Mon, 03 Jun 2019 04:43:29: 8000000 INFO @ Mon, 03 Jun 2019 04:43:33: #1 tag size is determined as 81 bps INFO @ Mon, 03 Jun 2019 04:43:33: #1 tag size = 81 INFO @ Mon, 03 Jun 2019 04:43:33: #1 total tags in treatment: 3848816 INFO @ Mon, 03 Jun 2019 04:43:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:43:33: #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 04:43:33: #1 tags after filtering in treatment: 3657512 INFO @ Mon, 03 Jun 2019 04:43:33: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 04:43:33: #1 finished! INFO @ Mon, 03 Jun 2019 04:43:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:43:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:43:34: #2 number of paired peaks: 3146 INFO @ Mon, 03 Jun 2019 04:43:34: start model_add_line... INFO @ Mon, 03 Jun 2019 04:43:34: start X-correlation... INFO @ Mon, 03 Jun 2019 04:43:34: end of X-cor INFO @ Mon, 03 Jun 2019 04:43:34: #2 finished! INFO @ Mon, 03 Jun 2019 04:43:34: #2 predicted fragment length is 217 bps INFO @ Mon, 03 Jun 2019 04:43:34: #2 alternative fragment length(s) may be 217 bps INFO @ Mon, 03 Jun 2019 04:43:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.05_model.r INFO @ Mon, 03 Jun 2019 04:43:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:43:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:43:37: #1 tag size is determined as 81 bps INFO @ Mon, 03 Jun 2019 04:43:37: #1 tag size = 81 INFO @ Mon, 03 Jun 2019 04:43:37: #1 total tags in treatment: 3848816 INFO @ Mon, 03 Jun 2019 04:43:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:43:37: #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 04:43:37: #1 tags after filtering in treatment: 3657512 INFO @ Mon, 03 Jun 2019 04:43:37: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 04:43:37: #1 finished! INFO @ Mon, 03 Jun 2019 04:43:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:43:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:43:37: #1 tag size is determined as 81 bps INFO @ Mon, 03 Jun 2019 04:43:37: #1 tag size = 81 INFO @ Mon, 03 Jun 2019 04:43:37: #1 total tags in treatment: 3848816 INFO @ Mon, 03 Jun 2019 04:43:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:43:37: #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 04:43:37: #1 tags after filtering in treatment: 3657512 INFO @ Mon, 03 Jun 2019 04:43:37: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 04:43:37: #1 finished! INFO @ Mon, 03 Jun 2019 04:43:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:43:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:43:38: #2 number of paired peaks: 3146 INFO @ Mon, 03 Jun 2019 04:43:38: start model_add_line... INFO @ Mon, 03 Jun 2019 04:43:38: start X-correlation... INFO @ Mon, 03 Jun 2019 04:43:38: end of X-cor INFO @ Mon, 03 Jun 2019 04:43:38: #2 finished! INFO @ Mon, 03 Jun 2019 04:43:38: #2 predicted fragment length is 217 bps INFO @ Mon, 03 Jun 2019 04:43:38: #2 alternative fragment length(s) may be 217 bps INFO @ Mon, 03 Jun 2019 04:43:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.10_model.r INFO @ Mon, 03 Jun 2019 04:43:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:43:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:43:38: #2 number of paired peaks: 3146 INFO @ Mon, 03 Jun 2019 04:43:38: start model_add_line... INFO @ Mon, 03 Jun 2019 04:43:38: start X-correlation... INFO @ Mon, 03 Jun 2019 04:43:38: end of X-cor INFO @ Mon, 03 Jun 2019 04:43:38: #2 finished! INFO @ Mon, 03 Jun 2019 04:43:38: #2 predicted fragment length is 217 bps INFO @ Mon, 03 Jun 2019 04:43:38: #2 alternative fragment length(s) may be 217 bps INFO @ Mon, 03 Jun 2019 04:43:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.20_model.r INFO @ Mon, 03 Jun 2019 04:43:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:43:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:43:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:43:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:43:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:43:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:43:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:43:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.05_summits.bed INFO @ Mon, 03 Jun 2019 04:43:52: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (5116 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:43:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:43:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:43:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.10_summits.bed INFO @ Mon, 03 Jun 2019 04:43:56: Done! INFO @ Mon, 03 Jun 2019 04:43:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:43:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:43:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763409/SRX1763409.20_summits.bed INFO @ Mon, 03 Jun 2019 04:43:56: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3655 records, 4 fields): 7 millis CompletedMACS2peakCalling pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2270 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。