Job ID = 1294040 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,718,830 reads read : 11,437,660 reads written : 11,437,660 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: 00:13:23 5718830 reads; of these: 5718830 (100.00%) were paired; of these: 886992 (15.51%) aligned concordantly 0 times 4042454 (70.69%) aligned concordantly exactly 1 time 789384 (13.80%) aligned concordantly >1 times ---- 886992 pairs aligned concordantly 0 times; of these: 369830 (41.69%) aligned discordantly 1 time ---- 517162 pairs aligned 0 times concordantly or discordantly; of these: 1034324 mates make up the pairs; of these: 689204 (66.63%) aligned 0 times 157566 (15.23%) aligned exactly 1 time 187554 (18.13%) aligned >1 times 93.97% overall alignment rate Time searching: 00:13:23 Overall time: 00:13:23 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] 207807 / 5195178 = 0.0400 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 04:43:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.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 04:43:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:43:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:43:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.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 04:43:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:43:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:43:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.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 04:43:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:43:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:44:00: 1000000 INFO @ Mon, 03 Jun 2019 04:44:01: 1000000 INFO @ Mon, 03 Jun 2019 04:44:01: 1000000 INFO @ Mon, 03 Jun 2019 04:44:07: 2000000 INFO @ Mon, 03 Jun 2019 04:44:10: 2000000 INFO @ Mon, 03 Jun 2019 04:44:10: 2000000 INFO @ Mon, 03 Jun 2019 04:44:15: 3000000 INFO @ Mon, 03 Jun 2019 04:44:18: 3000000 INFO @ Mon, 03 Jun 2019 04:44:19: 3000000 INFO @ Mon, 03 Jun 2019 04:44:22: 4000000 INFO @ Mon, 03 Jun 2019 04:44:27: 4000000 INFO @ Mon, 03 Jun 2019 04:44:28: 4000000 INFO @ Mon, 03 Jun 2019 04:44:30: 5000000 INFO @ Mon, 03 Jun 2019 04:44:36: 5000000 INFO @ Mon, 03 Jun 2019 04:44:37: 5000000 INFO @ Mon, 03 Jun 2019 04:44:37: 6000000 INFO @ Mon, 03 Jun 2019 04:44:45: 7000000 INFO @ Mon, 03 Jun 2019 04:44:45: 6000000 INFO @ Mon, 03 Jun 2019 04:44:46: 6000000 INFO @ Mon, 03 Jun 2019 04:44:52: 8000000 INFO @ Mon, 03 Jun 2019 04:44:53: 7000000 INFO @ Mon, 03 Jun 2019 04:44:54: 7000000 INFO @ Mon, 03 Jun 2019 04:45:00: 9000000 INFO @ Mon, 03 Jun 2019 04:45:01: 8000000 INFO @ Mon, 03 Jun 2019 04:45:03: 8000000 INFO @ Mon, 03 Jun 2019 04:45:07: 10000000 INFO @ Mon, 03 Jun 2019 04:45:10: #1 tag size is determined as 82 bps INFO @ Mon, 03 Jun 2019 04:45:10: #1 tag size = 82 INFO @ Mon, 03 Jun 2019 04:45:10: #1 total tags in treatment: 4630354 INFO @ Mon, 03 Jun 2019 04:45:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:45:10: #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 04:45:10: #1 tags after filtering in treatment: 4375975 INFO @ Mon, 03 Jun 2019 04:45:10: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 04:45:10: #1 finished! INFO @ Mon, 03 Jun 2019 04:45:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:45:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:45:10: 9000000 INFO @ Mon, 03 Jun 2019 04:45:10: #2 number of paired peaks: 3100 INFO @ Mon, 03 Jun 2019 04:45:10: start model_add_line... INFO @ Mon, 03 Jun 2019 04:45:10: start X-correlation... INFO @ Mon, 03 Jun 2019 04:45:10: end of X-cor INFO @ Mon, 03 Jun 2019 04:45:10: #2 finished! INFO @ Mon, 03 Jun 2019 04:45:10: #2 predicted fragment length is 216 bps INFO @ Mon, 03 Jun 2019 04:45:10: #2 alternative fragment length(s) may be 216 bps INFO @ Mon, 03 Jun 2019 04:45:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.20_model.r INFO @ Mon, 03 Jun 2019 04:45:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:45:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:45:12: 9000000 INFO @ Mon, 03 Jun 2019 04:45:18: 10000000 INFO @ Mon, 03 Jun 2019 04:45:21: 10000000 INFO @ Mon, 03 Jun 2019 04:45:21: #1 tag size is determined as 82 bps INFO @ Mon, 03 Jun 2019 04:45:21: #1 tag size = 82 INFO @ Mon, 03 Jun 2019 04:45:21: #1 total tags in treatment: 4630354 INFO @ Mon, 03 Jun 2019 04:45:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:45:21: #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 04:45:21: #1 tags after filtering in treatment: 4375975 INFO @ Mon, 03 Jun 2019 04:45:21: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 04:45:21: #1 finished! INFO @ Mon, 03 Jun 2019 04:45:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:45:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:45:22: #2 number of paired peaks: 3100 INFO @ Mon, 03 Jun 2019 04:45:22: start model_add_line... INFO @ Mon, 03 Jun 2019 04:45:22: start X-correlation... INFO @ Mon, 03 Jun 2019 04:45:22: end of X-cor INFO @ Mon, 03 Jun 2019 04:45:22: #2 finished! INFO @ Mon, 03 Jun 2019 04:45:22: #2 predicted fragment length is 216 bps INFO @ Mon, 03 Jun 2019 04:45:22: #2 alternative fragment length(s) may be 216 bps INFO @ Mon, 03 Jun 2019 04:45:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.10_model.r INFO @ Mon, 03 Jun 2019 04:45:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:45:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:45:24: #1 tag size is determined as 82 bps INFO @ Mon, 03 Jun 2019 04:45:24: #1 tag size = 82 INFO @ Mon, 03 Jun 2019 04:45:24: #1 total tags in treatment: 4630354 INFO @ Mon, 03 Jun 2019 04:45:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:45:24: #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 04:45:24: #1 tags after filtering in treatment: 4375975 INFO @ Mon, 03 Jun 2019 04:45:24: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 04:45:24: #1 finished! INFO @ Mon, 03 Jun 2019 04:45:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:45:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:45:24: #2 number of paired peaks: 3100 INFO @ Mon, 03 Jun 2019 04:45:24: start model_add_line... INFO @ Mon, 03 Jun 2019 04:45:24: start X-correlation... INFO @ Mon, 03 Jun 2019 04:45:24: end of X-cor INFO @ Mon, 03 Jun 2019 04:45:24: #2 finished! INFO @ Mon, 03 Jun 2019 04:45:24: #2 predicted fragment length is 216 bps INFO @ Mon, 03 Jun 2019 04:45:24: #2 alternative fragment length(s) may be 216 bps INFO @ Mon, 03 Jun 2019 04:45:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.05_model.r INFO @ Mon, 03 Jun 2019 04:45:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:45:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:45:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:45:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:45:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:45:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.20_summits.bed INFO @ Mon, 03 Jun 2019 04:45:32: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2642 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:45:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:45:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:45:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:45:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:45:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.10_summits.bed INFO @ Mon, 03 Jun 2019 04:45:43: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4064 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:45:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:45:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:45:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763406/SRX1763406.05_summits.bed INFO @ Mon, 03 Jun 2019 04:45:47: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (5693 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。