Job ID = 1294051 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,477,057 reads read : 10,954,114 reads written : 10,954,114 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: 00:13:12 5477057 reads; of these: 5477057 (100.00%) were paired; of these: 1337742 (24.42%) aligned concordantly 0 times 3413941 (62.33%) aligned concordantly exactly 1 time 725374 (13.24%) aligned concordantly >1 times ---- 1337742 pairs aligned concordantly 0 times; of these: 456693 (34.14%) aligned discordantly 1 time ---- 881049 pairs aligned 0 times concordantly or discordantly; of these: 1762098 mates make up the pairs; of these: 1384496 (78.57%) aligned 0 times 165135 (9.37%) aligned exactly 1 time 212467 (12.06%) aligned >1 times 87.36% overall alignment rate Time searching: 00:13:12 Overall time: 00:13:12 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] 121340 / 4590965 = 0.0264 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 04:48:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.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 04:48:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:48:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:48:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.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 04:48:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:48:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:48:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.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 04:48:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:48:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:48:46: 1000000 INFO @ Mon, 03 Jun 2019 04:48:46: 1000000 INFO @ Mon, 03 Jun 2019 04:48:48: 1000000 INFO @ Mon, 03 Jun 2019 04:48:55: 2000000 INFO @ Mon, 03 Jun 2019 04:48:55: 2000000 INFO @ Mon, 03 Jun 2019 04:49:00: 2000000 INFO @ Mon, 03 Jun 2019 04:49:05: 3000000 INFO @ Mon, 03 Jun 2019 04:49:05: 3000000 INFO @ Mon, 03 Jun 2019 04:49:10: 3000000 INFO @ Mon, 03 Jun 2019 04:49:14: 4000000 INFO @ Mon, 03 Jun 2019 04:49:14: 4000000 INFO @ Mon, 03 Jun 2019 04:49:21: 4000000 INFO @ Mon, 03 Jun 2019 04:49:24: 5000000 INFO @ Mon, 03 Jun 2019 04:49:26: 5000000 INFO @ Mon, 03 Jun 2019 04:49:32: 5000000 INFO @ Mon, 03 Jun 2019 04:49:34: 6000000 INFO @ Mon, 03 Jun 2019 04:49:35: 6000000 INFO @ Mon, 03 Jun 2019 04:49:42: 6000000 INFO @ Mon, 03 Jun 2019 04:49:43: 7000000 INFO @ Mon, 03 Jun 2019 04:49:45: 7000000 INFO @ Mon, 03 Jun 2019 04:49:52: 8000000 INFO @ Mon, 03 Jun 2019 04:49:53: 7000000 INFO @ Mon, 03 Jun 2019 04:49:54: 8000000 INFO @ Mon, 03 Jun 2019 04:50:01: 9000000 INFO @ Mon, 03 Jun 2019 04:50:03: 9000000 INFO @ Mon, 03 Jun 2019 04:50:03: 8000000 INFO @ Mon, 03 Jun 2019 04:50:04: #1 tag size is determined as 82 bps INFO @ Mon, 03 Jun 2019 04:50:04: #1 tag size = 82 INFO @ Mon, 03 Jun 2019 04:50:04: #1 total tags in treatment: 4024324 INFO @ Mon, 03 Jun 2019 04:50:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:50:04: #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 04:50:04: #1 tags after filtering in treatment: 3860642 INFO @ Mon, 03 Jun 2019 04:50:04: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 03 Jun 2019 04:50:04: #1 finished! INFO @ Mon, 03 Jun 2019 04:50:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:50:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:50:05: #2 number of paired peaks: 3149 INFO @ Mon, 03 Jun 2019 04:50:05: start model_add_line... INFO @ Mon, 03 Jun 2019 04:50:05: start X-correlation... INFO @ Mon, 03 Jun 2019 04:50:05: end of X-cor INFO @ Mon, 03 Jun 2019 04:50:05: #2 finished! INFO @ Mon, 03 Jun 2019 04:50:05: #2 predicted fragment length is 229 bps INFO @ Mon, 03 Jun 2019 04:50:05: #2 alternative fragment length(s) may be 229 bps INFO @ Mon, 03 Jun 2019 04:50:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.05_model.r INFO @ Mon, 03 Jun 2019 04:50:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:50:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:50:06: #1 tag size is determined as 82 bps INFO @ Mon, 03 Jun 2019 04:50:06: #1 tag size = 82 INFO @ Mon, 03 Jun 2019 04:50:06: #1 total tags in treatment: 4024324 INFO @ Mon, 03 Jun 2019 04:50:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:50:06: #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 04:50:06: #1 tags after filtering in treatment: 3860642 INFO @ Mon, 03 Jun 2019 04:50:06: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 03 Jun 2019 04:50:06: #1 finished! INFO @ Mon, 03 Jun 2019 04:50:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:50:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:50:06: #2 number of paired peaks: 3149 INFO @ Mon, 03 Jun 2019 04:50:06: start model_add_line... INFO @ Mon, 03 Jun 2019 04:50:06: start X-correlation... INFO @ Mon, 03 Jun 2019 04:50:06: end of X-cor INFO @ Mon, 03 Jun 2019 04:50:06: #2 finished! INFO @ Mon, 03 Jun 2019 04:50:06: #2 predicted fragment length is 229 bps INFO @ Mon, 03 Jun 2019 04:50:06: #2 alternative fragment length(s) may be 229 bps INFO @ Mon, 03 Jun 2019 04:50:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.20_model.r INFO @ Mon, 03 Jun 2019 04:50:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:50:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:50:13: 9000000 INFO @ Mon, 03 Jun 2019 04:50:17: #1 tag size is determined as 82 bps INFO @ Mon, 03 Jun 2019 04:50:17: #1 tag size = 82 INFO @ Mon, 03 Jun 2019 04:50:17: #1 total tags in treatment: 4024324 INFO @ Mon, 03 Jun 2019 04:50:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:50:17: #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 04:50:17: #1 tags after filtering in treatment: 3860642 INFO @ Mon, 03 Jun 2019 04:50:17: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 03 Jun 2019 04:50:17: #1 finished! INFO @ Mon, 03 Jun 2019 04:50:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:50:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:50:17: #2 number of paired peaks: 3149 INFO @ Mon, 03 Jun 2019 04:50:17: start model_add_line... INFO @ Mon, 03 Jun 2019 04:50:17: start X-correlation... INFO @ Mon, 03 Jun 2019 04:50:17: end of X-cor INFO @ Mon, 03 Jun 2019 04:50:17: #2 finished! INFO @ Mon, 03 Jun 2019 04:50:17: #2 predicted fragment length is 229 bps INFO @ Mon, 03 Jun 2019 04:50:17: #2 alternative fragment length(s) may be 229 bps INFO @ Mon, 03 Jun 2019 04:50:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.10_model.r INFO @ Mon, 03 Jun 2019 04:50:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:50:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:50:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:50:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:50:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:50:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:50:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.05_summits.bed INFO @ Mon, 03 Jun 2019 04:50:24: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5171 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:50:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:50:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:50:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.20_summits.bed INFO @ Mon, 03 Jun 2019 04:50:25: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (2061 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:50:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:50:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:50:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:50:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763414/SRX1763414.10_summits.bed INFO @ Mon, 03 Jun 2019 04:50:37: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3604 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。