Job ID = 1294048 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 8,358,859 reads read : 16,717,718 reads written : 16,717,718 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: 00:23:39 8358859 reads; of these: 8358859 (100.00%) were paired; of these: 1158126 (13.86%) aligned concordantly 0 times 5731943 (68.57%) aligned concordantly exactly 1 time 1468790 (17.57%) aligned concordantly >1 times ---- 1158126 pairs aligned concordantly 0 times; of these: 568439 (49.08%) aligned discordantly 1 time ---- 589687 pairs aligned 0 times concordantly or discordantly; of these: 1179374 mates make up the pairs; of these: 649346 (55.06%) aligned 0 times 241624 (20.49%) aligned exactly 1 time 288404 (24.45%) aligned >1 times 96.12% overall alignment rate Time searching: 00:23:39 Overall time: 00:23:39 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] 218295 / 7760936 = 0.0281 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 05:03:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.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 05:03:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:03:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:03:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.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 05:03:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:03:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:03:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.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 05:03:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:03:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:03:56: 1000000 INFO @ Mon, 03 Jun 2019 05:03:57: 1000000 INFO @ Mon, 03 Jun 2019 05:03:57: 1000000 INFO @ Mon, 03 Jun 2019 05:04:04: 2000000 INFO @ Mon, 03 Jun 2019 05:04:07: 2000000 INFO @ Mon, 03 Jun 2019 05:04:07: 2000000 INFO @ Mon, 03 Jun 2019 05:04:13: 3000000 INFO @ Mon, 03 Jun 2019 05:04:17: 3000000 INFO @ Mon, 03 Jun 2019 05:04:18: 3000000 INFO @ Mon, 03 Jun 2019 05:04:22: 4000000 INFO @ Mon, 03 Jun 2019 05:04:28: 4000000 INFO @ Mon, 03 Jun 2019 05:04:28: 4000000 INFO @ Mon, 03 Jun 2019 05:04:30: 5000000 INFO @ Mon, 03 Jun 2019 05:04:38: 5000000 INFO @ Mon, 03 Jun 2019 05:04:38: 5000000 INFO @ Mon, 03 Jun 2019 05:04:39: 6000000 INFO @ Mon, 03 Jun 2019 05:04:48: 7000000 INFO @ Mon, 03 Jun 2019 05:04:48: 6000000 INFO @ Mon, 03 Jun 2019 05:04:48: 6000000 INFO @ Mon, 03 Jun 2019 05:04:56: 8000000 INFO @ Mon, 03 Jun 2019 05:04:57: 7000000 INFO @ Mon, 03 Jun 2019 05:04:58: 7000000 INFO @ Mon, 03 Jun 2019 05:05:05: 9000000 INFO @ Mon, 03 Jun 2019 05:05:07: 8000000 INFO @ Mon, 03 Jun 2019 05:05:08: 8000000 INFO @ Mon, 03 Jun 2019 05:05:13: 10000000 INFO @ Mon, 03 Jun 2019 05:05:17: 9000000 INFO @ Mon, 03 Jun 2019 05:05:18: 9000000 INFO @ Mon, 03 Jun 2019 05:05:22: 11000000 INFO @ Mon, 03 Jun 2019 05:05:27: 10000000 INFO @ Mon, 03 Jun 2019 05:05:28: 10000000 INFO @ Mon, 03 Jun 2019 05:05:30: 12000000 INFO @ Mon, 03 Jun 2019 05:05:37: 11000000 INFO @ Mon, 03 Jun 2019 05:05:38: 11000000 INFO @ Mon, 03 Jun 2019 05:05:39: 13000000 INFO @ Mon, 03 Jun 2019 05:05:47: 12000000 INFO @ Mon, 03 Jun 2019 05:05:48: 14000000 INFO @ Mon, 03 Jun 2019 05:05:48: 12000000 INFO @ Mon, 03 Jun 2019 05:05:57: 15000000 INFO @ Mon, 03 Jun 2019 05:05:57: 13000000 INFO @ Mon, 03 Jun 2019 05:05:58: 13000000 INFO @ Mon, 03 Jun 2019 05:06:02: #1 tag size is determined as 82 bps INFO @ Mon, 03 Jun 2019 05:06:02: #1 tag size = 82 INFO @ Mon, 03 Jun 2019 05:06:02: #1 total tags in treatment: 6991754 INFO @ Mon, 03 Jun 2019 05:06:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:06:02: #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 05:06:02: #1 tags after filtering in treatment: 6772863 INFO @ Mon, 03 Jun 2019 05:06:02: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 05:06:02: #1 finished! INFO @ Mon, 03 Jun 2019 05:06:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:06:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:06:03: #2 number of paired peaks: 866 WARNING @ Mon, 03 Jun 2019 05:06:03: Fewer paired peaks (866) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 866 pairs to build model! INFO @ Mon, 03 Jun 2019 05:06:03: start model_add_line... INFO @ Mon, 03 Jun 2019 05:06:03: start X-correlation... INFO @ Mon, 03 Jun 2019 05:06:03: end of X-cor INFO @ Mon, 03 Jun 2019 05:06:03: #2 finished! INFO @ Mon, 03 Jun 2019 05:06:03: #2 predicted fragment length is 224 bps INFO @ Mon, 03 Jun 2019 05:06:03: #2 alternative fragment length(s) may be 224 bps INFO @ Mon, 03 Jun 2019 05:06:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.05_model.r INFO @ Mon, 03 Jun 2019 05:06:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:06:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:06:07: 14000000 INFO @ Mon, 03 Jun 2019 05:06:08: 14000000 INFO @ Mon, 03 Jun 2019 05:06:17: 15000000 INFO @ Mon, 03 Jun 2019 05:06:18: 15000000 INFO @ Mon, 03 Jun 2019 05:06:23: #1 tag size is determined as 82 bps INFO @ Mon, 03 Jun 2019 05:06:23: #1 tag size = 82 INFO @ Mon, 03 Jun 2019 05:06:23: #1 total tags in treatment: 6991754 INFO @ Mon, 03 Jun 2019 05:06:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:06:23: #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 05:06:24: #1 tags after filtering in treatment: 6772863 INFO @ Mon, 03 Jun 2019 05:06:24: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 05:06:24: #1 finished! INFO @ Mon, 03 Jun 2019 05:06:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:06:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:06:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:06:24: #2 number of paired peaks: 866 WARNING @ Mon, 03 Jun 2019 05:06:24: Fewer paired peaks (866) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 866 pairs to build model! INFO @ Mon, 03 Jun 2019 05:06:24: start model_add_line... INFO @ Mon, 03 Jun 2019 05:06:24: start X-correlation... INFO @ Mon, 03 Jun 2019 05:06:24: end of X-cor INFO @ Mon, 03 Jun 2019 05:06:24: #2 finished! INFO @ Mon, 03 Jun 2019 05:06:24: #2 predicted fragment length is 224 bps INFO @ Mon, 03 Jun 2019 05:06:24: #2 alternative fragment length(s) may be 224 bps INFO @ Mon, 03 Jun 2019 05:06:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.20_model.r INFO @ Mon, 03 Jun 2019 05:06:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:06:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:06:25: #1 tag size is determined as 82 bps INFO @ Mon, 03 Jun 2019 05:06:25: #1 tag size = 82 INFO @ Mon, 03 Jun 2019 05:06:25: #1 total tags in treatment: 6991754 INFO @ Mon, 03 Jun 2019 05:06:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:06:25: #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 05:06:25: #1 tags after filtering in treatment: 6772863 INFO @ Mon, 03 Jun 2019 05:06:25: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 05:06:25: #1 finished! INFO @ Mon, 03 Jun 2019 05:06:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:06:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:06:26: #2 number of paired peaks: 866 WARNING @ Mon, 03 Jun 2019 05:06:26: Fewer paired peaks (866) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 866 pairs to build model! INFO @ Mon, 03 Jun 2019 05:06:26: start model_add_line... INFO @ Mon, 03 Jun 2019 05:06:26: start X-correlation... INFO @ Mon, 03 Jun 2019 05:06:26: end of X-cor INFO @ Mon, 03 Jun 2019 05:06:26: #2 finished! INFO @ Mon, 03 Jun 2019 05:06:26: #2 predicted fragment length is 224 bps INFO @ Mon, 03 Jun 2019 05:06:26: #2 alternative fragment length(s) may be 224 bps INFO @ Mon, 03 Jun 2019 05:06:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.10_model.r INFO @ Mon, 03 Jun 2019 05:06:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:06:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:06:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:06:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:06:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.05_summits.bed INFO @ Mon, 03 Jun 2019 05:06:34: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3973 records, 4 fields): 261 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:06:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:06:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:06:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:06:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:06:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.20_summits.bed INFO @ Mon, 03 Jun 2019 05:06:55: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1211 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:06:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:06:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:06:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763412/SRX1763412.10_summits.bed INFO @ Mon, 03 Jun 2019 05:06:57: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2411 records, 4 fields): 26 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。