Job ID = 1293347 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 14,572,378 reads read : 29,144,756 reads written : 29,144,756 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:56:56 14572378 reads; of these: 14572378 (100.00%) were paired; of these: 3658882 (25.11%) aligned concordantly 0 times 6139053 (42.13%) aligned concordantly exactly 1 time 4774443 (32.76%) aligned concordantly >1 times ---- 3658882 pairs aligned concordantly 0 times; of these: 72671 (1.99%) aligned discordantly 1 time ---- 3586211 pairs aligned 0 times concordantly or discordantly; of these: 7172422 mates make up the pairs; of these: 6568217 (91.58%) aligned 0 times 294661 (4.11%) aligned exactly 1 time 309544 (4.32%) aligned >1 times 77.46% overall alignment rate Time searching: 00:56:57 Overall time: 00:56:57 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 12 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] 731109 / 10970575 = 0.0666 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 00:18:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.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 00:18:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:18:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:18:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.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 00:18:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:18:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:18:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.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 00:18:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:18:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:18:16: 1000000 INFO @ Mon, 03 Jun 2019 00:18:17: 1000000 INFO @ Mon, 03 Jun 2019 00:18:18: 1000000 INFO @ Mon, 03 Jun 2019 00:18:26: 2000000 INFO @ Mon, 03 Jun 2019 00:18:28: 2000000 INFO @ Mon, 03 Jun 2019 00:18:28: 2000000 INFO @ Mon, 03 Jun 2019 00:18:36: 3000000 INFO @ Mon, 03 Jun 2019 00:18:39: 3000000 INFO @ Mon, 03 Jun 2019 00:18:39: 3000000 INFO @ Mon, 03 Jun 2019 00:18:45: 4000000 INFO @ Mon, 03 Jun 2019 00:18:49: 4000000 INFO @ Mon, 03 Jun 2019 00:18:50: 4000000 INFO @ Mon, 03 Jun 2019 00:18:55: 5000000 INFO @ Mon, 03 Jun 2019 00:19:00: 5000000 INFO @ Mon, 03 Jun 2019 00:19:00: 5000000 INFO @ Mon, 03 Jun 2019 00:19:05: 6000000 INFO @ Mon, 03 Jun 2019 00:19:10: 6000000 INFO @ Mon, 03 Jun 2019 00:19:11: 6000000 INFO @ Mon, 03 Jun 2019 00:19:14: 7000000 INFO @ Mon, 03 Jun 2019 00:19:20: 7000000 INFO @ Mon, 03 Jun 2019 00:19:21: 7000000 INFO @ Mon, 03 Jun 2019 00:19:24: 8000000 INFO @ Mon, 03 Jun 2019 00:19:31: 8000000 INFO @ Mon, 03 Jun 2019 00:19:31: 8000000 INFO @ Mon, 03 Jun 2019 00:19:33: 9000000 INFO @ Mon, 03 Jun 2019 00:19:41: 9000000 INFO @ Mon, 03 Jun 2019 00:19:41: 9000000 INFO @ Mon, 03 Jun 2019 00:19:43: 10000000 INFO @ Mon, 03 Jun 2019 00:19:51: 10000000 INFO @ Mon, 03 Jun 2019 00:19:52: 10000000 INFO @ Mon, 03 Jun 2019 00:19:53: 11000000 INFO @ Mon, 03 Jun 2019 00:20:01: 11000000 INFO @ Mon, 03 Jun 2019 00:20:02: 11000000 INFO @ Mon, 03 Jun 2019 00:20:04: 12000000 INFO @ Mon, 03 Jun 2019 00:20:11: 12000000 INFO @ Mon, 03 Jun 2019 00:20:13: 12000000 INFO @ Mon, 03 Jun 2019 00:20:14: 13000000 INFO @ Mon, 03 Jun 2019 00:20:21: 13000000 INFO @ Mon, 03 Jun 2019 00:20:24: 13000000 INFO @ Mon, 03 Jun 2019 00:20:24: 14000000 INFO @ Mon, 03 Jun 2019 00:20:30: 14000000 INFO @ Mon, 03 Jun 2019 00:20:34: 14000000 INFO @ Mon, 03 Jun 2019 00:20:34: 15000000 INFO @ Mon, 03 Jun 2019 00:20:40: 15000000 INFO @ Mon, 03 Jun 2019 00:20:44: 16000000 INFO @ Mon, 03 Jun 2019 00:20:44: 15000000 INFO @ Mon, 03 Jun 2019 00:20:49: 16000000 INFO @ Mon, 03 Jun 2019 00:20:55: 16000000 INFO @ Mon, 03 Jun 2019 00:20:55: 17000000 INFO @ Mon, 03 Jun 2019 00:20:58: 17000000 INFO @ Mon, 03 Jun 2019 00:21:05: 18000000 INFO @ Mon, 03 Jun 2019 00:21:06: 17000000 INFO @ Mon, 03 Jun 2019 00:21:08: 18000000 INFO @ Mon, 03 Jun 2019 00:21:16: 19000000 INFO @ Mon, 03 Jun 2019 00:21:16: 18000000 INFO @ Mon, 03 Jun 2019 00:21:16: 19000000 INFO @ Mon, 03 Jun 2019 00:21:25: 20000000 INFO @ Mon, 03 Jun 2019 00:21:27: 20000000 INFO @ Mon, 03 Jun 2019 00:21:27: 19000000 INFO @ Mon, 03 Jun 2019 00:21:33: 21000000 INFO @ Mon, 03 Jun 2019 00:21:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 00:21:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 00:21:34: #1 total tags in treatment: 10185751 INFO @ Mon, 03 Jun 2019 00:21:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:21:34: #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 00:21:34: #1 tags after filtering in treatment: 9687650 INFO @ Mon, 03 Jun 2019 00:21:34: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 00:21:34: #1 finished! INFO @ Mon, 03 Jun 2019 00:21:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:21:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:21:35: #2 number of paired peaks: 357 WARNING @ Mon, 03 Jun 2019 00:21:35: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Mon, 03 Jun 2019 00:21:35: start model_add_line... INFO @ Mon, 03 Jun 2019 00:21:35: start X-correlation... INFO @ Mon, 03 Jun 2019 00:21:35: end of X-cor INFO @ Mon, 03 Jun 2019 00:21:35: #2 finished! INFO @ Mon, 03 Jun 2019 00:21:35: #2 predicted fragment length is 167 bps INFO @ Mon, 03 Jun 2019 00:21:35: #2 alternative fragment length(s) may be 167,597 bps INFO @ Mon, 03 Jun 2019 00:21:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.20_model.r INFO @ Mon, 03 Jun 2019 00:21:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:21:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:21:37: 21000000 INFO @ Mon, 03 Jun 2019 00:21:38: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 00:21:38: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 00:21:38: #1 total tags in treatment: 10185751 INFO @ Mon, 03 Jun 2019 00:21:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:21:38: #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 00:21:38: 20000000 INFO @ Mon, 03 Jun 2019 00:21:38: #1 tags after filtering in treatment: 9687650 INFO @ Mon, 03 Jun 2019 00:21:38: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 00:21:38: #1 finished! INFO @ Mon, 03 Jun 2019 00:21:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:21:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:21:39: #2 number of paired peaks: 357 WARNING @ Mon, 03 Jun 2019 00:21:39: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Mon, 03 Jun 2019 00:21:39: start model_add_line... INFO @ Mon, 03 Jun 2019 00:21:39: start X-correlation... INFO @ Mon, 03 Jun 2019 00:21:39: end of X-cor INFO @ Mon, 03 Jun 2019 00:21:39: #2 finished! INFO @ Mon, 03 Jun 2019 00:21:39: #2 predicted fragment length is 167 bps INFO @ Mon, 03 Jun 2019 00:21:39: #2 alternative fragment length(s) may be 167,597 bps INFO @ Mon, 03 Jun 2019 00:21:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.05_model.r INFO @ Mon, 03 Jun 2019 00:21:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:21:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:21:49: 21000000 INFO @ Mon, 03 Jun 2019 00:21:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 00:21:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 00:21:50: #1 total tags in treatment: 10185751 INFO @ Mon, 03 Jun 2019 00:21:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:21:50: #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 00:21:50: #1 tags after filtering in treatment: 9687650 INFO @ Mon, 03 Jun 2019 00:21:50: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 00:21:50: #1 finished! INFO @ Mon, 03 Jun 2019 00:21:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:21:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:21:51: #2 number of paired peaks: 357 WARNING @ Mon, 03 Jun 2019 00:21:51: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Mon, 03 Jun 2019 00:21:51: start model_add_line... INFO @ Mon, 03 Jun 2019 00:21:51: start X-correlation... INFO @ Mon, 03 Jun 2019 00:21:51: end of X-cor INFO @ Mon, 03 Jun 2019 00:21:51: #2 finished! INFO @ Mon, 03 Jun 2019 00:21:51: #2 predicted fragment length is 167 bps INFO @ Mon, 03 Jun 2019 00:21:51: #2 alternative fragment length(s) may be 167,597 bps INFO @ Mon, 03 Jun 2019 00:21:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.10_model.r INFO @ Mon, 03 Jun 2019 00:21:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:21:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:22:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:22:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:22:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.20_peaks.xls INFO @ Mon, 03 Jun 2019 00:22:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:22:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.20_summits.bed INFO @ Mon, 03 Jun 2019 00:22:21: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1723 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:22:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:22:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.05_peaks.xls INFO @ Mon, 03 Jun 2019 00:22:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:22:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.05_summits.bed INFO @ Mon, 03 Jun 2019 00:22:29: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7042 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:22:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.10_peaks.xls INFO @ Mon, 03 Jun 2019 00:22:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:22:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818273/ERX1818273.10_summits.bed INFO @ Mon, 03 Jun 2019 00:22:41: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4489 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。