Job ID = 1293346 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 31,735,482 reads read : 63,470,964 reads written : 63,470,964 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: 01:12:03 31735482 reads; of these: 31735482 (100.00%) were paired; of these: 9773529 (30.80%) aligned concordantly 0 times 14917716 (47.01%) aligned concordantly exactly 1 time 7044237 (22.20%) aligned concordantly >1 times ---- 9773529 pairs aligned concordantly 0 times; of these: 95173 (0.97%) aligned discordantly 1 time ---- 9678356 pairs aligned 0 times concordantly or discordantly; of these: 19356712 mates make up the pairs; of these: 18136417 (93.70%) aligned 0 times 627984 (3.24%) aligned exactly 1 time 592311 (3.06%) aligned >1 times 71.43% overall alignment rate Time searching: 01:12:03 Overall time: 01:12:03 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 20 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] 14207478 / 22039651 = 0.6446 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 00:55:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.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 00:55:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:55:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:55:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.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 00:55:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:55:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:55:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.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 00:55:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:55:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:55:27: 1000000 INFO @ Mon, 03 Jun 2019 00:55:29: 1000000 INFO @ Mon, 03 Jun 2019 00:55:29: 1000000 INFO @ Mon, 03 Jun 2019 00:55:36: 2000000 INFO @ Mon, 03 Jun 2019 00:55:39: 2000000 INFO @ Mon, 03 Jun 2019 00:55:41: 2000000 INFO @ Mon, 03 Jun 2019 00:55:45: 3000000 INFO @ Mon, 03 Jun 2019 00:55:49: 3000000 INFO @ Mon, 03 Jun 2019 00:55:52: 3000000 INFO @ Mon, 03 Jun 2019 00:55:54: 4000000 INFO @ Mon, 03 Jun 2019 00:55:59: 4000000 INFO @ Mon, 03 Jun 2019 00:56:03: 4000000 INFO @ Mon, 03 Jun 2019 00:56:03: 5000000 INFO @ Mon, 03 Jun 2019 00:56:09: 5000000 INFO @ Mon, 03 Jun 2019 00:56:11: 6000000 INFO @ Mon, 03 Jun 2019 00:56:14: 5000000 INFO @ Mon, 03 Jun 2019 00:56:20: 7000000 INFO @ Mon, 03 Jun 2019 00:56:20: 6000000 INFO @ Mon, 03 Jun 2019 00:56:25: 6000000 INFO @ Mon, 03 Jun 2019 00:56:28: 8000000 INFO @ Mon, 03 Jun 2019 00:56:30: 7000000 INFO @ Mon, 03 Jun 2019 00:56:36: 7000000 INFO @ Mon, 03 Jun 2019 00:56:36: 9000000 INFO @ Mon, 03 Jun 2019 00:56:39: 8000000 INFO @ Mon, 03 Jun 2019 00:56:44: 10000000 INFO @ Mon, 03 Jun 2019 00:56:47: 8000000 INFO @ Mon, 03 Jun 2019 00:56:50: 9000000 INFO @ Mon, 03 Jun 2019 00:56:52: 11000000 INFO @ Mon, 03 Jun 2019 00:56:59: 9000000 INFO @ Mon, 03 Jun 2019 00:57:00: 12000000 INFO @ Mon, 03 Jun 2019 00:57:01: 10000000 INFO @ Mon, 03 Jun 2019 00:57:08: 13000000 INFO @ Mon, 03 Jun 2019 00:57:09: 10000000 INFO @ Mon, 03 Jun 2019 00:57:11: 11000000 INFO @ Mon, 03 Jun 2019 00:57:16: 14000000 INFO @ Mon, 03 Jun 2019 00:57:20: 11000000 INFO @ Mon, 03 Jun 2019 00:57:21: 12000000 INFO @ Mon, 03 Jun 2019 00:57:25: 15000000 INFO @ Mon, 03 Jun 2019 00:57:29: 12000000 INFO @ Mon, 03 Jun 2019 00:57:30: 13000000 INFO @ Mon, 03 Jun 2019 00:57:33: 16000000 INFO @ Mon, 03 Jun 2019 00:57:38: 13000000 INFO @ Mon, 03 Jun 2019 00:57:39: 14000000 INFO @ Mon, 03 Jun 2019 00:57:40: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 00:57:40: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 00:57:40: #1 total tags in treatment: 7792455 INFO @ Mon, 03 Jun 2019 00:57:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:57:40: #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 00:57:41: #1 tags after filtering in treatment: 6959709 INFO @ Mon, 03 Jun 2019 00:57:41: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 00:57:41: #1 finished! INFO @ Mon, 03 Jun 2019 00:57:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:57:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:57:41: #2 number of paired peaks: 578 WARNING @ Mon, 03 Jun 2019 00:57:41: Fewer paired peaks (578) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 578 pairs to build model! INFO @ Mon, 03 Jun 2019 00:57:41: start model_add_line... INFO @ Mon, 03 Jun 2019 00:57:41: start X-correlation... INFO @ Mon, 03 Jun 2019 00:57:41: end of X-cor INFO @ Mon, 03 Jun 2019 00:57:41: #2 finished! INFO @ Mon, 03 Jun 2019 00:57:41: #2 predicted fragment length is 185 bps INFO @ Mon, 03 Jun 2019 00:57:41: #2 alternative fragment length(s) may be 185 bps INFO @ Mon, 03 Jun 2019 00:57:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.20_model.r INFO @ Mon, 03 Jun 2019 00:57:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:57:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:57:47: 14000000 INFO @ Mon, 03 Jun 2019 00:57:49: 15000000 INFO @ Mon, 03 Jun 2019 00:57:56: 15000000 INFO @ Mon, 03 Jun 2019 00:57:58: 16000000 INFO @ Mon, 03 Jun 2019 00:58:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:58:06: 16000000 INFO @ Mon, 03 Jun 2019 00:58:07: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 00:58:07: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 00:58:07: #1 total tags in treatment: 7792455 INFO @ Mon, 03 Jun 2019 00:58:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:58:07: #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 00:58:08: #1 tags after filtering in treatment: 6959709 INFO @ Mon, 03 Jun 2019 00:58:08: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 00:58:08: #1 finished! INFO @ Mon, 03 Jun 2019 00:58:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:58:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:58:08: #2 number of paired peaks: 578 WARNING @ Mon, 03 Jun 2019 00:58:08: Fewer paired peaks (578) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 578 pairs to build model! INFO @ Mon, 03 Jun 2019 00:58:08: start model_add_line... INFO @ Mon, 03 Jun 2019 00:58:08: start X-correlation... INFO @ Mon, 03 Jun 2019 00:58:08: end of X-cor INFO @ Mon, 03 Jun 2019 00:58:08: #2 finished! INFO @ Mon, 03 Jun 2019 00:58:08: #2 predicted fragment length is 185 bps INFO @ Mon, 03 Jun 2019 00:58:08: #2 alternative fragment length(s) may be 185 bps INFO @ Mon, 03 Jun 2019 00:58:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.10_model.r INFO @ Mon, 03 Jun 2019 00:58:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:58:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:58:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.20_peaks.xls INFO @ Mon, 03 Jun 2019 00:58:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:58:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.20_summits.bed INFO @ Mon, 03 Jun 2019 00:58:13: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (703 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:58:14: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 00:58:14: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 00:58:14: #1 total tags in treatment: 7792455 INFO @ Mon, 03 Jun 2019 00:58:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:58:14: #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 00:58:14: #1 tags after filtering in treatment: 6959709 INFO @ Mon, 03 Jun 2019 00:58:14: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 00:58:14: #1 finished! INFO @ Mon, 03 Jun 2019 00:58:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:58:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:58:15: #2 number of paired peaks: 578 WARNING @ Mon, 03 Jun 2019 00:58:15: Fewer paired peaks (578) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 578 pairs to build model! INFO @ Mon, 03 Jun 2019 00:58:15: start model_add_line... INFO @ Mon, 03 Jun 2019 00:58:15: start X-correlation... INFO @ Mon, 03 Jun 2019 00:58:15: end of X-cor INFO @ Mon, 03 Jun 2019 00:58:15: #2 finished! INFO @ Mon, 03 Jun 2019 00:58:15: #2 predicted fragment length is 185 bps INFO @ Mon, 03 Jun 2019 00:58:15: #2 alternative fragment length(s) may be 185 bps INFO @ Mon, 03 Jun 2019 00:58:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.05_model.r INFO @ Mon, 03 Jun 2019 00:58:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:58:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:58:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:58:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:58:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.10_peaks.xls INFO @ Mon, 03 Jun 2019 00:58:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:58:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.10_summits.bed INFO @ Mon, 03 Jun 2019 00:58:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2232 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:58:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.05_peaks.xls INFO @ Mon, 03 Jun 2019 00:58:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:58:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818272/ERX1818272.05_summits.bed INFO @ Mon, 03 Jun 2019 00:58:47: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5481 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。