Job ID = 1293398 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 29,054,256 reads read : 58,108,512 reads written : 58,108,512 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: 00:56:54 29054256 reads; of these: 29054256 (100.00%) were paired; of these: 5037935 (17.34%) aligned concordantly 0 times 20356745 (70.06%) aligned concordantly exactly 1 time 3659576 (12.60%) aligned concordantly >1 times ---- 5037935 pairs aligned concordantly 0 times; of these: 757532 (15.04%) aligned discordantly 1 time ---- 4280403 pairs aligned 0 times concordantly or discordantly; of these: 8560806 mates make up the pairs; of these: 7405852 (86.51%) aligned 0 times 766847 (8.96%) aligned exactly 1 time 388107 (4.53%) aligned >1 times 87.26% overall alignment rate Time searching: 00:56:54 Overall time: 00:56:54 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 24 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] 10947798 / 24748106 = 0.4424 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 01:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.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 01:04:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:04:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.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 01:04:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:04:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.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 01:04:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:04:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:05:07: 1000000 INFO @ Mon, 03 Jun 2019 01:05:08: 1000000 INFO @ Mon, 03 Jun 2019 01:05:08: 1000000 INFO @ Mon, 03 Jun 2019 01:05:16: 2000000 INFO @ Mon, 03 Jun 2019 01:05:18: 2000000 INFO @ Mon, 03 Jun 2019 01:05:18: 2000000 INFO @ Mon, 03 Jun 2019 01:05:25: 3000000 INFO @ Mon, 03 Jun 2019 01:05:28: 3000000 INFO @ Mon, 03 Jun 2019 01:05:29: 3000000 INFO @ Mon, 03 Jun 2019 01:05:34: 4000000 INFO @ Mon, 03 Jun 2019 01:05:39: 4000000 INFO @ Mon, 03 Jun 2019 01:05:39: 4000000 INFO @ Mon, 03 Jun 2019 01:05:42: 5000000 INFO @ Mon, 03 Jun 2019 01:05:49: 5000000 INFO @ Mon, 03 Jun 2019 01:05:49: 5000000 INFO @ Mon, 03 Jun 2019 01:05:51: 6000000 INFO @ Mon, 03 Jun 2019 01:05:59: 6000000 INFO @ Mon, 03 Jun 2019 01:05:59: 6000000 INFO @ Mon, 03 Jun 2019 01:05:59: 7000000 INFO @ Mon, 03 Jun 2019 01:06:07: 8000000 INFO @ Mon, 03 Jun 2019 01:06:08: 7000000 INFO @ Mon, 03 Jun 2019 01:06:08: 7000000 INFO @ Mon, 03 Jun 2019 01:06:16: 9000000 INFO @ Mon, 03 Jun 2019 01:06:18: 8000000 INFO @ Mon, 03 Jun 2019 01:06:18: 8000000 INFO @ Mon, 03 Jun 2019 01:06:24: 10000000 INFO @ Mon, 03 Jun 2019 01:06:27: 9000000 INFO @ Mon, 03 Jun 2019 01:06:27: 9000000 INFO @ Mon, 03 Jun 2019 01:06:32: 11000000 INFO @ Mon, 03 Jun 2019 01:06:37: 10000000 INFO @ Mon, 03 Jun 2019 01:06:37: 10000000 INFO @ Mon, 03 Jun 2019 01:06:40: 12000000 INFO @ Mon, 03 Jun 2019 01:06:46: 11000000 INFO @ Mon, 03 Jun 2019 01:06:46: 11000000 INFO @ Mon, 03 Jun 2019 01:06:48: 13000000 INFO @ Mon, 03 Jun 2019 01:06:56: 12000000 INFO @ Mon, 03 Jun 2019 01:06:56: 12000000 INFO @ Mon, 03 Jun 2019 01:06:56: 14000000 INFO @ Mon, 03 Jun 2019 01:07:04: 15000000 INFO @ Mon, 03 Jun 2019 01:07:05: 13000000 INFO @ Mon, 03 Jun 2019 01:07:05: 13000000 INFO @ Mon, 03 Jun 2019 01:07:12: 16000000 INFO @ Mon, 03 Jun 2019 01:07:13: 14000000 INFO @ Mon, 03 Jun 2019 01:07:13: 14000000 INFO @ Mon, 03 Jun 2019 01:07:21: 17000000 INFO @ Mon, 03 Jun 2019 01:07:23: 15000000 INFO @ Mon, 03 Jun 2019 01:07:23: 15000000 INFO @ Mon, 03 Jun 2019 01:07:29: 18000000 INFO @ Mon, 03 Jun 2019 01:07:32: 16000000 INFO @ Mon, 03 Jun 2019 01:07:32: 16000000 INFO @ Mon, 03 Jun 2019 01:07:38: 19000000 INFO @ Mon, 03 Jun 2019 01:07:42: 17000000 INFO @ Mon, 03 Jun 2019 01:07:42: 17000000 INFO @ Mon, 03 Jun 2019 01:07:46: 20000000 INFO @ Mon, 03 Jun 2019 01:07:52: 18000000 INFO @ Mon, 03 Jun 2019 01:07:52: 18000000 INFO @ Mon, 03 Jun 2019 01:07:55: 21000000 INFO @ Mon, 03 Jun 2019 01:08:02: 19000000 INFO @ Mon, 03 Jun 2019 01:08:02: 19000000 INFO @ Mon, 03 Jun 2019 01:08:03: 22000000 INFO @ Mon, 03 Jun 2019 01:08:12: 20000000 INFO @ Mon, 03 Jun 2019 01:08:12: 20000000 INFO @ Mon, 03 Jun 2019 01:08:12: 23000000 INFO @ Mon, 03 Jun 2019 01:08:20: 24000000 INFO @ Mon, 03 Jun 2019 01:08:21: 21000000 INFO @ Mon, 03 Jun 2019 01:08:21: 21000000 INFO @ Mon, 03 Jun 2019 01:08:28: 25000000 INFO @ Mon, 03 Jun 2019 01:08:30: 22000000 INFO @ Mon, 03 Jun 2019 01:08:31: 22000000 INFO @ Mon, 03 Jun 2019 01:08:37: 26000000 INFO @ Mon, 03 Jun 2019 01:08:40: 23000000 INFO @ Mon, 03 Jun 2019 01:08:40: 23000000 INFO @ Mon, 03 Jun 2019 01:08:45: 27000000 INFO @ Mon, 03 Jun 2019 01:08:49: 24000000 INFO @ Mon, 03 Jun 2019 01:08:49: 24000000 INFO @ Mon, 03 Jun 2019 01:08:53: 28000000 INFO @ Mon, 03 Jun 2019 01:08:58: 25000000 INFO @ Mon, 03 Jun 2019 01:08:59: 25000000 INFO @ Mon, 03 Jun 2019 01:09:00: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 01:09:00: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 01:09:00: #1 total tags in treatment: 13328912 INFO @ Mon, 03 Jun 2019 01:09:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:09:00: #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 01:09:00: #1 tags after filtering in treatment: 12541875 INFO @ Mon, 03 Jun 2019 01:09:00: #1 Redundant rate of treatment: 0.06 INFO @ Mon, 03 Jun 2019 01:09:00: #1 finished! INFO @ Mon, 03 Jun 2019 01:09:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:09:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:09:01: #2 number of paired peaks: 122 WARNING @ Mon, 03 Jun 2019 01:09:01: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Mon, 03 Jun 2019 01:09:01: start model_add_line... INFO @ Mon, 03 Jun 2019 01:09:01: start X-correlation... INFO @ Mon, 03 Jun 2019 01:09:01: end of X-cor INFO @ Mon, 03 Jun 2019 01:09:01: #2 finished! INFO @ Mon, 03 Jun 2019 01:09:01: #2 predicted fragment length is 186 bps INFO @ Mon, 03 Jun 2019 01:09:01: #2 alternative fragment length(s) may be 186 bps INFO @ Mon, 03 Jun 2019 01:09:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.20_model.r INFO @ Mon, 03 Jun 2019 01:09:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:09:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:09:08: 26000000 INFO @ Mon, 03 Jun 2019 01:09:08: 26000000 INFO @ Mon, 03 Jun 2019 01:09:18: 27000000 INFO @ Mon, 03 Jun 2019 01:09:18: 27000000 INFO @ Mon, 03 Jun 2019 01:09:27: 28000000 INFO @ Mon, 03 Jun 2019 01:09:28: 28000000 INFO @ Mon, 03 Jun 2019 01:09:34: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 01:09:34: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 01:09:34: #1 total tags in treatment: 13328912 INFO @ Mon, 03 Jun 2019 01:09:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:09:34: #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 01:09:34: #1 tags after filtering in treatment: 12541875 INFO @ Mon, 03 Jun 2019 01:09:34: #1 Redundant rate of treatment: 0.06 INFO @ Mon, 03 Jun 2019 01:09:34: #1 finished! INFO @ Mon, 03 Jun 2019 01:09:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:09:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:09:35: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 01:09:35: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 01:09:35: #1 total tags in treatment: 13328912 INFO @ Mon, 03 Jun 2019 01:09:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:09:35: #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 01:09:35: #1 tags after filtering in treatment: 12541875 INFO @ Mon, 03 Jun 2019 01:09:35: #1 Redundant rate of treatment: 0.06 INFO @ Mon, 03 Jun 2019 01:09:35: #1 finished! INFO @ Mon, 03 Jun 2019 01:09:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:09:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:09:36: #2 number of paired peaks: 122 WARNING @ Mon, 03 Jun 2019 01:09:36: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Mon, 03 Jun 2019 01:09:36: start model_add_line... INFO @ Mon, 03 Jun 2019 01:09:36: start X-correlation... INFO @ Mon, 03 Jun 2019 01:09:36: end of X-cor INFO @ Mon, 03 Jun 2019 01:09:36: #2 finished! INFO @ Mon, 03 Jun 2019 01:09:36: #2 predicted fragment length is 186 bps INFO @ Mon, 03 Jun 2019 01:09:36: #2 alternative fragment length(s) may be 186 bps INFO @ Mon, 03 Jun 2019 01:09:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.10_model.r INFO @ Mon, 03 Jun 2019 01:09:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:09:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:09:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:09:37: #2 number of paired peaks: 122 WARNING @ Mon, 03 Jun 2019 01:09:37: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Mon, 03 Jun 2019 01:09:37: start model_add_line... INFO @ Mon, 03 Jun 2019 01:09:37: start X-correlation... INFO @ Mon, 03 Jun 2019 01:09:37: end of X-cor INFO @ Mon, 03 Jun 2019 01:09:37: #2 finished! INFO @ Mon, 03 Jun 2019 01:09:37: #2 predicted fragment length is 186 bps INFO @ Mon, 03 Jun 2019 01:09:37: #2 alternative fragment length(s) may be 186 bps INFO @ Mon, 03 Jun 2019 01:09:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.05_model.r INFO @ Mon, 03 Jun 2019 01:09:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:09:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:09:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:09:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:09:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.20_summits.bed INFO @ Mon, 03 Jun 2019 01:09:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (784 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:10:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:10:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:10:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:10:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:10:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.10_summits.bed INFO @ Mon, 03 Jun 2019 01:10:29: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2209 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:10:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:10:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:10:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2075295/ERX2075295.05_summits.bed INFO @ Mon, 03 Jun 2019 01:10:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4459 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。