Job ID = 1293401 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 22,906,481 reads read : 45,812,962 reads written : 45,812,962 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: 00:51:42 22906481 reads; of these: 22906481 (100.00%) were paired; of these: 2724225 (11.89%) aligned concordantly 0 times 16799087 (73.34%) aligned concordantly exactly 1 time 3383169 (14.77%) aligned concordantly >1 times ---- 2724225 pairs aligned concordantly 0 times; of these: 547935 (20.11%) aligned discordantly 1 time ---- 2176290 pairs aligned 0 times concordantly or discordantly; of these: 4352580 mates make up the pairs; of these: 3257783 (74.85%) aligned 0 times 701378 (16.11%) aligned exactly 1 time 393419 (9.04%) aligned >1 times 92.89% overall alignment rate Time searching: 00:51:42 Overall time: 00:51:42 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] 6307324 / 20651004 = 0.3054 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 00:58:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.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 00:58:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.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 00:58:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:58:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:58:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:58:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:58:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.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 00:58:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:58:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:58:14: 1000000 INFO @ Mon, 03 Jun 2019 00:58:15: 1000000 INFO @ Mon, 03 Jun 2019 00:58:15: 1000000 INFO @ Mon, 03 Jun 2019 00:58:22: 2000000 INFO @ Mon, 03 Jun 2019 00:58:25: 2000000 INFO @ Mon, 03 Jun 2019 00:58:25: 2000000 INFO @ Mon, 03 Jun 2019 00:58:29: 3000000 INFO @ Mon, 03 Jun 2019 00:58:34: 3000000 INFO @ Mon, 03 Jun 2019 00:58:34: 3000000 INFO @ Mon, 03 Jun 2019 00:58:37: 4000000 INFO @ Mon, 03 Jun 2019 00:58:44: 4000000 INFO @ Mon, 03 Jun 2019 00:58:44: 4000000 INFO @ Mon, 03 Jun 2019 00:58:45: 5000000 INFO @ Mon, 03 Jun 2019 00:58:52: 6000000 INFO @ Mon, 03 Jun 2019 00:58:53: 5000000 INFO @ Mon, 03 Jun 2019 00:58:53: 5000000 INFO @ Mon, 03 Jun 2019 00:59:00: 7000000 INFO @ Mon, 03 Jun 2019 00:59:03: 6000000 INFO @ Mon, 03 Jun 2019 00:59:03: 6000000 INFO @ Mon, 03 Jun 2019 00:59:08: 8000000 INFO @ Mon, 03 Jun 2019 00:59:12: 7000000 INFO @ Mon, 03 Jun 2019 00:59:12: 7000000 INFO @ Mon, 03 Jun 2019 00:59:15: 9000000 INFO @ Mon, 03 Jun 2019 00:59:22: 8000000 INFO @ Mon, 03 Jun 2019 00:59:22: 8000000 INFO @ Mon, 03 Jun 2019 00:59:23: 10000000 INFO @ Mon, 03 Jun 2019 00:59:31: 11000000 INFO @ Mon, 03 Jun 2019 00:59:31: 9000000 INFO @ Mon, 03 Jun 2019 00:59:31: 9000000 INFO @ Mon, 03 Jun 2019 00:59:38: 12000000 INFO @ Mon, 03 Jun 2019 00:59:41: 10000000 INFO @ Mon, 03 Jun 2019 00:59:41: 10000000 INFO @ Mon, 03 Jun 2019 00:59:46: 13000000 INFO @ Mon, 03 Jun 2019 00:59:50: 11000000 INFO @ Mon, 03 Jun 2019 00:59:50: 11000000 INFO @ Mon, 03 Jun 2019 00:59:53: 14000000 INFO @ Mon, 03 Jun 2019 00:59:59: 12000000 INFO @ Mon, 03 Jun 2019 00:59:59: 12000000 INFO @ Mon, 03 Jun 2019 01:00:01: 15000000 INFO @ Mon, 03 Jun 2019 01:00:09: 13000000 INFO @ Mon, 03 Jun 2019 01:00:09: 16000000 INFO @ Mon, 03 Jun 2019 01:00:09: 13000000 INFO @ Mon, 03 Jun 2019 01:00:16: 17000000 INFO @ Mon, 03 Jun 2019 01:00:18: 14000000 INFO @ Mon, 03 Jun 2019 01:00:18: 14000000 INFO @ Mon, 03 Jun 2019 01:00:24: 18000000 INFO @ Mon, 03 Jun 2019 01:00:28: 15000000 INFO @ Mon, 03 Jun 2019 01:00:28: 15000000 INFO @ Mon, 03 Jun 2019 01:00:31: 19000000 INFO @ Mon, 03 Jun 2019 01:00:39: 16000000 INFO @ Mon, 03 Jun 2019 01:00:39: 16000000 INFO @ Mon, 03 Jun 2019 01:00:39: 20000000 INFO @ Mon, 03 Jun 2019 01:00:46: 21000000 INFO @ Mon, 03 Jun 2019 01:00:48: 17000000 INFO @ Mon, 03 Jun 2019 01:00:49: 17000000 INFO @ Mon, 03 Jun 2019 01:00:54: 22000000 INFO @ Mon, 03 Jun 2019 01:00:58: 18000000 INFO @ Mon, 03 Jun 2019 01:00:59: 18000000 INFO @ Mon, 03 Jun 2019 01:01:01: 23000000 INFO @ Mon, 03 Jun 2019 01:01:08: 19000000 INFO @ Mon, 03 Jun 2019 01:01:08: 19000000 INFO @ Mon, 03 Jun 2019 01:01:09: 24000000 INFO @ Mon, 03 Jun 2019 01:01:17: 25000000 INFO @ Mon, 03 Jun 2019 01:01:18: 20000000 INFO @ Mon, 03 Jun 2019 01:01:18: 20000000 INFO @ Mon, 03 Jun 2019 01:01:24: 26000000 INFO @ Mon, 03 Jun 2019 01:01:27: 21000000 INFO @ Mon, 03 Jun 2019 01:01:27: 21000000 INFO @ Mon, 03 Jun 2019 01:01:32: 27000000 INFO @ Mon, 03 Jun 2019 01:01:37: 22000000 INFO @ Mon, 03 Jun 2019 01:01:37: 22000000 INFO @ Mon, 03 Jun 2019 01:01:40: 28000000 INFO @ Mon, 03 Jun 2019 01:01:46: 23000000 INFO @ Mon, 03 Jun 2019 01:01:47: 23000000 INFO @ Mon, 03 Jun 2019 01:01:47: 29000000 INFO @ Mon, 03 Jun 2019 01:01:55: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 01:01:55: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 01:01:55: #1 total tags in treatment: 13994643 INFO @ Mon, 03 Jun 2019 01:01:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:01:55: #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 01:01:55: #1 tags after filtering in treatment: 12703312 INFO @ Mon, 03 Jun 2019 01:01:55: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 01:01:55: #1 finished! INFO @ Mon, 03 Jun 2019 01:01:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:01:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:01:56: 24000000 INFO @ Mon, 03 Jun 2019 01:01:56: #2 number of paired peaks: 127 WARNING @ Mon, 03 Jun 2019 01:01:56: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Mon, 03 Jun 2019 01:01:56: start model_add_line... INFO @ Mon, 03 Jun 2019 01:01:56: 24000000 INFO @ Mon, 03 Jun 2019 01:01:56: start X-correlation... INFO @ Mon, 03 Jun 2019 01:01:56: end of X-cor INFO @ Mon, 03 Jun 2019 01:01:56: #2 finished! INFO @ Mon, 03 Jun 2019 01:01:56: #2 predicted fragment length is 169 bps INFO @ Mon, 03 Jun 2019 01:01:56: #2 alternative fragment length(s) may be 169 bps INFO @ Mon, 03 Jun 2019 01:01:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.20_model.r INFO @ Mon, 03 Jun 2019 01:01:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:01:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:02:05: 25000000 INFO @ Mon, 03 Jun 2019 01:02:06: 25000000 INFO @ Mon, 03 Jun 2019 01:02:15: 26000000 INFO @ Mon, 03 Jun 2019 01:02:16: 26000000 INFO @ Mon, 03 Jun 2019 01:02:25: 27000000 INFO @ Mon, 03 Jun 2019 01:02:25: 27000000 INFO @ Mon, 03 Jun 2019 01:02:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:02:35: 28000000 INFO @ Mon, 03 Jun 2019 01:02:35: 28000000 INFO @ Mon, 03 Jun 2019 01:02:45: 29000000 INFO @ Mon, 03 Jun 2019 01:02:45: 29000000 INFO @ Mon, 03 Jun 2019 01:02:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:02:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:02:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.20_summits.bed INFO @ Mon, 03 Jun 2019 01:02:52: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (532 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:02:54: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 01:02:54: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 01:02:54: #1 total tags in treatment: 13994643 INFO @ Mon, 03 Jun 2019 01:02:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:02:54: #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 01:02:54: #1 tags after filtering in treatment: 12703312 INFO @ Mon, 03 Jun 2019 01:02:54: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 01:02:54: #1 finished! INFO @ Mon, 03 Jun 2019 01:02:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:02:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:02:54: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 01:02:54: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 01:02:54: #1 total tags in treatment: 13994643 INFO @ Mon, 03 Jun 2019 01:02:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:02:54: #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 01:02:55: #1 tags after filtering in treatment: 12703312 INFO @ Mon, 03 Jun 2019 01:02:55: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 01:02:55: #1 finished! INFO @ Mon, 03 Jun 2019 01:02:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:02:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:02:55: #2 number of paired peaks: 127 WARNING @ Mon, 03 Jun 2019 01:02:55: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Mon, 03 Jun 2019 01:02:55: start model_add_line... INFO @ Mon, 03 Jun 2019 01:02:55: start X-correlation... INFO @ Mon, 03 Jun 2019 01:02:55: end of X-cor INFO @ Mon, 03 Jun 2019 01:02:55: #2 finished! INFO @ Mon, 03 Jun 2019 01:02:55: #2 predicted fragment length is 169 bps INFO @ Mon, 03 Jun 2019 01:02:55: #2 alternative fragment length(s) may be 169 bps INFO @ Mon, 03 Jun 2019 01:02:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.05_model.r INFO @ Mon, 03 Jun 2019 01:02:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:02:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:02:56: #2 number of paired peaks: 127 WARNING @ Mon, 03 Jun 2019 01:02:56: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Mon, 03 Jun 2019 01:02:56: start model_add_line... INFO @ Mon, 03 Jun 2019 01:02:56: start X-correlation... INFO @ Mon, 03 Jun 2019 01:02:56: end of X-cor INFO @ Mon, 03 Jun 2019 01:02:56: #2 finished! INFO @ Mon, 03 Jun 2019 01:02:56: #2 predicted fragment length is 169 bps INFO @ Mon, 03 Jun 2019 01:02:56: #2 alternative fragment length(s) may be 169 bps INFO @ Mon, 03 Jun 2019 01:02:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.10_model.r INFO @ Mon, 03 Jun 2019 01:02:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:02:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:03:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:03:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:03:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:03:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:03:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.10_summits.bed INFO @ Mon, 03 Jun 2019 01:03:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1732 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:03:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:03:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:03:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2075298/ERX2075298.05_summits.bed INFO @ Mon, 03 Jun 2019 01:03:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4309 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。