Job ID = 1294046 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 8,071,297 reads read : 16,142,594 reads written : 16,142,594 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: 00:22:53 8071297 reads; of these: 8071297 (100.00%) were paired; of these: 989913 (12.26%) aligned concordantly 0 times 5631192 (69.77%) aligned concordantly exactly 1 time 1450192 (17.97%) aligned concordantly >1 times ---- 989913 pairs aligned concordantly 0 times; of these: 484361 (48.93%) aligned discordantly 1 time ---- 505552 pairs aligned 0 times concordantly or discordantly; of these: 1011104 mates make up the pairs; of these: 539837 (53.39%) aligned 0 times 220462 (21.80%) aligned exactly 1 time 250805 (24.81%) aligned >1 times 96.66% overall alignment rate Time searching: 00:22:53 Overall time: 00:22:53 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] 163523 / 7555388 = 0.0216 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 05:01:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.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 05:01:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:01:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:01:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.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 05:01:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:01:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:01:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.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 05:01:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:01:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:02:06: 1000000 INFO @ Mon, 03 Jun 2019 05:02:06: 1000000 INFO @ Mon, 03 Jun 2019 05:02:09: 1000000 INFO @ Mon, 03 Jun 2019 05:02:15: 2000000 INFO @ Mon, 03 Jun 2019 05:02:16: 2000000 INFO @ Mon, 03 Jun 2019 05:02:20: 2000000 INFO @ Mon, 03 Jun 2019 05:02:24: 3000000 INFO @ Mon, 03 Jun 2019 05:02:26: 3000000 INFO @ Mon, 03 Jun 2019 05:02:32: 3000000 INFO @ Mon, 03 Jun 2019 05:02:32: 4000000 INFO @ Mon, 03 Jun 2019 05:02:35: 4000000 INFO @ Mon, 03 Jun 2019 05:02:41: 5000000 INFO @ Mon, 03 Jun 2019 05:02:43: 4000000 INFO @ Mon, 03 Jun 2019 05:02:45: 5000000 INFO @ Mon, 03 Jun 2019 05:02:50: 6000000 INFO @ Mon, 03 Jun 2019 05:02:54: 5000000 INFO @ Mon, 03 Jun 2019 05:02:55: 6000000 INFO @ Mon, 03 Jun 2019 05:02:59: 7000000 INFO @ Mon, 03 Jun 2019 05:03:04: 7000000 INFO @ Mon, 03 Jun 2019 05:03:06: 6000000 INFO @ Mon, 03 Jun 2019 05:03:08: 8000000 INFO @ Mon, 03 Jun 2019 05:03:14: 8000000 INFO @ Mon, 03 Jun 2019 05:03:17: 7000000 INFO @ Mon, 03 Jun 2019 05:03:18: 9000000 INFO @ Mon, 03 Jun 2019 05:03:23: 9000000 INFO @ Mon, 03 Jun 2019 05:03:28: 8000000 INFO @ Mon, 03 Jun 2019 05:03:28: 10000000 INFO @ Mon, 03 Jun 2019 05:03:33: 10000000 INFO @ Mon, 03 Jun 2019 05:03:38: 11000000 INFO @ Mon, 03 Jun 2019 05:03:40: 9000000 INFO @ Mon, 03 Jun 2019 05:03:42: 11000000 INFO @ Mon, 03 Jun 2019 05:03:47: 12000000 INFO @ Mon, 03 Jun 2019 05:03:50: 12000000 INFO @ Mon, 03 Jun 2019 05:03:51: 10000000 INFO @ Mon, 03 Jun 2019 05:03:56: 13000000 INFO @ Mon, 03 Jun 2019 05:03:59: 13000000 INFO @ Mon, 03 Jun 2019 05:04:02: 11000000 INFO @ Mon, 03 Jun 2019 05:04:05: 14000000 INFO @ Mon, 03 Jun 2019 05:04:08: 14000000 INFO @ Mon, 03 Jun 2019 05:04:13: 12000000 INFO @ Mon, 03 Jun 2019 05:04:14: 15000000 INFO @ Mon, 03 Jun 2019 05:04:16: #1 tag size is determined as 81 bps INFO @ Mon, 03 Jun 2019 05:04:16: #1 tag size = 81 INFO @ Mon, 03 Jun 2019 05:04:16: #1 total tags in treatment: 6923326 INFO @ Mon, 03 Jun 2019 05:04:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:04:16: #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 05:04:16: #1 tags after filtering in treatment: 6711119 INFO @ Mon, 03 Jun 2019 05:04:16: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 05:04:16: #1 finished! INFO @ Mon, 03 Jun 2019 05:04:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:04:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:04:16: 15000000 INFO @ Mon, 03 Jun 2019 05:04:17: #2 number of paired peaks: 851 WARNING @ Mon, 03 Jun 2019 05:04:17: Fewer paired peaks (851) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 851 pairs to build model! INFO @ Mon, 03 Jun 2019 05:04:17: start model_add_line... INFO @ Mon, 03 Jun 2019 05:04:17: start X-correlation... INFO @ Mon, 03 Jun 2019 05:04:17: end of X-cor INFO @ Mon, 03 Jun 2019 05:04:17: #2 finished! INFO @ Mon, 03 Jun 2019 05:04:17: #2 predicted fragment length is 228 bps INFO @ Mon, 03 Jun 2019 05:04:17: #2 alternative fragment length(s) may be 228 bps INFO @ Mon, 03 Jun 2019 05:04:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.20_model.r INFO @ Mon, 03 Jun 2019 05:04:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:04:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:04:19: #1 tag size is determined as 81 bps INFO @ Mon, 03 Jun 2019 05:04:19: #1 tag size = 81 INFO @ Mon, 03 Jun 2019 05:04:19: #1 total tags in treatment: 6923326 INFO @ Mon, 03 Jun 2019 05:04:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:04:19: #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 05:04:19: #1 tags after filtering in treatment: 6711119 INFO @ Mon, 03 Jun 2019 05:04:19: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 05:04:19: #1 finished! INFO @ Mon, 03 Jun 2019 05:04:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:04:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:04:20: #2 number of paired peaks: 851 WARNING @ Mon, 03 Jun 2019 05:04:20: Fewer paired peaks (851) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 851 pairs to build model! INFO @ Mon, 03 Jun 2019 05:04:20: start model_add_line... INFO @ Mon, 03 Jun 2019 05:04:20: start X-correlation... INFO @ Mon, 03 Jun 2019 05:04:20: end of X-cor INFO @ Mon, 03 Jun 2019 05:04:20: #2 finished! INFO @ Mon, 03 Jun 2019 05:04:20: #2 predicted fragment length is 228 bps INFO @ Mon, 03 Jun 2019 05:04:20: #2 alternative fragment length(s) may be 228 bps INFO @ Mon, 03 Jun 2019 05:04:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.05_model.r INFO @ Mon, 03 Jun 2019 05:04:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:04:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:04:24: 13000000 INFO @ Mon, 03 Jun 2019 05:04:35: 14000000 INFO @ Mon, 03 Jun 2019 05:04:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:04:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:04:45: 15000000 INFO @ Mon, 03 Jun 2019 05:04:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:04:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:04:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.20_summits.bed INFO @ Mon, 03 Jun 2019 05:04:48: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (1149 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:04:49: #1 tag size is determined as 81 bps INFO @ Mon, 03 Jun 2019 05:04:49: #1 tag size = 81 INFO @ Mon, 03 Jun 2019 05:04:49: #1 total tags in treatment: 6923326 INFO @ Mon, 03 Jun 2019 05:04:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:04:49: #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 05:04:49: #1 tags after filtering in treatment: 6711119 INFO @ Mon, 03 Jun 2019 05:04:49: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 05:04:49: #1 finished! INFO @ Mon, 03 Jun 2019 05:04:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:04:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:04:49: #2 number of paired peaks: 851 WARNING @ Mon, 03 Jun 2019 05:04:49: Fewer paired peaks (851) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 851 pairs to build model! INFO @ Mon, 03 Jun 2019 05:04:49: start model_add_line... INFO @ Mon, 03 Jun 2019 05:04:49: start X-correlation... INFO @ Mon, 03 Jun 2019 05:04:49: end of X-cor INFO @ Mon, 03 Jun 2019 05:04:49: #2 finished! INFO @ Mon, 03 Jun 2019 05:04:49: #2 predicted fragment length is 228 bps INFO @ Mon, 03 Jun 2019 05:04:49: #2 alternative fragment length(s) may be 228 bps INFO @ Mon, 03 Jun 2019 05:04:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.10_model.r INFO @ Mon, 03 Jun 2019 05:04:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:04:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:04:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:04:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:04:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.05_summits.bed INFO @ Mon, 03 Jun 2019 05:04:50: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3884 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:05:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:05:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:05:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:05:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763411/SRX1763411.10_summits.bed INFO @ Mon, 03 Jun 2019 05:05:21: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2349 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。