Job ID = 2010915 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 14,216,369 reads read : 28,432,738 reads written : 28,432,738 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1104089.sra.cache’: 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: 00:21:55 14216369 reads; of these: 14216369 (100.00%) were paired; of these: 2974849 (20.93%) aligned concordantly 0 times 6010125 (42.28%) aligned concordantly exactly 1 time 5231395 (36.80%) aligned concordantly >1 times ---- 2974849 pairs aligned concordantly 0 times; of these: 54398 (1.83%) aligned discordantly 1 time ---- 2920451 pairs aligned 0 times concordantly or discordantly; of these: 5840902 mates make up the pairs; of these: 4475665 (76.63%) aligned 0 times 578470 (9.90%) aligned exactly 1 time 786767 (13.47%) aligned >1 times 84.26% overall alignment rate Time searching: 00:21:55 Overall time: 00:21:55 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 7953890 / 11256843 = 0.7066 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 @ Sat, 06 Jul 2019 01:47:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 06 Jul 2019 01:47:47: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:47:47: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:47:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 06 Jul 2019 01:47:48: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:47:48: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:47:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 06 Jul 2019 01:47:49: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:47:49: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:47:56: 1000000 INFO @ Sat, 06 Jul 2019 01:47:58: 1000000 INFO @ Sat, 06 Jul 2019 01:47:59: 1000000 INFO @ Sat, 06 Jul 2019 01:48:06: 2000000 INFO @ Sat, 06 Jul 2019 01:48:07: 2000000 INFO @ Sat, 06 Jul 2019 01:48:08: 2000000 INFO @ Sat, 06 Jul 2019 01:48:15: 3000000 INFO @ Sat, 06 Jul 2019 01:48:16: 3000000 INFO @ Sat, 06 Jul 2019 01:48:17: 3000000 INFO @ Sat, 06 Jul 2019 01:48:24: 4000000 INFO @ Sat, 06 Jul 2019 01:48:25: 4000000 INFO @ Sat, 06 Jul 2019 01:48:26: 4000000 INFO @ Sat, 06 Jul 2019 01:48:32: 5000000 INFO @ Sat, 06 Jul 2019 01:48:34: 5000000 INFO @ Sat, 06 Jul 2019 01:48:35: 5000000 INFO @ Sat, 06 Jul 2019 01:48:41: 6000000 INFO @ Sat, 06 Jul 2019 01:48:42: 6000000 INFO @ Sat, 06 Jul 2019 01:48:43: 6000000 INFO @ Sat, 06 Jul 2019 01:48:50: 7000000 INFO @ Sat, 06 Jul 2019 01:48:51: 7000000 INFO @ Sat, 06 Jul 2019 01:48:52: 7000000 INFO @ Sat, 06 Jul 2019 01:48:59: 8000000 INFO @ Sat, 06 Jul 2019 01:48:59: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:48:59: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:48:59: #1 total tags in treatment: 3296362 INFO @ Sat, 06 Jul 2019 01:48:59: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:48:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:48:59: #1 tags after filtering in treatment: 1830986 INFO @ Sat, 06 Jul 2019 01:48:59: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 06 Jul 2019 01:48:59: #1 finished! INFO @ Sat, 06 Jul 2019 01:48:59: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:48:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:48:59: #2 number of paired peaks: 120 WARNING @ Sat, 06 Jul 2019 01:48:59: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Sat, 06 Jul 2019 01:48:59: start model_add_line... INFO @ Sat, 06 Jul 2019 01:48:59: start X-correlation... INFO @ Sat, 06 Jul 2019 01:48:59: end of X-cor INFO @ Sat, 06 Jul 2019 01:48:59: #2 finished! INFO @ Sat, 06 Jul 2019 01:48:59: #2 predicted fragment length is 184 bps INFO @ Sat, 06 Jul 2019 01:48:59: #2 alternative fragment length(s) may be 4,184 bps INFO @ Sat, 06 Jul 2019 01:48:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.05_model.r INFO @ Sat, 06 Jul 2019 01:48:59: 8000000 WARNING @ Sat, 06 Jul 2019 01:48:59: #2 Since the d (184) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 01:48:59: #2 You may need to consider one of the other alternative d(s): 4,184 WARNING @ Sat, 06 Jul 2019 01:48:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 01:48:59: #3 Call peaks... INFO @ Sat, 06 Jul 2019 01:48:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 01:49:00: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:49:00: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:49:00: #1 total tags in treatment: 3296362 INFO @ Sat, 06 Jul 2019 01:49:00: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:49:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:49:00: #1 tags after filtering in treatment: 1830986 INFO @ Sat, 06 Jul 2019 01:49:00: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 06 Jul 2019 01:49:00: #1 finished! INFO @ Sat, 06 Jul 2019 01:49:00: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:49:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:49:00: #2 number of paired peaks: 120 WARNING @ Sat, 06 Jul 2019 01:49:00: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Sat, 06 Jul 2019 01:49:00: start model_add_line... INFO @ Sat, 06 Jul 2019 01:49:00: start X-correlation... INFO @ Sat, 06 Jul 2019 01:49:00: end of X-cor INFO @ Sat, 06 Jul 2019 01:49:00: #2 finished! INFO @ Sat, 06 Jul 2019 01:49:00: #2 predicted fragment length is 184 bps INFO @ Sat, 06 Jul 2019 01:49:00: #2 alternative fragment length(s) may be 4,184 bps INFO @ Sat, 06 Jul 2019 01:49:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.10_model.r WARNING @ Sat, 06 Jul 2019 01:49:00: #2 Since the d (184) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 01:49:00: #2 You may need to consider one of the other alternative d(s): 4,184 WARNING @ Sat, 06 Jul 2019 01:49:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 01:49:00: #3 Call peaks... INFO @ Sat, 06 Jul 2019 01:49:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 01:49:01: 8000000 INFO @ Sat, 06 Jul 2019 01:49:01: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:49:01: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:49:01: #1 total tags in treatment: 3296362 INFO @ Sat, 06 Jul 2019 01:49:01: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:49:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:49:01: #1 tags after filtering in treatment: 1830986 INFO @ Sat, 06 Jul 2019 01:49:01: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 06 Jul 2019 01:49:01: #1 finished! INFO @ Sat, 06 Jul 2019 01:49:01: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:49:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:49:01: #2 number of paired peaks: 120 WARNING @ Sat, 06 Jul 2019 01:49:01: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Sat, 06 Jul 2019 01:49:01: start model_add_line... INFO @ Sat, 06 Jul 2019 01:49:01: start X-correlation... INFO @ Sat, 06 Jul 2019 01:49:01: end of X-cor INFO @ Sat, 06 Jul 2019 01:49:01: #2 finished! INFO @ Sat, 06 Jul 2019 01:49:01: #2 predicted fragment length is 184 bps INFO @ Sat, 06 Jul 2019 01:49:01: #2 alternative fragment length(s) may be 4,184 bps INFO @ Sat, 06 Jul 2019 01:49:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.20_model.r WARNING @ Sat, 06 Jul 2019 01:49:01: #2 Since the d (184) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 01:49:01: #2 You may need to consider one of the other alternative d(s): 4,184 WARNING @ Sat, 06 Jul 2019 01:49:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 01:49:01: #3 Call peaks... INFO @ Sat, 06 Jul 2019 01:49:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 01:49:06: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 01:49:07: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 01:49:08: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 01:49:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.05_peaks.xls INFO @ Sat, 06 Jul 2019 01:49:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 01:49:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.05_summits.bed INFO @ Sat, 06 Jul 2019 01:49:08: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (582 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:49:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.10_peaks.xls INFO @ Sat, 06 Jul 2019 01:49:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 01:49:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.10_summits.bed INFO @ Sat, 06 Jul 2019 01:49:09: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (249 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:49:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.20_peaks.xls INFO @ Sat, 06 Jul 2019 01:49:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 01:49:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX423250/SRX423250.20_summits.bed INFO @ Sat, 06 Jul 2019 01:49:10: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (98 records, 4 fields): 44 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。