Job ID = 2010532 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 20,211,892 reads read : 40,423,784 reads written : 40,423,784 rm: cannot remove ‘[DSE]RR*’: 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: 00:10:33 20211892 reads; of these: 20211892 (100.00%) were paired; of these: 10784802 (53.36%) aligned concordantly 0 times 6206794 (30.71%) aligned concordantly exactly 1 time 3220296 (15.93%) aligned concordantly >1 times ---- 10784802 pairs aligned concordantly 0 times; of these: 97388 (0.90%) aligned discordantly 1 time ---- 10687414 pairs aligned 0 times concordantly or discordantly; of these: 21374828 mates make up the pairs; of these: 21089095 (98.66%) aligned 0 times 101517 (0.47%) aligned exactly 1 time 184216 (0.86%) aligned >1 times 47.83% overall alignment rate Time searching: 00:10:33 Overall time: 00:10:33 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 8 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] 3003339 / 9518287 = 0.3155 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 @ Fri, 05 Jul 2019 23:32:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.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 @ Fri, 05 Jul 2019 23:32:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:32:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:32:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.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 @ Fri, 05 Jul 2019 23:32:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:32:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:32:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.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 @ Fri, 05 Jul 2019 23:32:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:32:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:32:23: 1000000 INFO @ Fri, 05 Jul 2019 23:32:26: 1000000 INFO @ Fri, 05 Jul 2019 23:32:28: 1000000 INFO @ Fri, 05 Jul 2019 23:32:30: 2000000 INFO @ Fri, 05 Jul 2019 23:32:35: 2000000 INFO @ Fri, 05 Jul 2019 23:32:38: 3000000 INFO @ Fri, 05 Jul 2019 23:32:40: 2000000 INFO @ Fri, 05 Jul 2019 23:32:43: 3000000 INFO @ Fri, 05 Jul 2019 23:32:45: 4000000 INFO @ Fri, 05 Jul 2019 23:32:52: 3000000 INFO @ Fri, 05 Jul 2019 23:32:52: 4000000 INFO @ Fri, 05 Jul 2019 23:32:53: 5000000 INFO @ Fri, 05 Jul 2019 23:33:00: 6000000 INFO @ Fri, 05 Jul 2019 23:33:00: 5000000 INFO @ Fri, 05 Jul 2019 23:33:03: 4000000 INFO @ Fri, 05 Jul 2019 23:33:08: 7000000 INFO @ Fri, 05 Jul 2019 23:33:09: 6000000 INFO @ Fri, 05 Jul 2019 23:33:15: 5000000 INFO @ Fri, 05 Jul 2019 23:33:15: 8000000 INFO @ Fri, 05 Jul 2019 23:33:18: 7000000 INFO @ Fri, 05 Jul 2019 23:33:23: 9000000 INFO @ Fri, 05 Jul 2019 23:33:26: 8000000 INFO @ Fri, 05 Jul 2019 23:33:27: 6000000 INFO @ Fri, 05 Jul 2019 23:33:30: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:33:34: 9000000 INFO @ Fri, 05 Jul 2019 23:33:37: 11000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:33:39: 7000000 INFO @ Fri, 05 Jul 2019 23:33:43: 10000000 INFO @ Fri, 05 Jul 2019 23:33:45: 12000000 INFO @ Fri, 05 Jul 2019 23:33:51: 8000000 INFO @ Fri, 05 Jul 2019 23:33:51: 11000000 INFO @ Fri, 05 Jul 2019 23:33:52: 13000000 INFO @ Fri, 05 Jul 2019 23:33:55: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:33:55: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:33:55: #1 total tags in treatment: 6431725 INFO @ Fri, 05 Jul 2019 23:33:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:33:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:33:55: #1 tags after filtering in treatment: 2447535 INFO @ Fri, 05 Jul 2019 23:33:55: #1 Redundant rate of treatment: 0.62 INFO @ Fri, 05 Jul 2019 23:33:55: #1 finished! INFO @ Fri, 05 Jul 2019 23:33:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:33:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:33:55: #2 number of paired peaks: 975 WARNING @ Fri, 05 Jul 2019 23:33:55: Fewer paired peaks (975) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 975 pairs to build model! INFO @ Fri, 05 Jul 2019 23:33:55: start model_add_line... INFO @ Fri, 05 Jul 2019 23:33:55: start X-correlation... INFO @ Fri, 05 Jul 2019 23:33:55: end of X-cor INFO @ Fri, 05 Jul 2019 23:33:55: #2 finished! INFO @ Fri, 05 Jul 2019 23:33:55: #2 predicted fragment length is 11 bps INFO @ Fri, 05 Jul 2019 23:33:55: #2 alternative fragment length(s) may be 11,40,64,90,107,579 bps INFO @ Fri, 05 Jul 2019 23:33:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.05_model.r WARNING @ Fri, 05 Jul 2019 23:33:55: #2 Since the d (11) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 23:33:55: #2 You may need to consider one of the other alternative d(s): 11,40,64,90,107,579 WARNING @ Fri, 05 Jul 2019 23:33:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 23:33:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:33:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:34:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:34:00: 12000000 INFO @ Fri, 05 Jul 2019 23:34:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:34:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:34:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.05_summits.bed INFO @ Fri, 05 Jul 2019 23:34:02: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:34:02: 9000000 INFO @ Fri, 05 Jul 2019 23:34:08: 13000000 INFO @ Fri, 05 Jul 2019 23:34:11: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:34:11: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:34:11: #1 total tags in treatment: 6431725 INFO @ Fri, 05 Jul 2019 23:34:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:34:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:34:11: #1 tags after filtering in treatment: 2447535 INFO @ Fri, 05 Jul 2019 23:34:11: #1 Redundant rate of treatment: 0.62 INFO @ Fri, 05 Jul 2019 23:34:11: #1 finished! INFO @ Fri, 05 Jul 2019 23:34:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:34:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:34:12: #2 number of paired peaks: 975 WARNING @ Fri, 05 Jul 2019 23:34:12: Fewer paired peaks (975) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 975 pairs to build model! INFO @ Fri, 05 Jul 2019 23:34:12: start model_add_line... INFO @ Fri, 05 Jul 2019 23:34:12: start X-correlation... INFO @ Fri, 05 Jul 2019 23:34:12: end of X-cor INFO @ Fri, 05 Jul 2019 23:34:12: #2 finished! INFO @ Fri, 05 Jul 2019 23:34:12: #2 predicted fragment length is 11 bps INFO @ Fri, 05 Jul 2019 23:34:12: #2 alternative fragment length(s) may be 11,40,64,90,107,579 bps INFO @ Fri, 05 Jul 2019 23:34:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.20_model.r WARNING @ Fri, 05 Jul 2019 23:34:12: #2 Since the d (11) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 23:34:12: #2 You may need to consider one of the other alternative d(s): 11,40,64,90,107,579 WARNING @ Fri, 05 Jul 2019 23:34:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 23:34:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:34:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:34:13: 10000000 INFO @ Fri, 05 Jul 2019 23:34:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:34:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:34:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:34:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.20_summits.bed INFO @ Fri, 05 Jul 2019 23:34:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:34:24: 11000000 INFO @ Fri, 05 Jul 2019 23:34:34: 12000000 INFO @ Fri, 05 Jul 2019 23:34:45: 13000000 INFO @ Fri, 05 Jul 2019 23:34:48: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:34:48: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:34:48: #1 total tags in treatment: 6431725 INFO @ Fri, 05 Jul 2019 23:34:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:34:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:34:48: #1 tags after filtering in treatment: 2447535 INFO @ Fri, 05 Jul 2019 23:34:48: #1 Redundant rate of treatment: 0.62 INFO @ Fri, 05 Jul 2019 23:34:48: #1 finished! INFO @ Fri, 05 Jul 2019 23:34:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:34:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:34:49: #2 number of paired peaks: 975 WARNING @ Fri, 05 Jul 2019 23:34:49: Fewer paired peaks (975) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 975 pairs to build model! INFO @ Fri, 05 Jul 2019 23:34:49: start model_add_line... INFO @ Fri, 05 Jul 2019 23:34:49: start X-correlation... INFO @ Fri, 05 Jul 2019 23:34:49: end of X-cor INFO @ Fri, 05 Jul 2019 23:34:49: #2 finished! INFO @ Fri, 05 Jul 2019 23:34:49: #2 predicted fragment length is 11 bps INFO @ Fri, 05 Jul 2019 23:34:49: #2 alternative fragment length(s) may be 11,40,64,90,107,579 bps INFO @ Fri, 05 Jul 2019 23:34:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.10_model.r WARNING @ Fri, 05 Jul 2019 23:35:07: #2 Since the d (11) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 23:35:07: #2 You may need to consider one of the other alternative d(s): 11,40,64,90,107,579 WARNING @ Fri, 05 Jul 2019 23:35:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 23:35:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:35:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:35:12: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:35:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:35:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:35:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381235/SRX381235.10_summits.bed INFO @ Fri, 05 Jul 2019 23:35:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling