Job ID = 2008045 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,728,840 reads read : 3,457,680 reads written : 3,457,680 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: 00:01:59 1728840 reads; of these: 1728840 (100.00%) were paired; of these: 150001 (8.68%) aligned concordantly 0 times 1454418 (84.13%) aligned concordantly exactly 1 time 124421 (7.20%) aligned concordantly >1 times ---- 150001 pairs aligned concordantly 0 times; of these: 34479 (22.99%) aligned discordantly 1 time ---- 115522 pairs aligned 0 times concordantly or discordantly; of these: 231044 mates make up the pairs; of these: 203449 (88.06%) aligned 0 times 18274 (7.91%) aligned exactly 1 time 9321 (4.03%) aligned >1 times 94.12% overall alignment rate Time searching: 00:01:59 Overall time: 00:01:59 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_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] 114341 / 1605063 = 0.0712 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 17:20:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.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 17:20:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:20:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:20:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.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 17:20:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:20:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:20:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.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 17:20:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:20:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:20:33: 1000000 INFO @ Fri, 05 Jul 2019 17:20:35: 1000000 INFO @ Fri, 05 Jul 2019 17:20:39: 1000000 INFO @ Fri, 05 Jul 2019 17:20:42: 2000000 INFO @ Fri, 05 Jul 2019 17:20:45: 2000000 INFO @ Fri, 05 Jul 2019 17:20:54: 2000000 INFO @ Fri, 05 Jul 2019 17:20:55: 3000000 INFO @ Fri, 05 Jul 2019 17:20:55: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:20:55: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:20:55: #1 total tags in treatment: 1465443 INFO @ Fri, 05 Jul 2019 17:20:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:20:55: #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 17:20:55: #1 tags after filtering in treatment: 1368121 INFO @ Fri, 05 Jul 2019 17:20:55: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:20:55: #1 finished! INFO @ Fri, 05 Jul 2019 17:20:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:20:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:20:55: #2 number of paired peaks: 184 WARNING @ Fri, 05 Jul 2019 17:20:55: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Fri, 05 Jul 2019 17:20:55: start model_add_line... INFO @ Fri, 05 Jul 2019 17:20:55: start X-correlation... INFO @ Fri, 05 Jul 2019 17:20:55: end of X-cor INFO @ Fri, 05 Jul 2019 17:20:55: #2 finished! INFO @ Fri, 05 Jul 2019 17:20:55: #2 predicted fragment length is 185 bps INFO @ Fri, 05 Jul 2019 17:20:55: #2 alternative fragment length(s) may be 1,69,170,185,209,233,465,504,526,564 bps INFO @ Fri, 05 Jul 2019 17:20:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.10_model.r WARNING @ Fri, 05 Jul 2019 17:20:55: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:20:55: #2 You may need to consider one of the other alternative d(s): 1,69,170,185,209,233,465,504,526,564 WARNING @ Fri, 05 Jul 2019 17:20:55: #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 17:20:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:20:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:20:56: 3000000 INFO @ Fri, 05 Jul 2019 17:20:57: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:20:57: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:20:57: #1 total tags in treatment: 1465443 INFO @ Fri, 05 Jul 2019 17:20:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:20:57: #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 17:20:57: #1 tags after filtering in treatment: 1368121 INFO @ Fri, 05 Jul 2019 17:20:57: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:20:57: #1 finished! INFO @ Fri, 05 Jul 2019 17:20:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:20:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:20:57: #2 number of paired peaks: 184 WARNING @ Fri, 05 Jul 2019 17:20:57: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Fri, 05 Jul 2019 17:20:57: start model_add_line... INFO @ Fri, 05 Jul 2019 17:20:57: start X-correlation... INFO @ Fri, 05 Jul 2019 17:20:57: end of X-cor INFO @ Fri, 05 Jul 2019 17:20:57: #2 finished! INFO @ Fri, 05 Jul 2019 17:20:57: #2 predicted fragment length is 185 bps INFO @ Fri, 05 Jul 2019 17:20:57: #2 alternative fragment length(s) may be 1,69,170,185,209,233,465,504,526,564 bps INFO @ Fri, 05 Jul 2019 17:20:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.05_model.r WARNING @ Fri, 05 Jul 2019 17:20:57: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:20:57: #2 You may need to consider one of the other alternative d(s): 1,69,170,185,209,233,465,504,526,564 WARNING @ Fri, 05 Jul 2019 17:20:57: #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 17:20:57: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:20:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:21:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:21:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:21:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:21:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:21:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.10_summits.bed INFO @ Fri, 05 Jul 2019 17:21:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:21:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:21:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:21:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.05_summits.bed INFO @ Fri, 05 Jul 2019 17:21:03: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (110 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 17:21:06: 3000000 INFO @ Fri, 05 Jul 2019 17:21:06: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:21:06: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:21:06: #1 total tags in treatment: 1465443 INFO @ Fri, 05 Jul 2019 17:21:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:21:06: #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 17:21:06: #1 tags after filtering in treatment: 1368121 INFO @ Fri, 05 Jul 2019 17:21:06: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:21:06: #1 finished! INFO @ Fri, 05 Jul 2019 17:21:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:21:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:21:06: #2 number of paired peaks: 184 WARNING @ Fri, 05 Jul 2019 17:21:06: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Fri, 05 Jul 2019 17:21:06: start model_add_line... INFO @ Fri, 05 Jul 2019 17:21:06: start X-correlation... INFO @ Fri, 05 Jul 2019 17:21:06: end of X-cor INFO @ Fri, 05 Jul 2019 17:21:06: #2 finished! INFO @ Fri, 05 Jul 2019 17:21:06: #2 predicted fragment length is 185 bps INFO @ Fri, 05 Jul 2019 17:21:06: #2 alternative fragment length(s) may be 1,69,170,185,209,233,465,504,526,564 bps INFO @ Fri, 05 Jul 2019 17:21:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.20_model.r WARNING @ Fri, 05 Jul 2019 17:21:06: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:21:06: #2 You may need to consider one of the other alternative d(s): 1,69,170,185,209,233,465,504,526,564 WARNING @ Fri, 05 Jul 2019 17:21:06: #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 17:21:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:21:06: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:21:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:21:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:21:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:21:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471829/ERX471829.20_summits.bed INFO @ Fri, 05 Jul 2019 17:21:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (8 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。