Job ID = 2010011 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,480,120 reads read : 14,960,240 reads written : 14,960,240 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: 00:05:05 7480120 reads; of these: 7480120 (100.00%) were paired; of these: 2084684 (27.87%) aligned concordantly 0 times 3721018 (49.75%) aligned concordantly exactly 1 time 1674418 (22.38%) aligned concordantly >1 times ---- 2084684 pairs aligned concordantly 0 times; of these: 97624 (4.68%) aligned discordantly 1 time ---- 1987060 pairs aligned 0 times concordantly or discordantly; of these: 3974120 mates make up the pairs; of these: 3763097 (94.69%) aligned 0 times 81366 (2.05%) aligned exactly 1 time 129657 (3.26%) aligned >1 times 74.85% overall alignment rate Time searching: 00:05:05 Overall time: 00:05:05 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] 2952889 / 5474137 = 0.5394 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 21:07:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.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 21:07:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:07:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:07:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.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 21:07:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:07:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:07:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.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 21:07:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:07:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:07:30: 1000000 INFO @ Fri, 05 Jul 2019 21:07:31: 1000000 INFO @ Fri, 05 Jul 2019 21:07:33: 1000000 INFO @ Fri, 05 Jul 2019 21:07:39: 2000000 INFO @ Fri, 05 Jul 2019 21:07:39: 2000000 INFO @ Fri, 05 Jul 2019 21:07:42: 2000000 INFO @ Fri, 05 Jul 2019 21:07:47: 3000000 INFO @ Fri, 05 Jul 2019 21:07:47: 3000000 INFO @ Fri, 05 Jul 2019 21:07:50: 3000000 INFO @ Fri, 05 Jul 2019 21:07:55: 4000000 INFO @ Fri, 05 Jul 2019 21:07:56: 4000000 INFO @ Fri, 05 Jul 2019 21:07:58: 4000000 INFO @ Fri, 05 Jul 2019 21:08:03: 5000000 INFO @ Fri, 05 Jul 2019 21:08:03: 5000000 INFO @ Fri, 05 Jul 2019 21:08:05: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:08:05: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:08:05: #1 total tags in treatment: 2461749 INFO @ Fri, 05 Jul 2019 21:08:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:08:05: #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 21:08:05: #1 tags after filtering in treatment: 1553129 INFO @ Fri, 05 Jul 2019 21:08:05: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 05 Jul 2019 21:08:05: #1 finished! INFO @ Fri, 05 Jul 2019 21:08:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:08:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:08:06: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:08:06: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:08:06: #1 total tags in treatment: 2461749 INFO @ Fri, 05 Jul 2019 21:08:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:08:06: #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 21:08:06: #2 number of paired peaks: 605 WARNING @ Fri, 05 Jul 2019 21:08:06: Fewer paired peaks (605) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 605 pairs to build model! INFO @ Fri, 05 Jul 2019 21:08:06: start model_add_line... INFO @ Fri, 05 Jul 2019 21:08:06: #1 tags after filtering in treatment: 1553129 INFO @ Fri, 05 Jul 2019 21:08:06: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 05 Jul 2019 21:08:06: #1 finished! INFO @ Fri, 05 Jul 2019 21:08:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:08:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:08:06: start X-correlation... INFO @ Fri, 05 Jul 2019 21:08:06: end of X-cor INFO @ Fri, 05 Jul 2019 21:08:06: #2 finished! INFO @ Fri, 05 Jul 2019 21:08:06: #2 predicted fragment length is 243 bps INFO @ Fri, 05 Jul 2019 21:08:06: #2 alternative fragment length(s) may be 4,222,243 bps INFO @ Fri, 05 Jul 2019 21:08:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.10_model.r INFO @ Fri, 05 Jul 2019 21:08:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:08:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:08:06: #2 number of paired peaks: 605 WARNING @ Fri, 05 Jul 2019 21:08:06: Fewer paired peaks (605) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 605 pairs to build model! INFO @ Fri, 05 Jul 2019 21:08:06: start model_add_line... INFO @ Fri, 05 Jul 2019 21:08:06: start X-correlation... INFO @ Fri, 05 Jul 2019 21:08:06: end of X-cor INFO @ Fri, 05 Jul 2019 21:08:06: #2 finished! INFO @ Fri, 05 Jul 2019 21:08:06: #2 predicted fragment length is 243 bps INFO @ Fri, 05 Jul 2019 21:08:06: #2 alternative fragment length(s) may be 4,222,243 bps INFO @ Fri, 05 Jul 2019 21:08:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.05_model.r INFO @ Fri, 05 Jul 2019 21:08:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:08:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:08:06: 5000000 INFO @ Fri, 05 Jul 2019 21:08:08: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:08:08: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:08:08: #1 total tags in treatment: 2461749 INFO @ Fri, 05 Jul 2019 21:08:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:08:09: #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 21:08:09: #1 tags after filtering in treatment: 1553129 INFO @ Fri, 05 Jul 2019 21:08:09: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 05 Jul 2019 21:08:09: #1 finished! INFO @ Fri, 05 Jul 2019 21:08:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:08:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:08:09: #2 number of paired peaks: 605 WARNING @ Fri, 05 Jul 2019 21:08:09: Fewer paired peaks (605) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 605 pairs to build model! INFO @ Fri, 05 Jul 2019 21:08:09: start model_add_line... INFO @ Fri, 05 Jul 2019 21:08:09: start X-correlation... INFO @ Fri, 05 Jul 2019 21:08:09: end of X-cor INFO @ Fri, 05 Jul 2019 21:08:09: #2 finished! INFO @ Fri, 05 Jul 2019 21:08:09: #2 predicted fragment length is 243 bps INFO @ Fri, 05 Jul 2019 21:08:09: #2 alternative fragment length(s) may be 4,222,243 bps INFO @ Fri, 05 Jul 2019 21:08:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.20_model.r INFO @ Fri, 05 Jul 2019 21:08:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:08:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:08:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:08:14: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 21:08:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.10_peaks.xls INFO @ Fri, 05 Jul 2019 21:08:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:08:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.10_summits.bed INFO @ Fri, 05 Jul 2019 21:08:16: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (557 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 21:08:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.05_peaks.xls INFO @ Fri, 05 Jul 2019 21:08:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:08:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.05_summits.bed INFO @ Fri, 05 Jul 2019 21:08:16: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (630 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 21:08:17: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:08:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.20_peaks.xls INFO @ Fri, 05 Jul 2019 21:08:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:08:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339872/SRX2339872.20_summits.bed INFO @ Fri, 05 Jul 2019 21:08:19: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (323 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。