Job ID = 2008323 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,542,616 reads read : 25,085,232 reads written : 25,085,232 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628985.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: 00:08:32 12542616 reads; of these: 12542616 (100.00%) were paired; of these: 1066843 (8.51%) aligned concordantly 0 times 10742211 (85.65%) aligned concordantly exactly 1 time 733562 (5.85%) aligned concordantly >1 times ---- 1066843 pairs aligned concordantly 0 times; of these: 51867 (4.86%) aligned discordantly 1 time ---- 1014976 pairs aligned 0 times concordantly or discordantly; of these: 2029952 mates make up the pairs; of these: 1971734 (97.13%) aligned 0 times 41448 (2.04%) aligned exactly 1 time 16770 (0.83%) aligned >1 times 92.14% overall alignment rate Time searching: 00:08:32 Overall time: 00:08:32 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] 10693892 / 11512727 = 0.9289 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 18:52:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.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 18:52:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:52:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:52:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.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 18:52:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:52:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:52:43: 1000000 INFO @ Fri, 05 Jul 2019 18:52:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.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 18:52:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:52:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:52:44: 1000000 INFO @ Fri, 05 Jul 2019 18:52:47: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:52:47: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:52:47: #1 total tags in treatment: 804097 INFO @ Fri, 05 Jul 2019 18:52:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:52:47: #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 18:52:47: #1 tags after filtering in treatment: 656608 INFO @ Fri, 05 Jul 2019 18:52:47: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 05 Jul 2019 18:52:47: #1 finished! INFO @ Fri, 05 Jul 2019 18:52:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:52:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:52:47: #2 number of paired peaks: 127 WARNING @ Fri, 05 Jul 2019 18:52:47: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Fri, 05 Jul 2019 18:52:47: start model_add_line... INFO @ Fri, 05 Jul 2019 18:52:47: start X-correlation... INFO @ Fri, 05 Jul 2019 18:52:47: end of X-cor INFO @ Fri, 05 Jul 2019 18:52:47: #2 finished! INFO @ Fri, 05 Jul 2019 18:52:47: #2 predicted fragment length is 169 bps INFO @ Fri, 05 Jul 2019 18:52:47: #2 alternative fragment length(s) may be 53,84,169,229,275,324,373,430,445,475,481,506,540 bps INFO @ Fri, 05 Jul 2019 18:52:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.05_model.r INFO @ Fri, 05 Jul 2019 18:52:49: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:52:49: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:52:49: #1 total tags in treatment: 804097 INFO @ Fri, 05 Jul 2019 18:52:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:52:49: #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 18:52:49: #1 tags after filtering in treatment: 656608 INFO @ Fri, 05 Jul 2019 18:52:49: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 05 Jul 2019 18:52:49: #1 finished! INFO @ Fri, 05 Jul 2019 18:52:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:52:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:52:49: #2 number of paired peaks: 127 WARNING @ Fri, 05 Jul 2019 18:52:49: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Fri, 05 Jul 2019 18:52:49: start model_add_line... INFO @ Fri, 05 Jul 2019 18:52:49: start X-correlation... INFO @ Fri, 05 Jul 2019 18:52:49: end of X-cor INFO @ Fri, 05 Jul 2019 18:52:49: #2 finished! INFO @ Fri, 05 Jul 2019 18:52:49: #2 predicted fragment length is 169 bps INFO @ Fri, 05 Jul 2019 18:52:49: #2 alternative fragment length(s) may be 53,84,169,229,275,324,373,430,445,475,481,506,540 bps INFO @ Fri, 05 Jul 2019 18:52:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.10_model.r INFO @ Fri, 05 Jul 2019 18:52:49: 1000000 INFO @ Fri, 05 Jul 2019 18:52:54: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:52:54: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:52:54: #1 total tags in treatment: 804097 INFO @ Fri, 05 Jul 2019 18:52:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:52:54: #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 18:52:54: #1 tags after filtering in treatment: 656608 INFO @ Fri, 05 Jul 2019 18:52:54: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 05 Jul 2019 18:52:54: #1 finished! INFO @ Fri, 05 Jul 2019 18:52:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:52:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:52:54: #2 number of paired peaks: 127 WARNING @ Fri, 05 Jul 2019 18:52:54: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Fri, 05 Jul 2019 18:52:54: start model_add_line... INFO @ Fri, 05 Jul 2019 18:52:54: start X-correlation... INFO @ Fri, 05 Jul 2019 18:52:54: end of X-cor INFO @ Fri, 05 Jul 2019 18:52:54: #2 finished! INFO @ Fri, 05 Jul 2019 18:52:54: #2 predicted fragment length is 169 bps INFO @ Fri, 05 Jul 2019 18:52:54: #2 alternative fragment length(s) may be 53,84,169,229,275,324,373,430,445,475,481,506,540 bps INFO @ Fri, 05 Jul 2019 18:52:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.20_model.r INFO @ Fri, 05 Jul 2019 18:53:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:53:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:53:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:53:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:53:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:53:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:53:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:53:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:53:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:53:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:53:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:53:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.10_summits.bed INFO @ Fri, 05 Jul 2019 18:53:05: Done! INFO @ Fri, 05 Jul 2019 18:53:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:53:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:53:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:53:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:53:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.05_summits.bed INFO @ Fri, 05 Jul 2019 18:53:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585831/ERX585831.20_summits.bed INFO @ Fri, 05 Jul 2019 18:53:05: Done! INFO @ Fri, 05 Jul 2019 18:53:05: Done! pass1 - making usageList (4 chroms): 2 millis pass2 - checking and writing primary data (4 records, 4 fields): 2 millis pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (67 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。