Job ID = 2010535 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,572,844 reads read : 11,145,688 reads written : 11,145,688 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: 00:04:29 5572844 reads; of these: 5572844 (100.00%) were paired; of these: 1047637 (18.80%) aligned concordantly 0 times 3567408 (64.01%) aligned concordantly exactly 1 time 957799 (17.19%) aligned concordantly >1 times ---- 1047637 pairs aligned concordantly 0 times; of these: 43733 (4.17%) aligned discordantly 1 time ---- 1003904 pairs aligned 0 times concordantly or discordantly; of these: 2007808 mates make up the pairs; of these: 1902614 (94.76%) aligned 0 times 57058 (2.84%) aligned exactly 1 time 48136 (2.40%) aligned >1 times 82.93% overall alignment rate Time searching: 00:04:29 Overall time: 00:04:29 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] 289594 / 4564405 = 0.0634 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 23:06:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.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 23:06:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:06:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:06:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.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 23:06:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:06:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:06:52: 1000000 INFO @ Fri, 05 Jul 2019 23:06:54: 1000000 INFO @ Fri, 05 Jul 2019 23:06:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.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 23:06:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:06:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:06:59: 2000000 INFO @ Fri, 05 Jul 2019 23:07:00: 2000000 INFO @ Fri, 05 Jul 2019 23:07:06: 3000000 INFO @ Fri, 05 Jul 2019 23:07:07: 1000000 INFO @ Fri, 05 Jul 2019 23:07:08: 3000000 INFO @ Fri, 05 Jul 2019 23:07:13: 4000000 INFO @ Fri, 05 Jul 2019 23:07:15: 4000000 INFO @ Fri, 05 Jul 2019 23:07:15: 2000000 INFO @ Fri, 05 Jul 2019 23:07:20: 5000000 INFO @ Fri, 05 Jul 2019 23:07:21: 5000000 INFO @ Fri, 05 Jul 2019 23:07:23: 3000000 INFO @ Fri, 05 Jul 2019 23:07:27: 6000000 INFO @ Fri, 05 Jul 2019 23:07:28: 6000000 INFO @ Fri, 05 Jul 2019 23:07:31: 4000000 INFO @ Fri, 05 Jul 2019 23:07:34: 7000000 INFO @ Fri, 05 Jul 2019 23:07:35: 7000000 INFO @ Fri, 05 Jul 2019 23:07:39: 5000000 INFO @ Fri, 05 Jul 2019 23:07:41: 8000000 INFO @ Fri, 05 Jul 2019 23:07:42: 8000000 INFO @ Fri, 05 Jul 2019 23:07:46: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:07:46: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:07:46: #1 total tags in treatment: 4236312 INFO @ Fri, 05 Jul 2019 23:07:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:07:46: #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 23:07:46: #1 tags after filtering in treatment: 2876099 INFO @ Fri, 05 Jul 2019 23:07:46: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 05 Jul 2019 23:07:46: #1 finished! INFO @ Fri, 05 Jul 2019 23:07:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:07:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:07:46: #2 number of paired peaks: 101 WARNING @ Fri, 05 Jul 2019 23:07:46: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Fri, 05 Jul 2019 23:07:46: start model_add_line... INFO @ Fri, 05 Jul 2019 23:07:46: start X-correlation... INFO @ Fri, 05 Jul 2019 23:07:46: end of X-cor INFO @ Fri, 05 Jul 2019 23:07:46: #2 finished! INFO @ Fri, 05 Jul 2019 23:07:46: #2 predicted fragment length is 281 bps INFO @ Fri, 05 Jul 2019 23:07:46: #2 alternative fragment length(s) may be 1,40,60,83,117,142,185,214,241,260,281,312,331,362,401,454,566 bps INFO @ Fri, 05 Jul 2019 23:07:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.05_model.r INFO @ Fri, 05 Jul 2019 23:07:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:07:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:07:47: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:07:47: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:07:47: #1 total tags in treatment: 4236312 INFO @ Fri, 05 Jul 2019 23:07:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:07:47: #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 23:07:47: #1 tags after filtering in treatment: 2876099 INFO @ Fri, 05 Jul 2019 23:07:47: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 05 Jul 2019 23:07:47: #1 finished! INFO @ Fri, 05 Jul 2019 23:07:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:07:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:07:47: #2 number of paired peaks: 101 WARNING @ Fri, 05 Jul 2019 23:07:47: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Fri, 05 Jul 2019 23:07:47: start model_add_line... INFO @ Fri, 05 Jul 2019 23:07:47: start X-correlation... INFO @ Fri, 05 Jul 2019 23:07:47: end of X-cor INFO @ Fri, 05 Jul 2019 23:07:47: #2 finished! INFO @ Fri, 05 Jul 2019 23:07:47: #2 predicted fragment length is 281 bps INFO @ Fri, 05 Jul 2019 23:07:47: #2 alternative fragment length(s) may be 1,40,60,83,117,142,185,214,241,260,281,312,331,362,401,454,566 bps INFO @ Fri, 05 Jul 2019 23:07:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.10_model.r INFO @ Fri, 05 Jul 2019 23:07:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:07:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:07:48: 6000000 INFO @ Fri, 05 Jul 2019 23:07:57: 7000000 INFO @ Fri, 05 Jul 2019 23:08:02: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:08:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:08:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:08:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:08:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.05_summits.bed INFO @ Fri, 05 Jul 2019 23:08:05: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (575 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:08:05: 8000000 INFO @ Fri, 05 Jul 2019 23:08:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:08:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:08:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.10_summits.bed INFO @ Fri, 05 Jul 2019 23:08:06: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (299 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:08:11: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:08:11: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:08:11: #1 total tags in treatment: 4236312 INFO @ Fri, 05 Jul 2019 23:08:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:08:11: #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 23:08:11: #1 tags after filtering in treatment: 2876099 INFO @ Fri, 05 Jul 2019 23:08:11: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 05 Jul 2019 23:08:11: #1 finished! INFO @ Fri, 05 Jul 2019 23:08:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:08:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:08:11: #2 number of paired peaks: 101 WARNING @ Fri, 05 Jul 2019 23:08:11: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Fri, 05 Jul 2019 23:08:11: start model_add_line... INFO @ Fri, 05 Jul 2019 23:08:11: start X-correlation... INFO @ Fri, 05 Jul 2019 23:08:11: end of X-cor INFO @ Fri, 05 Jul 2019 23:08:11: #2 finished! INFO @ Fri, 05 Jul 2019 23:08:11: #2 predicted fragment length is 281 bps INFO @ Fri, 05 Jul 2019 23:08:11: #2 alternative fragment length(s) may be 1,40,60,83,117,142,185,214,241,260,281,312,331,362,401,454,566 bps INFO @ Fri, 05 Jul 2019 23:08:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.20_model.r INFO @ Fri, 05 Jul 2019 23:08:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:08:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:08:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:08:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:08:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:08:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381238/SRX381238.20_summits.bed INFO @ Fri, 05 Jul 2019 23:08:30: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (66 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。