Job ID = 2011753 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,802,339 reads read : 11,604,678 reads written : 11,604,678 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: 00:03:58 5802339 reads; of these: 5802339 (100.00%) were paired; of these: 2831883 (48.81%) aligned concordantly 0 times 2628396 (45.30%) aligned concordantly exactly 1 time 342060 (5.90%) aligned concordantly >1 times ---- 2831883 pairs aligned concordantly 0 times; of these: 30013 (1.06%) aligned discordantly 1 time ---- 2801870 pairs aligned 0 times concordantly or discordantly; of these: 5603740 mates make up the pairs; of these: 3480493 (62.11%) aligned 0 times 1944465 (34.70%) aligned exactly 1 time 178782 (3.19%) aligned >1 times 70.01% overall alignment rate Time searching: 00:03:58 Overall time: 00:03:58 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] 2530555 / 2991818 = 0.8458 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 @ Sat, 06 Jul 2019 02:30:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.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 @ Sat, 06 Jul 2019 02:30:32: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:30:32: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:30:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.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 @ Sat, 06 Jul 2019 02:30:33: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:30:33: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:30:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.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 @ Sat, 06 Jul 2019 02:30:34: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:30:34: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:30:41: 1000000 INFO @ Sat, 06 Jul 2019 02:30:42: 1000000 INFO @ Sat, 06 Jul 2019 02:30:42: 1000000 INFO @ Sat, 06 Jul 2019 02:30:49: 2000000 INFO @ Sat, 06 Jul 2019 02:30:50: 2000000 INFO @ Sat, 06 Jul 2019 02:30:51: 2000000 INFO @ Sat, 06 Jul 2019 02:30:56: 3000000 INFO @ Sat, 06 Jul 2019 02:30:57: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:30:57: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:30:57: #1 total tags in treatment: 448047 INFO @ Sat, 06 Jul 2019 02:30:57: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:30:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:30:57: #1 tags after filtering in treatment: 418947 INFO @ Sat, 06 Jul 2019 02:30:57: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 06 Jul 2019 02:30:57: #1 finished! INFO @ Sat, 06 Jul 2019 02:30:57: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:30:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:30:57: #2 number of paired peaks: 310 WARNING @ Sat, 06 Jul 2019 02:30:57: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Sat, 06 Jul 2019 02:30:57: start model_add_line... INFO @ Sat, 06 Jul 2019 02:30:57: start X-correlation... INFO @ Sat, 06 Jul 2019 02:30:57: end of X-cor INFO @ Sat, 06 Jul 2019 02:30:57: #2 finished! INFO @ Sat, 06 Jul 2019 02:30:57: #2 predicted fragment length is 195 bps INFO @ Sat, 06 Jul 2019 02:30:57: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 06 Jul 2019 02:30:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.10_model.r INFO @ Sat, 06 Jul 2019 02:30:57: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:30:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:30:58: 3000000 INFO @ Sat, 06 Jul 2019 02:30:58: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:30:58: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:30:58: #1 total tags in treatment: 448047 INFO @ Sat, 06 Jul 2019 02:30:58: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:30:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:30:58: #1 tags after filtering in treatment: 418947 INFO @ Sat, 06 Jul 2019 02:30:58: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 06 Jul 2019 02:30:58: #1 finished! INFO @ Sat, 06 Jul 2019 02:30:58: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:30:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:30:59: #2 number of paired peaks: 310 WARNING @ Sat, 06 Jul 2019 02:30:59: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Sat, 06 Jul 2019 02:30:59: start model_add_line... INFO @ Sat, 06 Jul 2019 02:30:59: start X-correlation... INFO @ Sat, 06 Jul 2019 02:30:59: end of X-cor INFO @ Sat, 06 Jul 2019 02:30:59: #2 finished! INFO @ Sat, 06 Jul 2019 02:30:59: #2 predicted fragment length is 195 bps INFO @ Sat, 06 Jul 2019 02:30:59: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 06 Jul 2019 02:30:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.05_model.r INFO @ Sat, 06 Jul 2019 02:30:59: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:30:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:30:59: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:30:59: 3000000 INFO @ Sat, 06 Jul 2019 02:30:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.10_peaks.xls INFO @ Sat, 06 Jul 2019 02:30:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:30:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.10_summits.bed INFO @ Sat, 06 Jul 2019 02:30:59: Done! INFO @ Sat, 06 Jul 2019 02:31:00: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:31:00: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:31:00: #1 total tags in treatment: 448047 INFO @ Sat, 06 Jul 2019 02:31:00: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:31:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:31:00: #1 tags after filtering in treatment: 418947 INFO @ Sat, 06 Jul 2019 02:31:00: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 06 Jul 2019 02:31:00: #1 finished! INFO @ Sat, 06 Jul 2019 02:31:00: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:31:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:31:00: #2 number of paired peaks: 310 WARNING @ Sat, 06 Jul 2019 02:31:00: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Sat, 06 Jul 2019 02:31:00: start model_add_line... INFO @ Sat, 06 Jul 2019 02:31:00: start X-correlation... INFO @ Sat, 06 Jul 2019 02:31:00: end of X-cor INFO @ Sat, 06 Jul 2019 02:31:00: #2 finished! INFO @ Sat, 06 Jul 2019 02:31:00: #2 predicted fragment length is 195 bps INFO @ Sat, 06 Jul 2019 02:31:00: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 06 Jul 2019 02:31:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.20_model.r INFO @ Sat, 06 Jul 2019 02:31:00: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:31:00: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (343 records, 4 fields): 4 millis INFO @ Sat, 06 Jul 2019 02:31:00: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:31:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.05_peaks.xls INFO @ Sat, 06 Jul 2019 02:31:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:31:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.05_summits.bed INFO @ Sat, 06 Jul 2019 02:31:01: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (603 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:31:01: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:31:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.20_peaks.xls INFO @ Sat, 06 Jul 2019 02:31:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:31:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX497381/SRX497381.20_summits.bed INFO @ Sat, 06 Jul 2019 02:31:02: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (155 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。