Job ID = 2011910 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,994,452 reads read : 7,988,904 reads written : 7,988,904 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: 00:02:37 3994452 reads; of these: 3994452 (100.00%) were paired; of these: 432149 (10.82%) aligned concordantly 0 times 3038985 (76.08%) aligned concordantly exactly 1 time 523318 (13.10%) aligned concordantly >1 times ---- 432149 pairs aligned concordantly 0 times; of these: 227365 (52.61%) aligned discordantly 1 time ---- 204784 pairs aligned 0 times concordantly or discordantly; of these: 409568 mates make up the pairs; of these: 256238 (62.56%) aligned 0 times 70541 (17.22%) aligned exactly 1 time 82789 (20.21%) aligned >1 times 96.79% overall alignment rate Time searching: 00:02:37 Overall time: 00:02:37 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] 171267 / 3787936 = 0.0452 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 03:17:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.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 03:17:54: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:17:54: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:17:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.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 03:17:55: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:17:55: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:17:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.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 03:17:56: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:17:56: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:18:01: 1000000 INFO @ Sat, 06 Jul 2019 03:18:03: 1000000 INFO @ Sat, 06 Jul 2019 03:18:04: 1000000 INFO @ Sat, 06 Jul 2019 03:18:09: 2000000 INFO @ Sat, 06 Jul 2019 03:18:11: 2000000 INFO @ Sat, 06 Jul 2019 03:18:12: 2000000 INFO @ Sat, 06 Jul 2019 03:18:17: 3000000 INFO @ Sat, 06 Jul 2019 03:18:20: 3000000 INFO @ Sat, 06 Jul 2019 03:18:20: 3000000 INFO @ Sat, 06 Jul 2019 03:18:24: 4000000 INFO @ Sat, 06 Jul 2019 03:18:27: 4000000 INFO @ Sat, 06 Jul 2019 03:18:28: 4000000 INFO @ Sat, 06 Jul 2019 03:18:32: 5000000 INFO @ Sat, 06 Jul 2019 03:18:35: 5000000 INFO @ Sat, 06 Jul 2019 03:18:36: 5000000 INFO @ Sat, 06 Jul 2019 03:18:40: 6000000 INFO @ Sat, 06 Jul 2019 03:18:43: 6000000 INFO @ Sat, 06 Jul 2019 03:18:44: 6000000 INFO @ Sat, 06 Jul 2019 03:18:47: 7000000 INFO @ Sat, 06 Jul 2019 03:18:50: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:18:50: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:18:50: #1 total tags in treatment: 3397966 INFO @ Sat, 06 Jul 2019 03:18:50: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:18:50: #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 03:18:50: #1 tags after filtering in treatment: 2843186 INFO @ Sat, 06 Jul 2019 03:18:50: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 06 Jul 2019 03:18:50: #1 finished! INFO @ Sat, 06 Jul 2019 03:18:50: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:18:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:18:50: 7000000 INFO @ Sat, 06 Jul 2019 03:18:51: #2 number of paired peaks: 123 WARNING @ Sat, 06 Jul 2019 03:18:51: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sat, 06 Jul 2019 03:18:51: start model_add_line... INFO @ Sat, 06 Jul 2019 03:18:51: start X-correlation... INFO @ Sat, 06 Jul 2019 03:18:51: end of X-cor INFO @ Sat, 06 Jul 2019 03:18:51: #2 finished! INFO @ Sat, 06 Jul 2019 03:18:51: #2 predicted fragment length is 276 bps INFO @ Sat, 06 Jul 2019 03:18:51: #2 alternative fragment length(s) may be 1,235,276,293,298,334 bps INFO @ Sat, 06 Jul 2019 03:18:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.05_model.r INFO @ Sat, 06 Jul 2019 03:18:51: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:18:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:18:51: 7000000 INFO @ Sat, 06 Jul 2019 03:18:53: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:18:53: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:18:53: #1 total tags in treatment: 3397966 INFO @ Sat, 06 Jul 2019 03:18:53: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:18:53: #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 03:18:53: #1 tags after filtering in treatment: 2843186 INFO @ Sat, 06 Jul 2019 03:18:53: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 06 Jul 2019 03:18:53: #1 finished! INFO @ Sat, 06 Jul 2019 03:18:53: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:18:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:18:54: #2 number of paired peaks: 123 WARNING @ Sat, 06 Jul 2019 03:18:54: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sat, 06 Jul 2019 03:18:54: start model_add_line... INFO @ Sat, 06 Jul 2019 03:18:54: start X-correlation... INFO @ Sat, 06 Jul 2019 03:18:54: end of X-cor INFO @ Sat, 06 Jul 2019 03:18:54: #2 finished! INFO @ Sat, 06 Jul 2019 03:18:54: #2 predicted fragment length is 276 bps INFO @ Sat, 06 Jul 2019 03:18:54: #2 alternative fragment length(s) may be 1,235,276,293,298,334 bps INFO @ Sat, 06 Jul 2019 03:18:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.20_model.r INFO @ Sat, 06 Jul 2019 03:18:54: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:18:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:18:54: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:18:54: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:18:54: #1 total tags in treatment: 3397966 INFO @ Sat, 06 Jul 2019 03:18:54: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:18:54: #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 03:18:54: #1 tags after filtering in treatment: 2843186 INFO @ Sat, 06 Jul 2019 03:18:54: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 06 Jul 2019 03:18:54: #1 finished! INFO @ Sat, 06 Jul 2019 03:18:54: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:18:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:18:55: #2 number of paired peaks: 123 WARNING @ Sat, 06 Jul 2019 03:18:55: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sat, 06 Jul 2019 03:18:55: start model_add_line... INFO @ Sat, 06 Jul 2019 03:18:55: start X-correlation... INFO @ Sat, 06 Jul 2019 03:18:55: end of X-cor INFO @ Sat, 06 Jul 2019 03:18:55: #2 finished! INFO @ Sat, 06 Jul 2019 03:18:55: #2 predicted fragment length is 276 bps INFO @ Sat, 06 Jul 2019 03:18:55: #2 alternative fragment length(s) may be 1,235,276,293,298,334 bps INFO @ Sat, 06 Jul 2019 03:18:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.10_model.r INFO @ Sat, 06 Jul 2019 03:18:55: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:18:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:18:59: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:19:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:19:02: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:19:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:19:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.05_summits.bed INFO @ Sat, 06 Jul 2019 03:19:02: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (153 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:19:03: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:19:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.20_peaks.xls INFO @ Sat, 06 Jul 2019 03:19:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:19:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.20_summits.bed INFO @ Sat, 06 Jul 2019 03:19:05: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (11 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:19:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:19:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:19:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383683/SRX5383683.10_summits.bed INFO @ Sat, 06 Jul 2019 03:19:06: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (23 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。