Job ID = 2641108 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,208,115 reads read : 22,416,230 reads written : 22,416,230 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: 00:16:00 11208115 reads; of these: 11208115 (100.00%) were paired; of these: 6822382 (60.87%) aligned concordantly 0 times 3953094 (35.27%) aligned concordantly exactly 1 time 432639 (3.86%) aligned concordantly >1 times ---- 6822382 pairs aligned concordantly 0 times; of these: 4658935 (68.29%) aligned discordantly 1 time ---- 2163447 pairs aligned 0 times concordantly or discordantly; of these: 4326894 mates make up the pairs; of these: 2799847 (64.71%) aligned 0 times 435621 (10.07%) aligned exactly 1 time 1091426 (25.22%) aligned >1 times 87.51% overall alignment rate Time searching: 00:16:00 Overall time: 00:16:00 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] 158822 / 9032969 = 0.0176 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:07:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.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, 24 Aug 2019 22:07:35: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:07:35: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:07:43: 1000000 INFO @ Sat, 24 Aug 2019 22:07:51: 2000000 INFO @ Sat, 24 Aug 2019 22:07:58: 3000000 INFO @ Sat, 24 Aug 2019 22:08:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.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, 24 Aug 2019 22:08:05: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:08:05: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:08:06: 4000000 INFO @ Sat, 24 Aug 2019 22:08:14: 5000000 INFO @ Sat, 24 Aug 2019 22:08:16: 1000000 INFO @ Sat, 24 Aug 2019 22:08:22: 6000000 INFO @ Sat, 24 Aug 2019 22:08:27: 2000000 INFO @ Sat, 24 Aug 2019 22:08:30: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:08:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.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, 24 Aug 2019 22:08:35: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:08:35: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:08:38: 8000000 INFO @ Sat, 24 Aug 2019 22:08:38: 3000000 INFO @ Sat, 24 Aug 2019 22:08:46: 9000000 INFO @ Sat, 24 Aug 2019 22:08:47: 1000000 INFO @ Sat, 24 Aug 2019 22:08:50: 4000000 INFO @ Sat, 24 Aug 2019 22:08:54: 10000000 INFO @ Sat, 24 Aug 2019 22:08:59: 2000000 INFO @ Sat, 24 Aug 2019 22:09:02: 11000000 INFO @ Sat, 24 Aug 2019 22:09:02: 5000000 INFO @ Sat, 24 Aug 2019 22:09:10: 12000000 INFO @ Sat, 24 Aug 2019 22:09:11: 3000000 INFO @ Sat, 24 Aug 2019 22:09:14: 6000000 INFO @ Sat, 24 Aug 2019 22:09:18: 13000000 INFO @ Sat, 24 Aug 2019 22:09:23: 4000000 INFO @ Sat, 24 Aug 2019 22:09:26: 14000000 INFO @ Sat, 24 Aug 2019 22:09:26: 7000000 INFO @ Sat, 24 Aug 2019 22:09:33: 15000000 INFO @ Sat, 24 Aug 2019 22:09:35: 5000000 INFO @ Sat, 24 Aug 2019 22:09:38: 8000000 INFO @ Sat, 24 Aug 2019 22:09:41: 16000000 INFO @ Sat, 24 Aug 2019 22:09:47: 6000000 INFO @ Sat, 24 Aug 2019 22:09:49: 17000000 INFO @ Sat, 24 Aug 2019 22:09:50: 9000000 INFO @ Sat, 24 Aug 2019 22:09:57: 18000000 INFO @ Sat, 24 Aug 2019 22:09:58: 7000000 INFO @ Sat, 24 Aug 2019 22:10:02: 10000000 INFO @ Sat, 24 Aug 2019 22:10:05: 19000000 INFO @ Sat, 24 Aug 2019 22:10:08: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:10:08: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:10:08: #1 total tags in treatment: 4313532 INFO @ Sat, 24 Aug 2019 22:10:08: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:10:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:10:08: #1 tags after filtering in treatment: 3846692 INFO @ Sat, 24 Aug 2019 22:10:08: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 24 Aug 2019 22:10:08: #1 finished! INFO @ Sat, 24 Aug 2019 22:10:08: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:10:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:10:08: #2 number of paired peaks: 25 WARNING @ Sat, 24 Aug 2019 22:10:08: Too few paired peaks (25) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 22:10:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:10:10: 8000000 INFO @ Sat, 24 Aug 2019 22:10:13: 11000000 INFO @ Sat, 24 Aug 2019 22:10:22: 9000000 INFO @ Sat, 24 Aug 2019 22:10:25: 12000000 INFO @ Sat, 24 Aug 2019 22:10:34: 10000000 INFO @ Sat, 24 Aug 2019 22:10:36: 13000000 INFO @ Sat, 24 Aug 2019 22:10:45: 11000000 INFO @ Sat, 24 Aug 2019 22:10:46: 14000000 INFO @ Sat, 24 Aug 2019 22:10:55: 12000000 INFO @ Sat, 24 Aug 2019 22:10:57: 15000000 INFO @ Sat, 24 Aug 2019 22:11:06: 13000000 INFO @ Sat, 24 Aug 2019 22:11:09: 16000000 INFO @ Sat, 24 Aug 2019 22:11:17: 14000000 INFO @ Sat, 24 Aug 2019 22:11:20: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:11:28: 15000000 INFO @ Sat, 24 Aug 2019 22:11:28: 18000000 INFO @ Sat, 24 Aug 2019 22:11:36: 19000000 INFO @ Sat, 24 Aug 2019 22:11:38: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:11:38: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:11:38: #1 total tags in treatment: 4313532 INFO @ Sat, 24 Aug 2019 22:11:38: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:11:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:11:38: #1 tags after filtering in treatment: 3846692 INFO @ Sat, 24 Aug 2019 22:11:38: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 24 Aug 2019 22:11:38: #1 finished! INFO @ Sat, 24 Aug 2019 22:11:38: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:11:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:11:39: #2 number of paired peaks: 25 WARNING @ Sat, 24 Aug 2019 22:11:39: Too few paired peaks (25) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 22:11:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:11:39: 16000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:11:49: 17000000 INFO @ Sat, 24 Aug 2019 22:12:00: 18000000 INFO @ Sat, 24 Aug 2019 22:12:10: 19000000 INFO @ Sat, 24 Aug 2019 22:12:14: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:12:14: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:12:14: #1 total tags in treatment: 4313532 INFO @ Sat, 24 Aug 2019 22:12:14: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:12:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:12:14: #1 tags after filtering in treatment: 3846692 INFO @ Sat, 24 Aug 2019 22:12:14: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 24 Aug 2019 22:12:14: #1 finished! INFO @ Sat, 24 Aug 2019 22:12:14: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:12:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:12:14: #2 number of paired peaks: 25 WARNING @ Sat, 24 Aug 2019 22:12:14: Too few paired peaks (25) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 22:12:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546549/SRX5546549.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling