Job ID = 2641119 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,252,622 reads read : 22,505,244 reads written : 22,505,244 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: 00:16:53 11252622 reads; of these: 11252622 (100.00%) were paired; of these: 7565356 (67.23%) aligned concordantly 0 times 3312007 (29.43%) aligned concordantly exactly 1 time 375259 (3.33%) aligned concordantly >1 times ---- 7565356 pairs aligned concordantly 0 times; of these: 5197376 (68.70%) aligned discordantly 1 time ---- 2367980 pairs aligned 0 times concordantly or discordantly; of these: 4735960 mates make up the pairs; of these: 3019536 (63.76%) aligned 0 times 473209 (9.99%) aligned exactly 1 time 1243215 (26.25%) aligned >1 times 86.58% overall alignment rate Time searching: 00:16:53 Overall time: 00:16:53 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] 162401 / 8874772 = 0.0183 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:09:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.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 22:09:56: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:09:56: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:10:07: 1000000 INFO @ Sat, 24 Aug 2019 22:10:19: 2000000 INFO @ Sat, 24 Aug 2019 22:10:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.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 22:10:26: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:10:26: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:10:30: 3000000 INFO @ Sat, 24 Aug 2019 22:10:34: 1000000 INFO @ Sat, 24 Aug 2019 22:10:41: 4000000 INFO @ Sat, 24 Aug 2019 22:10:42: 2000000 INFO @ Sat, 24 Aug 2019 22:10:50: 3000000 INFO @ Sat, 24 Aug 2019 22:10:53: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:10:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.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 22:10:56: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:10:56: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:10:59: 4000000 INFO @ Sat, 24 Aug 2019 22:11:06: 6000000 INFO @ Sat, 24 Aug 2019 22:11:07: 5000000 INFO @ Sat, 24 Aug 2019 22:11:10: 1000000 INFO @ Sat, 24 Aug 2019 22:11:15: 6000000 INFO @ Sat, 24 Aug 2019 22:11:20: 7000000 INFO @ Sat, 24 Aug 2019 22:11:23: 7000000 INFO @ Sat, 24 Aug 2019 22:11:24: 2000000 INFO @ Sat, 24 Aug 2019 22:11:31: 8000000 INFO @ Sat, 24 Aug 2019 22:11:33: 8000000 INFO @ Sat, 24 Aug 2019 22:11:37: 3000000 INFO @ Sat, 24 Aug 2019 22:11:39: 9000000 INFO @ Sat, 24 Aug 2019 22:11:47: 9000000 INFO @ Sat, 24 Aug 2019 22:11:48: 10000000 INFO @ Sat, 24 Aug 2019 22:11:51: 4000000 INFO @ Sat, 24 Aug 2019 22:11:56: 11000000 INFO @ Sat, 24 Aug 2019 22:12:00: 10000000 INFO @ Sat, 24 Aug 2019 22:12:04: 12000000 INFO @ Sat, 24 Aug 2019 22:12:05: 5000000 INFO @ Sat, 24 Aug 2019 22:12:12: 13000000 INFO @ Sat, 24 Aug 2019 22:12:14: 11000000 INFO @ Sat, 24 Aug 2019 22:12:18: 6000000 INFO @ Sat, 24 Aug 2019 22:12:20: 14000000 INFO @ Sat, 24 Aug 2019 22:12:27: 12000000 INFO @ Sat, 24 Aug 2019 22:12:28: 15000000 INFO @ Sat, 24 Aug 2019 22:12:32: 7000000 INFO @ Sat, 24 Aug 2019 22:12:37: 16000000 INFO @ Sat, 24 Aug 2019 22:12:40: 13000000 INFO @ Sat, 24 Aug 2019 22:12:45: 17000000 INFO @ Sat, 24 Aug 2019 22:12:45: 8000000 INFO @ Sat, 24 Aug 2019 22:12:53: 18000000 INFO @ Sat, 24 Aug 2019 22:12:54: 14000000 INFO @ Sat, 24 Aug 2019 22:12:58: 9000000 INFO @ Sat, 24 Aug 2019 22:13:01: 19000000 INFO @ Sat, 24 Aug 2019 22:13:02: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:13:02: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:13:02: #1 total tags in treatment: 3624747 INFO @ Sat, 24 Aug 2019 22:13:02: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:13:02: #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 22:13:02: #1 tags after filtering in treatment: 3268862 INFO @ Sat, 24 Aug 2019 22:13:02: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 24 Aug 2019 22:13:02: #1 finished! INFO @ Sat, 24 Aug 2019 22:13:02: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:13:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:13:03: #2 number of paired peaks: 28 WARNING @ Sat, 24 Aug 2019 22:13:03: Too few paired peaks (28) 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 22:13:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.10_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/SRX5546557/SRX5546557.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:13:07: 15000000 INFO @ Sat, 24 Aug 2019 22:13:12: 10000000 INFO @ Sat, 24 Aug 2019 22:13:20: 16000000 INFO @ Sat, 24 Aug 2019 22:13:25: 11000000 INFO @ Sat, 24 Aug 2019 22:13:33: 17000000 INFO @ Sat, 24 Aug 2019 22:13:38: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:13:46: 18000000 INFO @ Sat, 24 Aug 2019 22:13:51: 13000000 INFO @ Sat, 24 Aug 2019 22:13:59: 19000000 INFO @ Sat, 24 Aug 2019 22:14:01: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:14:01: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:14:01: #1 total tags in treatment: 3624747 INFO @ Sat, 24 Aug 2019 22:14:01: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:14:01: #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 22:14:01: #1 tags after filtering in treatment: 3268862 INFO @ Sat, 24 Aug 2019 22:14:01: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 24 Aug 2019 22:14:01: #1 finished! INFO @ Sat, 24 Aug 2019 22:14:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:14:01: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:14:01: #2 number of paired peaks: 28 WARNING @ Sat, 24 Aug 2019 22:14:01: Too few paired peaks (28) 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 22:14:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.05_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/SRX5546557/SRX5546557.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:14:04: 14000000 INFO @ Sat, 24 Aug 2019 22:14:15: 15000000 INFO @ Sat, 24 Aug 2019 22:14:26: 16000000 INFO @ Sat, 24 Aug 2019 22:14:37: 17000000 INFO @ Sat, 24 Aug 2019 22:14:49: 18000000 INFO @ Sat, 24 Aug 2019 22:15:00: 19000000 INFO @ Sat, 24 Aug 2019 22:15:02: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:15:02: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:15:02: #1 total tags in treatment: 3624747 INFO @ Sat, 24 Aug 2019 22:15:02: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:15:02: #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 22:15:02: #1 tags after filtering in treatment: 3268862 INFO @ Sat, 24 Aug 2019 22:15:02: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 24 Aug 2019 22:15:02: #1 finished! INFO @ Sat, 24 Aug 2019 22:15:02: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:15:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:15:02: #2 number of paired peaks: 28 WARNING @ Sat, 24 Aug 2019 22:15:02: Too few paired peaks (28) 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 22:15:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.20_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/SRX5546557/SRX5546557.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546557/SRX5546557.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling