Job ID = 2010992 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,056,174 reads read : 8,112,348 reads written : 8,112,348 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: 00:02:28 4056174 reads; of these: 4056174 (100.00%) were paired; of these: 1992593 (49.12%) aligned concordantly 0 times 1767056 (43.56%) aligned concordantly exactly 1 time 296525 (7.31%) aligned concordantly >1 times ---- 1992593 pairs aligned concordantly 0 times; of these: 11589 (0.58%) aligned discordantly 1 time ---- 1981004 pairs aligned 0 times concordantly or discordantly; of these: 3962008 mates make up the pairs; of these: 2308607 (58.27%) aligned 0 times 1428839 (36.06%) aligned exactly 1 time 224562 (5.67%) aligned >1 times 71.54% overall alignment rate Time searching: 00:02:28 Overall time: 00:02:28 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] 110480 / 2074787 = 0.0532 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 01:39:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.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 01:39:34: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:39:34: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:39:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.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 01:39:35: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:39:35: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:39:40: 1000000 INFO @ Sat, 06 Jul 2019 01:39:44: 1000000 INFO @ Sat, 06 Jul 2019 01:39:47: 2000000 INFO @ Sat, 06 Jul 2019 01:39:52: 2000000 INFO @ Sat, 06 Jul 2019 01:39:53: 3000000 INFO @ Sat, 06 Jul 2019 01:39:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.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 01:39:54: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:39:54: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:39:59: 4000000 INFO @ Sat, 06 Jul 2019 01:40:01: 1000000 INFO @ Sat, 06 Jul 2019 01:40:01: 3000000 INFO @ Sat, 06 Jul 2019 01:40:06: 5000000 INFO @ Sat, 06 Jul 2019 01:40:08: 2000000 INFO @ Sat, 06 Jul 2019 01:40:09: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:40:09: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:40:09: #1 total tags in treatment: 1953206 INFO @ Sat, 06 Jul 2019 01:40:09: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:40:09: #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 01:40:09: #1 tags after filtering in treatment: 1449465 INFO @ Sat, 06 Jul 2019 01:40:09: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 01:40:09: #1 finished! INFO @ Sat, 06 Jul 2019 01:40:09: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:40:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:40:10: #2 number of paired peaks: 16 WARNING @ Sat, 06 Jul 2019 01:40:10: Too few paired peaks (16) 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, 06 Jul 2019 01:40:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.05_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/SRX4342938/SRX4342938.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:40:10: 4000000 INFO @ Sat, 06 Jul 2019 01:40:15: 3000000 INFO @ Sat, 06 Jul 2019 01:40:19: 5000000 INFO @ Sat, 06 Jul 2019 01:40:21: 4000000 INFO @ Sat, 06 Jul 2019 01:40:24: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:40:24: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:40:24: #1 total tags in treatment: 1953206 INFO @ Sat, 06 Jul 2019 01:40:24: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:40:24: #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 01:40:24: #1 tags after filtering in treatment: 1449465 INFO @ Sat, 06 Jul 2019 01:40:24: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 01:40:24: #1 finished! INFO @ Sat, 06 Jul 2019 01:40:24: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:40:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:40:24: #2 number of paired peaks: 16 WARNING @ Sat, 06 Jul 2019 01:40:24: Too few paired peaks (16) 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, 06 Jul 2019 01:40:24: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 01:40:28: 5000000 INFO @ Sat, 06 Jul 2019 01:40:32: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:40:32: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:40:32: #1 total tags in treatment: 1953206 INFO @ Sat, 06 Jul 2019 01:40:32: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:40:32: #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 01:40:32: #1 tags after filtering in treatment: 1449465 INFO @ Sat, 06 Jul 2019 01:40:32: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 01:40:32: #1 finished! INFO @ Sat, 06 Jul 2019 01:40:32: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:40:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:40:32: #2 number of paired peaks: 16 WARNING @ Sat, 06 Jul 2019 01:40:32: Too few paired peaks (16) 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, 06 Jul 2019 01:40:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.10_*.xls’rm: : No such file or directorycannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.20_model.r’ : No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.10_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342938/SRX4342938.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。