Job ID = 2011947 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,257,282 reads read : 22,514,564 reads written : 22,514,564 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: 00:08:49 11257282 reads; of these: 11257282 (100.00%) were paired; of these: 7306997 (64.91%) aligned concordantly 0 times 3307868 (29.38%) aligned concordantly exactly 1 time 642417 (5.71%) aligned concordantly >1 times ---- 7306997 pairs aligned concordantly 0 times; of these: 1758627 (24.07%) aligned discordantly 1 time ---- 5548370 pairs aligned 0 times concordantly or discordantly; of these: 11096740 mates make up the pairs; of these: 10014210 (90.24%) aligned 0 times 360048 (3.24%) aligned exactly 1 time 722482 (6.51%) aligned >1 times 55.52% overall alignment rate Time searching: 00:08:49 Overall time: 00:08:49 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] 873628 / 5592300 = 0.1562 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 03:50:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.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 03:50:13: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:50:13: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:50:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.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 03:50:14: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:50:14: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:50:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.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 03:50:15: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:50:15: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:50:21: 1000000 INFO @ Sat, 06 Jul 2019 03:50:23: 1000000 INFO @ Sat, 06 Jul 2019 03:50:25: 1000000 INFO @ Sat, 06 Jul 2019 03:50:28: 2000000 INFO @ Sat, 06 Jul 2019 03:50:31: 2000000 INFO @ Sat, 06 Jul 2019 03:50:36: 2000000 INFO @ Sat, 06 Jul 2019 03:50:36: 3000000 INFO @ Sat, 06 Jul 2019 03:50:40: 3000000 INFO @ Sat, 06 Jul 2019 03:50:44: 4000000 INFO @ Sat, 06 Jul 2019 03:50:46: 3000000 INFO @ Sat, 06 Jul 2019 03:50:48: 4000000 INFO @ Sat, 06 Jul 2019 03:50:51: 5000000 INFO @ Sat, 06 Jul 2019 03:50:56: 5000000 INFO @ Sat, 06 Jul 2019 03:50:57: 4000000 INFO @ Sat, 06 Jul 2019 03:50:59: 6000000 INFO @ Sat, 06 Jul 2019 03:51:05: 6000000 INFO @ Sat, 06 Jul 2019 03:51:08: 7000000 INFO @ Sat, 06 Jul 2019 03:51:08: 5000000 INFO @ Sat, 06 Jul 2019 03:51:13: 7000000 INFO @ Sat, 06 Jul 2019 03:51:16: 8000000 INFO @ Sat, 06 Jul 2019 03:51:19: 6000000 INFO @ Sat, 06 Jul 2019 03:51:22: 8000000 INFO @ Sat, 06 Jul 2019 03:51:25: 9000000 INFO @ Sat, 06 Jul 2019 03:51:30: 9000000 INFO @ Sat, 06 Jul 2019 03:51:30: 7000000 INFO @ Sat, 06 Jul 2019 03:51:33: 10000000 INFO @ Sat, 06 Jul 2019 03:51:38: 10000000 INFO @ Sat, 06 Jul 2019 03:51:40: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:51:40: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:51:40: #1 total tags in treatment: 3353589 INFO @ Sat, 06 Jul 2019 03:51:40: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:51:40: #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 03:51:41: #1 tags after filtering in treatment: 2395471 INFO @ Sat, 06 Jul 2019 03:51:41: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 06 Jul 2019 03:51:41: #1 finished! INFO @ Sat, 06 Jul 2019 03:51:41: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:51:41: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 03:51:41: 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, 06 Jul 2019 03:51:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.05_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/SRX5624306/SRX5624306.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:51:44: 8000000 INFO @ Sat, 06 Jul 2019 03:51:44: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:51:44: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:51:44: #1 total tags in treatment: 3353589 INFO @ Sat, 06 Jul 2019 03:51:44: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:51:44: #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 03:51:44: #1 tags after filtering in treatment: 2395471 INFO @ Sat, 06 Jul 2019 03:51:44: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 06 Jul 2019 03:51:44: #1 finished! INFO @ Sat, 06 Jul 2019 03:51:44: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:51:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:51:45: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 03:51:45: 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, 06 Jul 2019 03:51:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.20_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/SRX5624306/SRX5624306.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:51:56: 9000000 INFO @ Sat, 06 Jul 2019 03:52:08: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:52:18: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:52:18: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:52:18: #1 total tags in treatment: 3353589 INFO @ Sat, 06 Jul 2019 03:52:18: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:52:18: #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 03:52:18: #1 tags after filtering in treatment: 2395471 INFO @ Sat, 06 Jul 2019 03:52:18: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 06 Jul 2019 03:52:18: #1 finished! INFO @ Sat, 06 Jul 2019 03:52:18: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:52:18: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 03:52:18: 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, 06 Jul 2019 03:52:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.10_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/SRX5624306/SRX5624306.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624306/SRX5624306.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。