Job ID = 2010327 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,888,440 reads read : 25,776,880 reads written : 25,776,880 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1009164.sra.cache’: 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: 00:14:13 12888440 reads; of these: 12888440 (100.00%) were paired; of these: 3964311 (30.76%) aligned concordantly 0 times 6636347 (51.49%) aligned concordantly exactly 1 time 2287782 (17.75%) aligned concordantly >1 times ---- 3964311 pairs aligned concordantly 0 times; of these: 46860 (1.18%) aligned discordantly 1 time ---- 3917451 pairs aligned 0 times concordantly or discordantly; of these: 7834902 mates make up the pairs; of these: 7119672 (90.87%) aligned 0 times 489378 (6.25%) aligned exactly 1 time 225852 (2.88%) aligned >1 times 72.38% overall alignment rate Time searching: 00:14:13 Overall time: 00:14:13 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] 4118164 / 8951023 = 0.4601 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 @ Fri, 05 Jul 2019 22:36:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.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 @ Fri, 05 Jul 2019 22:36:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:36:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:36:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.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 @ Fri, 05 Jul 2019 22:36:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:36:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:36:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.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 @ Fri, 05 Jul 2019 22:36:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:36:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:36:58: 1000000 INFO @ Fri, 05 Jul 2019 22:36:59: 1000000 INFO @ Fri, 05 Jul 2019 22:36:59: 1000000 INFO @ Fri, 05 Jul 2019 22:37:07: 2000000 INFO @ Fri, 05 Jul 2019 22:37:08: 2000000 INFO @ Fri, 05 Jul 2019 22:37:09: 2000000 INFO @ Fri, 05 Jul 2019 22:37:16: 3000000 INFO @ Fri, 05 Jul 2019 22:37:17: 3000000 INFO @ Fri, 05 Jul 2019 22:37:20: 3000000 INFO @ Fri, 05 Jul 2019 22:37:25: 4000000 INFO @ Fri, 05 Jul 2019 22:37:26: 4000000 INFO @ Fri, 05 Jul 2019 22:37:30: 4000000 INFO @ Fri, 05 Jul 2019 22:37:33: 5000000 INFO @ Fri, 05 Jul 2019 22:37:34: 5000000 INFO @ Fri, 05 Jul 2019 22:37:40: 5000000 INFO @ Fri, 05 Jul 2019 22:37:42: 6000000 INFO @ Fri, 05 Jul 2019 22:37:43: 6000000 INFO @ Fri, 05 Jul 2019 22:37:50: 6000000 INFO @ Fri, 05 Jul 2019 22:37:50: 7000000 INFO @ Fri, 05 Jul 2019 22:37:52: 7000000 INFO @ Fri, 05 Jul 2019 22:37:59: 8000000 INFO @ Fri, 05 Jul 2019 22:37:59: 7000000 INFO @ Fri, 05 Jul 2019 22:38:00: 8000000 INFO @ Fri, 05 Jul 2019 22:38:07: 9000000 INFO @ Fri, 05 Jul 2019 22:38:08: 9000000 INFO @ Fri, 05 Jul 2019 22:38:09: 8000000 INFO @ Fri, 05 Jul 2019 22:38:15: 10000000 INFO @ Fri, 05 Jul 2019 22:38:17: 10000000 INFO @ Fri, 05 Jul 2019 22:38:18: 9000000 INFO @ Fri, 05 Jul 2019 22:38:19: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 22:38:19: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 22:38:19: #1 total tags in treatment: 4808172 INFO @ Fri, 05 Jul 2019 22:38:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:38:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 22:38:19: #1 tags after filtering in treatment: 3472778 INFO @ Fri, 05 Jul 2019 22:38:19: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 05 Jul 2019 22:38:19: #1 finished! INFO @ Fri, 05 Jul 2019 22:38:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:38:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:38:19: #2 number of paired peaks: 29 WARNING @ Fri, 05 Jul 2019 22:38:19: Too few paired peaks (29) 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 @ Fri, 05 Jul 2019 22:38:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.10_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/SRX363275/SRX363275.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:38:20: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 22:38:20: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 22:38:20: #1 total tags in treatment: 4808172 INFO @ Fri, 05 Jul 2019 22:38:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:38:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 22:38:20: #1 tags after filtering in treatment: 3472778 INFO @ Fri, 05 Jul 2019 22:38:20: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 05 Jul 2019 22:38:20: #1 finished! INFO @ Fri, 05 Jul 2019 22:38:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:38:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:38:21: #2 number of paired peaks: 29 WARNING @ Fri, 05 Jul 2019 22:38:21: Too few paired peaks (29) 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 @ Fri, 05 Jul 2019 22:38:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.20_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/SRX363275/SRX363275.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:38:27: 10000000 INFO @ Fri, 05 Jul 2019 22:38:31: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 22:38:31: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 22:38:31: #1 total tags in treatment: 4808172 INFO @ Fri, 05 Jul 2019 22:38:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:38:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 22:38:31: #1 tags after filtering in treatment: 3472778 INFO @ Fri, 05 Jul 2019 22:38:31: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 05 Jul 2019 22:38:31: #1 finished! INFO @ Fri, 05 Jul 2019 22:38:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:38:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:38:32: #2 number of paired peaks: 29 WARNING @ Fri, 05 Jul 2019 22:38:32: Too few paired peaks (29) 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 @ Fri, 05 Jul 2019 22:38:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.05_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/SRX363275/SRX363275.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363275/SRX363275.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。