Job ID = 2010010 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,988,078 reads read : 13,976,156 reads written : 13,976,156 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5008430.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: 00:05:11 6988078 reads; of these: 6988078 (100.00%) were paired; of these: 1503511 (21.52%) aligned concordantly 0 times 3573449 (51.14%) aligned concordantly exactly 1 time 1911118 (27.35%) aligned concordantly >1 times ---- 1503511 pairs aligned concordantly 0 times; of these: 39272 (2.61%) aligned discordantly 1 time ---- 1464239 pairs aligned 0 times concordantly or discordantly; of these: 2928478 mates make up the pairs; of these: 2703585 (92.32%) aligned 0 times 115292 (3.94%) aligned exactly 1 time 109601 (3.74%) aligned >1 times 80.66% overall alignment rate Time searching: 00:05:11 Overall time: 00:05:11 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] 1083977 / 5515665 = 0.1965 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 21:00:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.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 21:00:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:00:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:00:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.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 21:00:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:00:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:00:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.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 21:00:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:00:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:00:51: 1000000 INFO @ Fri, 05 Jul 2019 21:00:52: 1000000 INFO @ Fri, 05 Jul 2019 21:00:53: 1000000 INFO @ Fri, 05 Jul 2019 21:01:00: 2000000 INFO @ Fri, 05 Jul 2019 21:01:01: 2000000 INFO @ Fri, 05 Jul 2019 21:01:02: 2000000 INFO @ Fri, 05 Jul 2019 21:01:09: 3000000 INFO @ Fri, 05 Jul 2019 21:01:10: 3000000 INFO @ Fri, 05 Jul 2019 21:01:11: 3000000 INFO @ Fri, 05 Jul 2019 21:01:18: 4000000 INFO @ Fri, 05 Jul 2019 21:01:19: 4000000 INFO @ Fri, 05 Jul 2019 21:01:20: 4000000 INFO @ Fri, 05 Jul 2019 21:01:26: 5000000 INFO @ Fri, 05 Jul 2019 21:01:27: 5000000 INFO @ Fri, 05 Jul 2019 21:01:28: 5000000 INFO @ Fri, 05 Jul 2019 21:01:35: 6000000 INFO @ Fri, 05 Jul 2019 21:01:36: 6000000 INFO @ Fri, 05 Jul 2019 21:01:37: 6000000 INFO @ Fri, 05 Jul 2019 21:01:44: 7000000 INFO @ Fri, 05 Jul 2019 21:01:45: 7000000 INFO @ Fri, 05 Jul 2019 21:01:46: 7000000 INFO @ Fri, 05 Jul 2019 21:01:52: 8000000 INFO @ Fri, 05 Jul 2019 21:01:53: 8000000 INFO @ Fri, 05 Jul 2019 21:01:54: 8000000 INFO @ Fri, 05 Jul 2019 21:02:01: 9000000 INFO @ Fri, 05 Jul 2019 21:02:02: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:02:02: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:02:02: #1 total tags in treatment: 4401772 INFO @ Fri, 05 Jul 2019 21:02:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:02:02: #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 21:02:02: #1 tags after filtering in treatment: 2630015 INFO @ Fri, 05 Jul 2019 21:02:02: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 05 Jul 2019 21:02:02: #1 finished! INFO @ Fri, 05 Jul 2019 21:02:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:02:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:02:02: 9000000 INFO @ Fri, 05 Jul 2019 21:02:02: #2 number of paired peaks: 97 WARNING @ Fri, 05 Jul 2019 21:02:02: Too few paired peaks (97) 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 21:02:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.05_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/SRX2339871/SRX2339871.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:02:03: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:02:03: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:02:03: #1 total tags in treatment: 4401772 INFO @ Fri, 05 Jul 2019 21:02:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:02:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 21:02:03: #1 tags after filtering in treatment: 2630015 INFO @ Fri, 05 Jul 2019 21:02:03: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 05 Jul 2019 21:02:03: #1 finished! INFO @ Fri, 05 Jul 2019 21:02:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:02:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:02:03: 9000000 INFO @ Fri, 05 Jul 2019 21:02:03: #2 number of paired peaks: 97 WARNING @ Fri, 05 Jul 2019 21:02:03: Too few paired peaks (97) 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 21:02:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.10_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/SRX2339871/SRX2339871.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:02:04: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:02:04: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:02:04: #1 total tags in treatment: 4401772 INFO @ Fri, 05 Jul 2019 21:02:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:02:04: #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 21:02:04: #1 tags after filtering in treatment: 2630015 INFO @ Fri, 05 Jul 2019 21:02:04: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 05 Jul 2019 21:02:04: #1 finished! INFO @ Fri, 05 Jul 2019 21:02:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:02:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:02:04: #2 number of paired peaks: 97 WARNING @ Fri, 05 Jul 2019 21:02:04: Too few paired peaks (97) 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 21:02:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.20_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/SRX2339871/SRX2339871.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339871/SRX2339871.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。