Job ID = 2008268 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,623,897 reads read : 11,247,794 reads written : 11,247,794 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: 00:06:58 5623897 reads; of these: 5623897 (100.00%) were paired; of these: 769382 (13.68%) aligned concordantly 0 times 4401294 (78.26%) aligned concordantly exactly 1 time 453221 (8.06%) aligned concordantly >1 times ---- 769382 pairs aligned concordantly 0 times; of these: 157116 (20.42%) aligned discordantly 1 time ---- 612266 pairs aligned 0 times concordantly or discordantly; of these: 1224532 mates make up the pairs; of these: 1046652 (85.47%) aligned 0 times 118818 (9.70%) aligned exactly 1 time 59062 (4.82%) aligned >1 times 90.69% overall alignment rate Time searching: 00:06:58 Overall time: 00:06:58 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] 667060 / 4989578 = 0.1337 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 18:39:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.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 18:39:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:39:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:39:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.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 18:39:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:39:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:39:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.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 18:39:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:39:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:39:45: 1000000 INFO @ Fri, 05 Jul 2019 18:39:47: 1000000 INFO @ Fri, 05 Jul 2019 18:39:50: 1000000 INFO @ Fri, 05 Jul 2019 18:39:55: 2000000 INFO @ Fri, 05 Jul 2019 18:39:58: 2000000 INFO @ Fri, 05 Jul 2019 18:40:02: 2000000 INFO @ Fri, 05 Jul 2019 18:40:04: 3000000 INFO @ Fri, 05 Jul 2019 18:40:08: 3000000 INFO @ Fri, 05 Jul 2019 18:40:14: 4000000 INFO @ Fri, 05 Jul 2019 18:40:15: 3000000 INFO @ Fri, 05 Jul 2019 18:40:19: 4000000 INFO @ Fri, 05 Jul 2019 18:40:23: 5000000 INFO @ Fri, 05 Jul 2019 18:40:28: 4000000 INFO @ Fri, 05 Jul 2019 18:40:29: 5000000 INFO @ Fri, 05 Jul 2019 18:40:32: 6000000 INFO @ Fri, 05 Jul 2019 18:40:40: 6000000 INFO @ Fri, 05 Jul 2019 18:40:40: 5000000 INFO @ Fri, 05 Jul 2019 18:40:41: 7000000 INFO @ Fri, 05 Jul 2019 18:40:51: 8000000 INFO @ Fri, 05 Jul 2019 18:40:52: 7000000 INFO @ Fri, 05 Jul 2019 18:40:53: 6000000 INFO @ Fri, 05 Jul 2019 18:40:59: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:40:59: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:40:59: #1 total tags in treatment: 4193735 INFO @ Fri, 05 Jul 2019 18:40:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:40:59: #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 18:40:59: #1 tags after filtering in treatment: 2819186 INFO @ Fri, 05 Jul 2019 18:40:59: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 05 Jul 2019 18:40:59: #1 finished! INFO @ Fri, 05 Jul 2019 18:40:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:40:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:40:59: #2 number of paired peaks: 3 WARNING @ Fri, 05 Jul 2019 18:40:59: Too few paired peaks (3) 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 18:40:59: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 18:41:03: 8000000 cut: /home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.10_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/ERX585790/ERX585790.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:41:06: 7000000 INFO @ Fri, 05 Jul 2019 18:41:12: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:41:12: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:41:12: #1 total tags in treatment: 4193735 INFO @ Fri, 05 Jul 2019 18:41:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:41:12: #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 18:41:12: #1 tags after filtering in treatment: 2819186 INFO @ Fri, 05 Jul 2019 18:41:12: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 05 Jul 2019 18:41:12: #1 finished! INFO @ Fri, 05 Jul 2019 18:41:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:41:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:41:13: #2 number of paired peaks: 3 WARNING @ Fri, 05 Jul 2019 18:41:13: Too few paired peaks (3) 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 18:41:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.05_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/ERX585790/ERX585790.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:41:18: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 18:41:28: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:41:28: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:41:28: #1 total tags in treatment: 4193735 INFO @ Fri, 05 Jul 2019 18:41:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:41:28: #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 18:41:28: #1 tags after filtering in treatment: 2819186 INFO @ Fri, 05 Jul 2019 18:41:28: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 05 Jul 2019 18:41:28: #1 finished! INFO @ Fri, 05 Jul 2019 18:41:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:41:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:41:28: #2 number of paired peaks: 3 WARNING @ Fri, 05 Jul 2019 18:41:28: Too few paired peaks (3) 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 18:41:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.20_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/ERX585790/ERX585790.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585790/ERX585790.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。