Job ID = 2011939 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 15,512,128 reads read : 31,024,256 reads written : 31,024,256 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: 00:11:58 15512128 reads; of these: 15512128 (100.00%) were paired; of these: 11540705 (74.40%) aligned concordantly 0 times 3370310 (21.73%) aligned concordantly exactly 1 time 601113 (3.88%) aligned concordantly >1 times ---- 11540705 pairs aligned concordantly 0 times; of these: 2467811 (21.38%) aligned discordantly 1 time ---- 9072894 pairs aligned 0 times concordantly or discordantly; of these: 18145788 mates make up the pairs; of these: 16678647 (91.91%) aligned 0 times 533810 (2.94%) aligned exactly 1 time 933331 (5.14%) aligned >1 times 46.24% overall alignment rate Time searching: 00:11:58 Overall time: 00:11:58 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] 1040880 / 6286414 = 0.1656 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 03:57:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.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 03:57:24: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:57:24: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:57:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.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 03:57:25: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:57:25: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:57:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.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 03:57:26: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:57:26: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:57:34: 1000000 INFO @ Sat, 06 Jul 2019 03:57:35: 1000000 INFO @ Sat, 06 Jul 2019 03:57:36: 1000000 INFO @ Sat, 06 Jul 2019 03:57:43: 2000000 INFO @ Sat, 06 Jul 2019 03:57:46: 2000000 INFO @ Sat, 06 Jul 2019 03:57:48: 2000000 INFO @ Sat, 06 Jul 2019 03:57:50: 3000000 INFO @ Sat, 06 Jul 2019 03:57:58: 3000000 INFO @ Sat, 06 Jul 2019 03:57:58: 4000000 INFO @ Sat, 06 Jul 2019 03:57:59: 3000000 INFO @ Sat, 06 Jul 2019 03:58:06: 5000000 INFO @ Sat, 06 Jul 2019 03:58:09: 4000000 INFO @ Sat, 06 Jul 2019 03:58:10: 4000000 INFO @ Sat, 06 Jul 2019 03:58:15: 6000000 INFO @ Sat, 06 Jul 2019 03:58:20: 5000000 INFO @ Sat, 06 Jul 2019 03:58:23: 5000000 INFO @ Sat, 06 Jul 2019 03:58:28: 7000000 INFO @ Sat, 06 Jul 2019 03:58:30: 6000000 INFO @ Sat, 06 Jul 2019 03:58:36: 6000000 INFO @ Sat, 06 Jul 2019 03:58:39: 7000000 INFO @ Sat, 06 Jul 2019 03:58:40: 8000000 INFO @ Sat, 06 Jul 2019 03:58:46: 7000000 INFO @ Sat, 06 Jul 2019 03:58:47: 8000000 INFO @ Sat, 06 Jul 2019 03:58:52: 9000000 INFO @ Sat, 06 Jul 2019 03:58:56: 8000000 INFO @ Sat, 06 Jul 2019 03:58:56: 9000000 INFO @ Sat, 06 Jul 2019 03:59:03: 10000000 INFO @ Sat, 06 Jul 2019 03:59:05: 10000000 INFO @ Sat, 06 Jul 2019 03:59:05: 9000000 INFO @ Sat, 06 Jul 2019 03:59:14: 11000000 INFO @ Sat, 06 Jul 2019 03:59:14: 10000000 INFO @ Sat, 06 Jul 2019 03:59:14: 11000000 INFO @ Sat, 06 Jul 2019 03:59:24: 11000000 INFO @ Sat, 06 Jul 2019 03:59:24: 12000000 INFO @ Sat, 06 Jul 2019 03:59:24: 12000000 INFO @ Sat, 06 Jul 2019 03:59:26: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:59:26: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:59:26: #1 total tags in treatment: 3375671 INFO @ Sat, 06 Jul 2019 03:59:26: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:59:26: #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 03:59:26: #1 tags after filtering in treatment: 2445357 INFO @ Sat, 06 Jul 2019 03:59:26: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 06 Jul 2019 03:59:26: #1 finished! INFO @ Sat, 06 Jul 2019 03:59:26: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:59:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:59:26: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 03:59:26: 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 03:59:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.05_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/SRX5624298/SRX5624298.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:59:27: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:59:27: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:59:27: #1 total tags in treatment: 3375671 INFO @ Sat, 06 Jul 2019 03:59:27: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:59:27: #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 03:59:27: #1 tags after filtering in treatment: 2445357 INFO @ Sat, 06 Jul 2019 03:59:27: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 06 Jul 2019 03:59:27: #1 finished! INFO @ Sat, 06 Jul 2019 03:59:27: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:59:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:59:27: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 03:59:27: 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 03:59:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:59:34: 12000000 INFO @ Sat, 06 Jul 2019 03:59:36: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:59:36: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:59:36: #1 total tags in treatment: 3375671 INFO @ Sat, 06 Jul 2019 03:59:36: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:59:36: #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 03:59:36: #1 tags after filtering in treatment: 2445357 INFO @ Sat, 06 Jul 2019 03:59:36: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 06 Jul 2019 03:59:36: #1 finished! INFO @ Sat, 06 Jul 2019 03:59:36: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:59:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:59:36: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 03:59:36: 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 03:59:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.20_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/SRX5624298/SRX5624298.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624298/SRX5624298.20_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。