Job ID = 2011905 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,877,017 reads read : 7,754,034 reads written : 7,754,034 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: 00:02:36 3877017 reads; of these: 3877017 (100.00%) were paired; of these: 355972 (9.18%) aligned concordantly 0 times 3014136 (77.74%) aligned concordantly exactly 1 time 506909 (13.07%) aligned concordantly >1 times ---- 355972 pairs aligned concordantly 0 times; of these: 174457 (49.01%) aligned discordantly 1 time ---- 181515 pairs aligned 0 times concordantly or discordantly; of these: 363030 mates make up the pairs; of these: 242959 (66.93%) aligned 0 times 54432 (14.99%) aligned exactly 1 time 65639 (18.08%) aligned >1 times 96.87% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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_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] 175401 / 3693588 = 0.0475 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 03:14:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.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 03:14:28: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:14:28: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:14:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.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 03:14:29: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:14:29: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:14:36: 1000000 INFO @ Sat, 06 Jul 2019 03:14:37: 1000000 INFO @ Sat, 06 Jul 2019 03:14:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.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 03:14:43: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:14:43: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:14:43: 2000000 INFO @ Sat, 06 Jul 2019 03:14:45: 2000000 INFO @ Sat, 06 Jul 2019 03:14:50: 1000000 INFO @ Sat, 06 Jul 2019 03:14:51: 3000000 INFO @ Sat, 06 Jul 2019 03:14:53: 3000000 INFO @ Sat, 06 Jul 2019 03:14:57: 2000000 INFO @ Sat, 06 Jul 2019 03:14:58: 4000000 INFO @ Sat, 06 Jul 2019 03:15:02: 4000000 INFO @ Sat, 06 Jul 2019 03:15:04: 3000000 INFO @ Sat, 06 Jul 2019 03:15:05: 5000000 INFO @ Sat, 06 Jul 2019 03:15:10: 5000000 INFO @ Sat, 06 Jul 2019 03:15:11: 4000000 INFO @ Sat, 06 Jul 2019 03:15:12: 6000000 INFO @ Sat, 06 Jul 2019 03:15:18: 6000000 INFO @ Sat, 06 Jul 2019 03:15:18: 5000000 INFO @ Sat, 06 Jul 2019 03:15:19: 7000000 INFO @ Sat, 06 Jul 2019 03:15:20: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:15:20: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:15:20: #1 total tags in treatment: 3350946 INFO @ Sat, 06 Jul 2019 03:15:20: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:15:20: #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 03:15:20: #1 tags after filtering in treatment: 2870957 INFO @ Sat, 06 Jul 2019 03:15:20: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 06 Jul 2019 03:15:20: #1 finished! INFO @ Sat, 06 Jul 2019 03:15:20: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:15:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:15:21: #2 number of paired peaks: 33 WARNING @ Sat, 06 Jul 2019 03:15:21: Too few paired peaks (33) 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 03:15:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.10_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/SRX5383678/SRX5383678.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:15:25: 6000000 INFO @ Sat, 06 Jul 2019 03:15:26: 7000000 INFO @ Sat, 06 Jul 2019 03:15:27: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:15:27: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:15:27: #1 total tags in treatment: 3350946 INFO @ Sat, 06 Jul 2019 03:15:27: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:15:27: #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 03:15:28: #1 tags after filtering in treatment: 2870957 INFO @ Sat, 06 Jul 2019 03:15:28: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 06 Jul 2019 03:15:28: #1 finished! INFO @ Sat, 06 Jul 2019 03:15:28: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:15:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:15:28: #2 number of paired peaks: 33 WARNING @ Sat, 06 Jul 2019 03:15:28: Too few paired peaks (33) 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 03:15:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.05_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/SRX5383678/SRX5383678.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:15:32: 7000000 INFO @ Sat, 06 Jul 2019 03:15:33: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:15:33: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:15:33: #1 total tags in treatment: 3350946 INFO @ Sat, 06 Jul 2019 03:15:33: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:15:33: #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 03:15:33: #1 tags after filtering in treatment: 2870957 INFO @ Sat, 06 Jul 2019 03:15:33: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 06 Jul 2019 03:15:33: #1 finished! INFO @ Sat, 06 Jul 2019 03:15:33: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:15:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:15:33: #2 number of paired peaks: 33 WARNING @ Sat, 06 Jul 2019 03:15:33: Too few paired peaks (33) 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 03:15:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.20_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/SRX5383678/SRX5383678.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5383678/SRX5383678.20_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。