Job ID = 2008228 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 9,548,559 reads read : 19,097,118 reads written : 19,097,118 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: 00:11:59 9548559 reads; of these: 9548559 (100.00%) were paired; of these: 869031 (9.10%) aligned concordantly 0 times 7442870 (77.95%) aligned concordantly exactly 1 time 1236658 (12.95%) aligned concordantly >1 times ---- 869031 pairs aligned concordantly 0 times; of these: 468424 (53.90%) aligned discordantly 1 time ---- 400607 pairs aligned 0 times concordantly or discordantly; of these: 801214 mates make up the pairs; of these: 530100 (66.16%) aligned 0 times 121648 (15.18%) aligned exactly 1 time 149466 (18.65%) aligned >1 times 97.22% overall alignment rate Time searching: 00:11:59 Overall time: 00:11:59 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] 1337258 / 9085260 = 0.1472 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 18:32:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.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 18:32:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:32:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:32:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.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 18:32:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:32:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:32:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.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 18:32:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:32:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:32:53: 1000000 INFO @ Fri, 05 Jul 2019 18:32:53: 1000000 INFO @ Fri, 05 Jul 2019 18:32:55: 1000000 INFO @ Fri, 05 Jul 2019 18:33:04: 2000000 INFO @ Fri, 05 Jul 2019 18:33:04: 2000000 INFO @ Fri, 05 Jul 2019 18:33:05: 2000000 INFO @ Fri, 05 Jul 2019 18:33:14: 3000000 INFO @ Fri, 05 Jul 2019 18:33:14: 3000000 INFO @ Fri, 05 Jul 2019 18:33:15: 3000000 INFO @ Fri, 05 Jul 2019 18:33:23: 4000000 INFO @ Fri, 05 Jul 2019 18:33:25: 4000000 INFO @ Fri, 05 Jul 2019 18:33:25: 4000000 INFO @ Fri, 05 Jul 2019 18:33:33: 5000000 INFO @ Fri, 05 Jul 2019 18:33:36: 5000000 INFO @ Fri, 05 Jul 2019 18:33:36: 5000000 INFO @ Fri, 05 Jul 2019 18:33:43: 6000000 INFO @ Fri, 05 Jul 2019 18:33:46: 6000000 INFO @ Fri, 05 Jul 2019 18:33:46: 6000000 INFO @ Fri, 05 Jul 2019 18:33:53: 7000000 INFO @ Fri, 05 Jul 2019 18:33:56: 7000000 INFO @ Fri, 05 Jul 2019 18:33:56: 7000000 INFO @ Fri, 05 Jul 2019 18:34:02: 8000000 INFO @ Fri, 05 Jul 2019 18:34:06: 8000000 INFO @ Fri, 05 Jul 2019 18:34:06: 8000000 INFO @ Fri, 05 Jul 2019 18:34:12: 9000000 INFO @ Fri, 05 Jul 2019 18:34:16: 9000000 INFO @ Fri, 05 Jul 2019 18:34:17: 9000000 INFO @ Fri, 05 Jul 2019 18:34:22: 10000000 INFO @ Fri, 05 Jul 2019 18:34:27: 10000000 INFO @ Fri, 05 Jul 2019 18:34:28: 10000000 INFO @ Fri, 05 Jul 2019 18:34:31: 11000000 INFO @ Fri, 05 Jul 2019 18:34:38: 11000000 INFO @ Fri, 05 Jul 2019 18:34:39: 11000000 INFO @ Fri, 05 Jul 2019 18:34:41: 12000000 INFO @ Fri, 05 Jul 2019 18:34:49: 12000000 INFO @ Fri, 05 Jul 2019 18:34:49: 12000000 INFO @ Fri, 05 Jul 2019 18:34:51: 13000000 INFO @ Fri, 05 Jul 2019 18:35:00: 13000000 INFO @ Fri, 05 Jul 2019 18:35:00: 13000000 INFO @ Fri, 05 Jul 2019 18:35:00: 14000000 INFO @ Fri, 05 Jul 2019 18:35:10: 15000000 INFO @ Fri, 05 Jul 2019 18:35:10: 14000000 INFO @ Fri, 05 Jul 2019 18:35:10: 14000000 INFO @ Fri, 05 Jul 2019 18:35:18: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:35:18: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:35:18: #1 total tags in treatment: 7362250 INFO @ Fri, 05 Jul 2019 18:35:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:35:18: #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 18:35:19: #1 tags after filtering in treatment: 4237582 INFO @ Fri, 05 Jul 2019 18:35:19: #1 Redundant rate of treatment: 0.42 INFO @ Fri, 05 Jul 2019 18:35:19: #1 finished! INFO @ Fri, 05 Jul 2019 18:35:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:35:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:35:19: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:35:19: Too few paired peaks (0) 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 18:35:19: Process for pairing-model is terminated! BedGraph に変換しました。 INFO @ Fri, 05 Jul 2019 18:35:20: 15000000 INFO @ Fri, 05 Jul 2019 18:35:20: 15000000 cut: /home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.10_peaks.narrowPeak: No such file or directory BigWig に変換中... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:35:30: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:35:30: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:35:30: #1 total tags in treatment: 7362250 INFO @ Fri, 05 Jul 2019 18:35:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:35:30: #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 18:35:30: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:35:30: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:35:30: #1 total tags in treatment: 7362250 INFO @ Fri, 05 Jul 2019 18:35:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:35:30: #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 18:35:30: #1 tags after filtering in treatment: 4237582 INFO @ Fri, 05 Jul 2019 18:35:30: #1 Redundant rate of treatment: 0.42 INFO @ Fri, 05 Jul 2019 18:35:30: #1 finished! INFO @ Fri, 05 Jul 2019 18:35:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:35:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:35:30: #1 tags after filtering in treatment: 4237582 INFO @ Fri, 05 Jul 2019 18:35:30: #1 Redundant rate of treatment: 0.42 INFO @ Fri, 05 Jul 2019 18:35:30: #1 finished! INFO @ Fri, 05 Jul 2019 18:35:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:35:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:35:30: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:35:30: Too few paired peaks (0) 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 18:35:30: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 18:35:30: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:35:30: Too few paired peaks (0) 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 18:35:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.05_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585752/ERX585752.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。