Job ID = 2009741 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 33,301,765 reads read : 66,603,530 reads written : 66,603,530 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: 00:24:26 33301765 reads; of these: 33301765 (100.00%) were paired; of these: 7601566 (22.83%) aligned concordantly 0 times 22466053 (67.46%) aligned concordantly exactly 1 time 3234146 (9.71%) aligned concordantly >1 times ---- 7601566 pairs aligned concordantly 0 times; of these: 1191718 (15.68%) aligned discordantly 1 time ---- 6409848 pairs aligned 0 times concordantly or discordantly; of these: 12819696 mates make up the pairs; of these: 11925705 (93.03%) aligned 0 times 418226 (3.26%) aligned exactly 1 time 475765 (3.71%) aligned >1 times 82.09% overall alignment rate Time searching: 00:24:26 Overall time: 00:24:26 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 24 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] 18020390 / 26517672 = 0.6796 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 21:06:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.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 21:06:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:06:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:06:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.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 21:06:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:06:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:06:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.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 21:06:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:06:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:06:57: 1000000 INFO @ Fri, 05 Jul 2019 21:06:58: 1000000 INFO @ Fri, 05 Jul 2019 21:07:00: 1000000 INFO @ Fri, 05 Jul 2019 21:07:04: 2000000 INFO @ Fri, 05 Jul 2019 21:07:06: 2000000 INFO @ Fri, 05 Jul 2019 21:07:09: 2000000 INFO @ Fri, 05 Jul 2019 21:07:11: 3000000 INFO @ Fri, 05 Jul 2019 21:07:14: 3000000 INFO @ Fri, 05 Jul 2019 21:07:18: 4000000 INFO @ Fri, 05 Jul 2019 21:07:18: 3000000 INFO @ Fri, 05 Jul 2019 21:07:22: 4000000 INFO @ Fri, 05 Jul 2019 21:07:25: 5000000 INFO @ Fri, 05 Jul 2019 21:07:28: 4000000 INFO @ Fri, 05 Jul 2019 21:07:30: 5000000 INFO @ Fri, 05 Jul 2019 21:07:33: 6000000 INFO @ Fri, 05 Jul 2019 21:07:37: 5000000 INFO @ Fri, 05 Jul 2019 21:07:39: 6000000 INFO @ Fri, 05 Jul 2019 21:07:40: 7000000 INFO @ Fri, 05 Jul 2019 21:07:46: 6000000 INFO @ Fri, 05 Jul 2019 21:07:47: 7000000 INFO @ Fri, 05 Jul 2019 21:07:47: 8000000 INFO @ Fri, 05 Jul 2019 21:07:54: 9000000 INFO @ Fri, 05 Jul 2019 21:07:54: 8000000 INFO @ Fri, 05 Jul 2019 21:07:55: 7000000 INFO @ Fri, 05 Jul 2019 21:08:02: 10000000 INFO @ Fri, 05 Jul 2019 21:08:02: 9000000 INFO @ Fri, 05 Jul 2019 21:08:06: 8000000 INFO @ Fri, 05 Jul 2019 21:08:11: 10000000 INFO @ Fri, 05 Jul 2019 21:08:11: 11000000 INFO @ Fri, 05 Jul 2019 21:08:15: 9000000 INFO @ Fri, 05 Jul 2019 21:08:19: 11000000 INFO @ Fri, 05 Jul 2019 21:08:21: 12000000 INFO @ Fri, 05 Jul 2019 21:08:24: 10000000 INFO @ Fri, 05 Jul 2019 21:08:27: 12000000 INFO @ Fri, 05 Jul 2019 21:08:30: 13000000 INFO @ Fri, 05 Jul 2019 21:08:33: 11000000 INFO @ Fri, 05 Jul 2019 21:08:36: 13000000 INFO @ Fri, 05 Jul 2019 21:08:41: 14000000 INFO @ Fri, 05 Jul 2019 21:08:43: 12000000 INFO @ Fri, 05 Jul 2019 21:08:44: 14000000 INFO @ Fri, 05 Jul 2019 21:08:51: 15000000 INFO @ Fri, 05 Jul 2019 21:08:52: 15000000 INFO @ Fri, 05 Jul 2019 21:08:52: 13000000 INFO @ Fri, 05 Jul 2019 21:09:00: 16000000 INFO @ Fri, 05 Jul 2019 21:09:01: 16000000 INFO @ Fri, 05 Jul 2019 21:09:02: 14000000 INFO @ Fri, 05 Jul 2019 21:09:08: 17000000 INFO @ Fri, 05 Jul 2019 21:09:10: 17000000 INFO @ Fri, 05 Jul 2019 21:09:11: 15000000 INFO @ Fri, 05 Jul 2019 21:09:16: 18000000 INFO @ Fri, 05 Jul 2019 21:09:20: 18000000 INFO @ Fri, 05 Jul 2019 21:09:20: 16000000 INFO @ Fri, 05 Jul 2019 21:09:21: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 21:09:21: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 21:09:21: #1 total tags in treatment: 8170615 INFO @ Fri, 05 Jul 2019 21:09:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:09:21: #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 21:09:21: #1 tags after filtering in treatment: 5224894 INFO @ Fri, 05 Jul 2019 21:09:21: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 05 Jul 2019 21:09:21: #1 finished! INFO @ Fri, 05 Jul 2019 21:09:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:09:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:09:22: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:09:22: 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 21:09:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.10_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/SRX1462590/SRX1462590.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:09:26: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 21:09:26: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 21:09:26: #1 total tags in treatment: 8170615 INFO @ Fri, 05 Jul 2019 21:09:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:09:26: #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 21:09:26: #1 tags after filtering in treatment: 5224894 INFO @ Fri, 05 Jul 2019 21:09:26: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 05 Jul 2019 21:09:26: #1 finished! INFO @ Fri, 05 Jul 2019 21:09:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:09:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:09:26: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:09:26: 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 21:09:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.05_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/SRX1462590/SRX1462590.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:09:29: 17000000 INFO @ Fri, 05 Jul 2019 21:09:38: 18000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 21:09:43: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 21:09:43: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 21:09:43: #1 total tags in treatment: 8170615 INFO @ Fri, 05 Jul 2019 21:09:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:09:43: #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 21:09:43: #1 tags after filtering in treatment: 5224894 INFO @ Fri, 05 Jul 2019 21:09:43: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 05 Jul 2019 21:09:43: #1 finished! INFO @ Fri, 05 Jul 2019 21:09:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:09:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:09:44: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:09:44: 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 21:09:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.20_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/SRX1462590/SRX1462590.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462590/SRX1462590.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling