Job ID = 2009920 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,354,046 reads read : 10,708,092 reads written : 10,708,092 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: 00:04:13 5354046 reads; of these: 5354046 (100.00%) were paired; of these: 595712 (11.13%) aligned concordantly 0 times 3831271 (71.56%) aligned concordantly exactly 1 time 927063 (17.32%) aligned concordantly >1 times ---- 595712 pairs aligned concordantly 0 times; of these: 63544 (10.67%) aligned discordantly 1 time ---- 532168 pairs aligned 0 times concordantly or discordantly; of these: 1064336 mates make up the pairs; of these: 809507 (76.06%) aligned 0 times 177630 (16.69%) aligned exactly 1 time 77199 (7.25%) aligned >1 times 92.44% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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] 149181 / 4806158 = 0.0310 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 20:55:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.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 20:55:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:55:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:55:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.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 20:55:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:55:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:56:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.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 20:56:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:56:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:56:06: 1000000 INFO @ Fri, 05 Jul 2019 20:56:07: 1000000 INFO @ Fri, 05 Jul 2019 20:56:09: 1000000 INFO @ Fri, 05 Jul 2019 20:56:13: 2000000 INFO @ Fri, 05 Jul 2019 20:56:16: 2000000 INFO @ Fri, 05 Jul 2019 20:56:17: 2000000 INFO @ Fri, 05 Jul 2019 20:56:19: 3000000 INFO @ Fri, 05 Jul 2019 20:56:25: 3000000 INFO @ Fri, 05 Jul 2019 20:56:26: 3000000 INFO @ Fri, 05 Jul 2019 20:56:26: 4000000 INFO @ Fri, 05 Jul 2019 20:56:33: 5000000 INFO @ Fri, 05 Jul 2019 20:56:34: 4000000 INFO @ Fri, 05 Jul 2019 20:56:34: 4000000 INFO @ Fri, 05 Jul 2019 20:56:40: 6000000 INFO @ Fri, 05 Jul 2019 20:56:43: 5000000 INFO @ Fri, 05 Jul 2019 20:56:44: 5000000 INFO @ Fri, 05 Jul 2019 20:56:46: 7000000 INFO @ Fri, 05 Jul 2019 20:56:52: 6000000 INFO @ Fri, 05 Jul 2019 20:56:53: 6000000 INFO @ Fri, 05 Jul 2019 20:56:53: 8000000 INFO @ Fri, 05 Jul 2019 20:57:00: 9000000 INFO @ Fri, 05 Jul 2019 20:57:01: 7000000 INFO @ Fri, 05 Jul 2019 20:57:02: 7000000 INFO @ Fri, 05 Jul 2019 20:57:04: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:57:04: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:57:04: #1 total tags in treatment: 4609477 INFO @ Fri, 05 Jul 2019 20:57:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:57:04: #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 20:57:04: #1 tags after filtering in treatment: 3229258 INFO @ Fri, 05 Jul 2019 20:57:04: #1 Redundant rate of treatment: 0.30 INFO @ Fri, 05 Jul 2019 20:57:04: #1 finished! INFO @ Fri, 05 Jul 2019 20:57:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:57:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:57:04: #2 number of paired peaks: 80 WARNING @ Fri, 05 Jul 2019 20:57:04: Too few paired peaks (80) 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 20:57:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.10_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/SRX2339855/SRX2339855.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:57:09: 8000000 INFO @ Fri, 05 Jul 2019 20:57:10: 8000000 INFO @ Fri, 05 Jul 2019 20:57:18: 9000000 INFO @ Fri, 05 Jul 2019 20:57:19: 9000000 INFO @ Fri, 05 Jul 2019 20:57:23: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:57:23: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:57:23: #1 total tags in treatment: 4609477 INFO @ Fri, 05 Jul 2019 20:57:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:57:23: #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 20:57:23: #1 tags after filtering in treatment: 3229258 INFO @ Fri, 05 Jul 2019 20:57:23: #1 Redundant rate of treatment: 0.30 INFO @ Fri, 05 Jul 2019 20:57:23: #1 finished! INFO @ Fri, 05 Jul 2019 20:57:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:57:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:57:23: #2 number of paired peaks: 80 WARNING @ Fri, 05 Jul 2019 20:57:23: Too few paired peaks (80) 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 20:57:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.20_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/SRX2339855/SRX2339855.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:57:24: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:57:24: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:57:24: #1 total tags in treatment: 4609477 INFO @ Fri, 05 Jul 2019 20:57:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:57:24: #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 20:57:24: #1 tags after filtering in treatment: 3229258 INFO @ Fri, 05 Jul 2019 20:57:24: #1 Redundant rate of treatment: 0.30 INFO @ Fri, 05 Jul 2019 20:57:24: #1 finished! INFO @ Fri, 05 Jul 2019 20:57:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:57:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:57:24: #2 number of paired peaks: 80 WARNING @ Fri, 05 Jul 2019 20:57:24: Too few paired peaks (80) 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 20:57:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.05_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/SRX2339855/SRX2339855.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339855/SRX2339855.05_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。