Job ID = 2011846 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,829,437 reads read : 23,658,874 reads written : 23,658,874 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 Warning: skipping mate #1 of read 'SRR8313293.2817547 2817547 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313293.2817547 2817547 length=1' because it was < 2 characters long Multiseed full-index search: 00:11:51 11829437 reads; of these: 11829437 (100.00%) were paired; of these: 422078 (3.57%) aligned concordantly 0 times 9446702 (79.86%) aligned concordantly exactly 1 time 1960657 (16.57%) aligned concordantly >1 times ---- 422078 pairs aligned concordantly 0 times; of these: 6990 (1.66%) aligned discordantly 1 time ---- 415088 pairs aligned 0 times concordantly or discordantly; of these: 830176 mates make up the pairs; of these: 684372 (82.44%) aligned 0 times 101411 (12.22%) aligned exactly 1 time 44393 (5.35%) aligned >1 times 97.11% overall alignment rate Time searching: 00:11:51 Overall time: 00:11:51 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 12 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] 9647198 / 11413246 = 0.8453 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 03:17:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.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 03:17:25: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:17:25: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:17:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.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 03:17:26: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:17:26: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:17:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.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 03:17:27: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:17:27: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:17:36: 1000000 INFO @ Sat, 06 Jul 2019 03:17:37: 1000000 INFO @ Sat, 06 Jul 2019 03:17:38: 1000000 INFO @ Sat, 06 Jul 2019 03:17:45: 2000000 INFO @ Sat, 06 Jul 2019 03:17:47: 2000000 INFO @ Sat, 06 Jul 2019 03:17:48: 2000000 INFO @ Sat, 06 Jul 2019 03:17:54: 3000000 INFO @ Sat, 06 Jul 2019 03:17:58: 3000000 INFO @ Sat, 06 Jul 2019 03:17:58: 3000000 INFO @ Sat, 06 Jul 2019 03:17:59: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:17:59: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:17:59: #1 total tags in treatment: 1762524 INFO @ Sat, 06 Jul 2019 03:17:59: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:17:59: #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 03:17:59: #1 tags after filtering in treatment: 1364265 INFO @ Sat, 06 Jul 2019 03:17:59: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 06 Jul 2019 03:17:59: #1 finished! INFO @ Sat, 06 Jul 2019 03:17:59: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:17:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:18:00: #2 number of paired peaks: 60 WARNING @ Sat, 06 Jul 2019 03:18:00: Too few paired peaks (60) 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 03:18:00: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 03:18:05: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:18:05: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:18:05: #1 total tags in treatment: 1762524 INFO @ Sat, 06 Jul 2019 03:18:05: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:18:05: #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 03:18:05: #1 tags after filtering in treatment: 1364265 INFO @ Sat, 06 Jul 2019 03:18:05: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 06 Jul 2019 03:18:05: #1 finished! INFO @ Sat, 06 Jul 2019 03:18:05: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:18:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:18:05: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:18:05: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:18:05: #1 total tags in treatment: 1762524 INFO @ Sat, 06 Jul 2019 03:18:05: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:18:05: #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 03:18:05: #1 tags after filtering in treatment: 1364265 INFO @ Sat, 06 Jul 2019 03:18:05: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 06 Jul 2019 03:18:05: #1 finished! INFO @ Sat, 06 Jul 2019 03:18:05: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:18:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:18:05: #2 number of paired peaks: 60 WARNING @ Sat, 06 Jul 2019 03:18:05: Too few paired peaks (60) 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 03:18:05: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 03:18:05: #2 number of paired peaks: 60 WARNING @ Sat, 06 Jul 2019 03:18:05: Too few paired peaks (60) 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 03:18:05: Process for pairing-model is terminated! BedGraph に変換しました。 cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.05_peaks.narrowPeakcut: : No such file or directory/home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.20_peaks.narrowPeak : No such file or directory BigWig に変換中... pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 2 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/SRX5126601/SRX5126601.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.10_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126601/SRX5126601.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。