Job ID = 11632750 sra ファイルのダウンロード中... Completed: 205240K bytes transferred in 5 seconds (335849K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Read 1975648 spots for /home/okishinya/chipatlas/results/sacCer3/DRX123820/DRR131082.sra Written 1975648 spots for /home/okishinya/chipatlas/results/sacCer3/DRX123820/DRR131082.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:02:18 1975648 reads; of these: 1975648 (100.00%) were paired; of these: 291108 (14.73%) aligned concordantly 0 times 1146329 (58.02%) aligned concordantly exactly 1 time 538211 (27.24%) aligned concordantly >1 times ---- 291108 pairs aligned concordantly 0 times; of these: 93345 (32.07%) aligned discordantly 1 time ---- 197763 pairs aligned 0 times concordantly or discordantly; of these: 395526 mates make up the pairs; of these: 278483 (70.41%) aligned 0 times 25546 (6.46%) aligned exactly 1 time 91497 (23.13%) aligned >1 times 92.95% overall alignment rate Time searching: 00:02:18 Overall time: 00:02:18 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] 143758 / 1776070 = 0.0809 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, 15 Feb 2019 07:35:46: # Command line: callpeak -t DRX123820.bam -f BAM -g 12100000 -n DRX123820.05 -q 1e-05 # ARGUMENTS LIST: # name = DRX123820.05 # format = BAM # ChIP-seq file = ['DRX123820.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, 15 Feb 2019 07:35:46: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:35:46: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:35:46: # Command line: callpeak -t DRX123820.bam -f BAM -g 12100000 -n DRX123820.10 -q 1e-10 # ARGUMENTS LIST: # name = DRX123820.10 # format = BAM # ChIP-seq file = ['DRX123820.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, 15 Feb 2019 07:35:46: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:35:46: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:35:46: # Command line: callpeak -t DRX123820.bam -f BAM -g 12100000 -n DRX123820.20 -q 1e-20 # ARGUMENTS LIST: # name = DRX123820.20 # format = BAM # ChIP-seq file = ['DRX123820.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, 15 Feb 2019 07:35:46: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:35:46: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:35:55: 1000000 INFO @ Fri, 15 Feb 2019 07:35:55: 1000000 INFO @ Fri, 15 Feb 2019 07:35:55: 1000000 INFO @ Fri, 15 Feb 2019 07:36:04: 2000000 INFO @ Fri, 15 Feb 2019 07:36:04: 2000000 INFO @ Fri, 15 Feb 2019 07:36:04: 2000000 INFO @ Fri, 15 Feb 2019 07:36:13: 3000000 INFO @ Fri, 15 Feb 2019 07:36:13: 3000000 INFO @ Fri, 15 Feb 2019 07:36:13: 3000000 INFO @ Fri, 15 Feb 2019 07:36:17: #1 tag size is determined as 74 bps INFO @ Fri, 15 Feb 2019 07:36:17: #1 tag size = 74 INFO @ Fri, 15 Feb 2019 07:36:17: #1 total tags in treatment: 1540974 INFO @ Fri, 15 Feb 2019 07:36:17: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:36:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:36:17: #1 tag size is determined as 74 bps INFO @ Fri, 15 Feb 2019 07:36:17: #1 tag size = 74 INFO @ Fri, 15 Feb 2019 07:36:17: #1 total tags in treatment: 1540974 INFO @ Fri, 15 Feb 2019 07:36:17: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:36:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:36:17: #1 tags after filtering in treatment: 1213894 INFO @ Fri, 15 Feb 2019 07:36:17: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 15 Feb 2019 07:36:17: #1 finished! INFO @ Fri, 15 Feb 2019 07:36:17: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:36:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:36:17: #1 tags after filtering in treatment: 1213894 INFO @ Fri, 15 Feb 2019 07:36:17: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 15 Feb 2019 07:36:17: #1 finished! INFO @ Fri, 15 Feb 2019 07:36:17: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:36:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:36:17: #2 number of paired peaks: 35 WARNING @ Fri, 15 Feb 2019 07:36:17: Too few paired peaks (35) 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, 15 Feb 2019 07:36:17: Process for pairing-model is terminated! INFO @ Fri, 15 Feb 2019 07:36:17: #1 tag size is determined as 74 bps INFO @ Fri, 15 Feb 2019 07:36:17: #1 tag size = 74 INFO @ Fri, 15 Feb 2019 07:36:17: #1 total tags in treatment: 1540974 INFO @ Fri, 15 Feb 2019 07:36:17: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:36:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) cat: INFO @ Fri, 15 Feb 2019 07:36:17: #2 number of paired peaks: 35 WARNING @ Fri, 15 Feb 2019 07:36:17: Too few paired peaks (35) 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, 15 Feb 2019 07:36:17: Process for pairing-model is terminated! DRX123820.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: DRX123820.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Fri, 15 Feb 2019 07:36:17: #1 tags after filtering in treatment: 1213894 INFO @ Fri, 15 Feb 2019 07:36:17: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 15 Feb 2019 07:36:17: #1 finished! INFO @ Fri, 15 Feb 2019 07:36:17: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:36:17: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (0 chroms): 14 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 9 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `DRX123820.05_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `DRX123820.05_*.xls': そのようなファイルやディレクトリはありません INFO @ Fri, 15 Feb 2019 07:36:17: #2 number of paired peaks: 35 WARNING @ Fri, 15 Feb 2019 07:36:17: Too few paired peaks (35) 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, 15 Feb 2019 07:36:17: Process for pairing-model is terminated! rm: cannot remove `DRX123820.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `DRX123820.10_model.r': そのようなファイルやディレクトリはありません cat: DRX123820.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません CompletedMACS2peakCalling rm: cannot remove `DRX123820.10_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `DRX123820.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 7 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `DRX123820.20_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `DRX123820.20_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `DRX123820.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。