Job ID = 9384124 sra ファイルのダウンロード中... Completed: 582454K bytes transferred in 14 seconds (322467K bits/sec), in 1 file, 2 directories. 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... Written 3940707 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2963108/SRR5763439.sra Written 3940707 spots total 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: 00:03:54 3940707 reads; of these: 3940707 (100.00%) were paired; of these: 1645433 (41.75%) aligned concordantly 0 times 1877221 (47.64%) aligned concordantly exactly 1 time 418053 (10.61%) aligned concordantly >1 times ---- 1645433 pairs aligned concordantly 0 times; of these: 90610 (5.51%) aligned discordantly 1 time ---- 1554823 pairs aligned 0 times concordantly or discordantly; of these: 3109646 mates make up the pairs; of these: 2948571 (94.82%) aligned 0 times 110137 (3.54%) aligned exactly 1 time 50938 (1.64%) aligned >1 times 62.59% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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] 138499 / 2381818 = 0.0581 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 @ Sun, 06 Aug 2017 00:48:59: # Command line: callpeak -t SRX2963108.bam -f BAM -g 12100000 -n SRX2963108.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2963108.05 # format = BAM # ChIP-seq file = ['SRX2963108.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 @ Sun, 06 Aug 2017 00:48:59: #1 read tag files... INFO @ Sun, 06 Aug 2017 00:48:59: #1 read treatment tags... INFO @ Sun, 06 Aug 2017 00:48:59: # Command line: callpeak -t SRX2963108.bam -f BAM -g 12100000 -n SRX2963108.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2963108.10 # format = BAM # ChIP-seq file = ['SRX2963108.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 @ Sun, 06 Aug 2017 00:48:59: #1 read tag files... INFO @ Sun, 06 Aug 2017 00:48:59: #1 read treatment tags... INFO @ Sun, 06 Aug 2017 00:48:59: # Command line: callpeak -t SRX2963108.bam -f BAM -g 12100000 -n SRX2963108.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2963108.20 # format = BAM # ChIP-seq file = ['SRX2963108.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 @ Sun, 06 Aug 2017 00:48:59: #1 read tag files... INFO @ Sun, 06 Aug 2017 00:48:59: #1 read treatment tags... INFO @ Sun, 06 Aug 2017 00:49:10: 1000000 INFO @ Sun, 06 Aug 2017 00:49:10: 1000000 INFO @ Sun, 06 Aug 2017 00:49:11: 1000000 INFO @ Sun, 06 Aug 2017 00:49:20: 2000000 INFO @ Sun, 06 Aug 2017 00:49:20: 2000000 INFO @ Sun, 06 Aug 2017 00:49:23: 2000000 INFO @ Sun, 06 Aug 2017 00:49:30: 3000000 INFO @ Sun, 06 Aug 2017 00:49:30: 3000000 INFO @ Sun, 06 Aug 2017 00:49:35: 3000000 INFO @ Sun, 06 Aug 2017 00:49:40: 4000000 INFO @ Sun, 06 Aug 2017 00:49:42: 4000000 INFO @ Sun, 06 Aug 2017 00:49:45: 4000000 INFO @ Sun, 06 Aug 2017 00:49:46: #1 tag size is determined as 101 bps INFO @ Sun, 06 Aug 2017 00:49:46: #1 tag size = 101 INFO @ Sun, 06 Aug 2017 00:49:46: #1 total tags in treatment: 2159379 INFO @ Sun, 06 Aug 2017 00:49:46: #1 user defined the maximum tags... INFO @ Sun, 06 Aug 2017 00:49:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 06 Aug 2017 00:49:46: #1 tags after filtering in treatment: 1797347 INFO @ Sun, 06 Aug 2017 00:49:46: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 06 Aug 2017 00:49:46: #1 finished! INFO @ Sun, 06 Aug 2017 00:49:46: #2 Build Peak Model... INFO @ Sun, 06 Aug 2017 00:49:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 06 Aug 2017 00:49:46: #2 number of paired peaks: 33 WARNING @ Sun, 06 Aug 2017 00:49:46: Too few paired peaks (33) 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 @ Sun, 06 Aug 2017 00:49:46: Process for pairing-model is terminated! cat: SRX2963108.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2963108.05_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 `SRX2963108.05_*.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 `SRX2963108.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Sun, 06 Aug 2017 00:49:49: #1 tag size is determined as 101 bps INFO @ Sun, 06 Aug 2017 00:49:49: #1 tag size = 101 INFO @ Sun, 06 Aug 2017 00:49:49: #1 total tags in treatment: 2159379 INFO @ Sun, 06 Aug 2017 00:49:49: #1 user defined the maximum tags... INFO @ Sun, 06 Aug 2017 00:49:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 06 Aug 2017 00:49:49: #1 tags after filtering in treatment: 1797347 INFO @ Sun, 06 Aug 2017 00:49:49: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 06 Aug 2017 00:49:49: #1 finished! INFO @ Sun, 06 Aug 2017 00:49:49: #2 Build Peak Model... INFO @ Sun, 06 Aug 2017 00:49:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 06 Aug 2017 00:49:49: #2 number of paired peaks: 33 WARNING @ Sun, 06 Aug 2017 00:49:49: Too few paired peaks (33) 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 @ Sun, 06 Aug 2017 00:49:49: Process for pairing-model is terminated! cat: SRX2963108.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2963108.20_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 `SRX2963108.20_*.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 `SRX2963108.20_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 INFO @ Sun, 06 Aug 2017 00:49:52: #1 tag size is determined as 101 bps INFO @ Sun, 06 Aug 2017 00:49:52: #1 tag size = 101 INFO @ Sun, 06 Aug 2017 00:49:52: #1 total tags in treatment: 2159379 INFO @ Sun, 06 Aug 2017 00:49:52: #1 user defined the maximum tags... INFO @ Sun, 06 Aug 2017 00:49:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 06 Aug 2017 00:49:52: #1 tags after filtering in treatment: 1797347 INFO @ Sun, 06 Aug 2017 00:49:52: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 06 Aug 2017 00:49:52: #1 finished! INFO @ Sun, 06 Aug 2017 00:49:52: #2 Build Peak Model... INFO @ Sun, 06 Aug 2017 00:49:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 06 Aug 2017 00:49:52: #2 number of paired peaks: 33 WARNING @ Sun, 06 Aug 2017 00:49:52: Too few paired peaks (33) 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 @ Sun, 06 Aug 2017 00:49:52: Process for pairing-model is terminated! cat: SRX2963108.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2963108.10_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX2963108.10_*.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 `SRX2963108.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。