Job ID = 10937563 sra ファイルのダウンロード中... Completed: 515125K bytes transferred in 16 seconds (254315K bits/sec), in 1 file. Completed: 579563K bytes transferred in 41 seconds (113440K 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 5255577 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010341/SRR5833341.sra Written 5255577 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010341/SRR5833341.sra Read 6270549 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010341/SRR5833342.sra Written 6270549 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010341/SRR5833342.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 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: 00:03:13 11526126 reads; of these: 11526126 (100.00%) were paired; of these: 10319577 (89.53%) aligned concordantly 0 times 804673 (6.98%) aligned concordantly exactly 1 time 401876 (3.49%) aligned concordantly >1 times ---- 10319577 pairs aligned concordantly 0 times; of these: 8494 (0.08%) aligned discordantly 1 time ---- 10311083 pairs aligned 0 times concordantly or discordantly; of these: 20622166 mates make up the pairs; of these: 20599699 (99.89%) aligned 0 times 11121 (0.05%) aligned exactly 1 time 11346 (0.06%) aligned >1 times 10.64% overall alignment rate Time searching: 00:03:13 Overall time: 00:03:13 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_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] 189954 / 1214569 = 0.1564 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, 10 Aug 2018 02:39:35: # Command line: callpeak -t SRX3010341.bam -f BAM -g 12100000 -n SRX3010341.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3010341.20 # format = BAM # ChIP-seq file = ['SRX3010341.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, 10 Aug 2018 02:39:35: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:39:35: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:39:35: # Command line: callpeak -t SRX3010341.bam -f BAM -g 12100000 -n SRX3010341.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3010341.10 # format = BAM # ChIP-seq file = ['SRX3010341.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, 10 Aug 2018 02:39:35: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:39:35: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:39:35: # Command line: callpeak -t SRX3010341.bam -f BAM -g 12100000 -n SRX3010341.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3010341.05 # format = BAM # ChIP-seq file = ['SRX3010341.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, 10 Aug 2018 02:39:35: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:39:35: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:39:44: 1000000 INFO @ Fri, 10 Aug 2018 02:39:47: 1000000 INFO @ Fri, 10 Aug 2018 02:39:47: 1000000 INFO @ Fri, 10 Aug 2018 02:39:53: 2000000 INFO @ Fri, 10 Aug 2018 02:39:54: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:39:54: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:39:54: #1 total tags in treatment: 1017320 INFO @ Fri, 10 Aug 2018 02:39:54: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:39:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:39:54: #1 tags after filtering in treatment: 700539 INFO @ Fri, 10 Aug 2018 02:39:54: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 10 Aug 2018 02:39:54: #1 finished! INFO @ Fri, 10 Aug 2018 02:39:54: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:39:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:39:54: #2 number of paired peaks: 91 WARNING @ Fri, 10 Aug 2018 02:39:54: Too few paired peaks (91) 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, 10 Aug 2018 02:39:54: Process for pairing-model is terminated! cat: SRX3010341.10_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3010341.10_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 `SRX3010341.10_*.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 `SRX3010341.10_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 INFO @ Fri, 10 Aug 2018 02:39:58: 2000000 INFO @ Fri, 10 Aug 2018 02:39:58: 2000000 INFO @ Fri, 10 Aug 2018 02:39:58: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:39:58: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:39:58: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:39:58: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:39:58: #1 total tags in treatment: 1017320 INFO @ Fri, 10 Aug 2018 02:39:58: #1 total tags in treatment: 1017320 INFO @ Fri, 10 Aug 2018 02:39:58: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:39:58: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:39:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:39:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:39:59: #1 tags after filtering in treatment: 700539 INFO @ Fri, 10 Aug 2018 02:39:59: #1 tags after filtering in treatment: 700539 INFO @ Fri, 10 Aug 2018 02:39:59: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 10 Aug 2018 02:39:59: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 10 Aug 2018 02:39:59: #1 finished! INFO @ Fri, 10 Aug 2018 02:39:59: #1 finished! INFO @ Fri, 10 Aug 2018 02:39:59: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:39:59: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:39:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:39:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:39:59: #2 number of paired peaks: 91 WARNING @ Fri, 10 Aug 2018 02:39:59: Too few paired peaks (91) 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, 10 Aug 2018 02:39:59: Process for pairing-model is terminated! INFO @ Fri, 10 Aug 2018 02:39:59: #2 number of paired peaks: 91 WARNING @ Fri, 10 Aug 2018 02:39:59: Too few paired peaks (91) 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, 10 Aug 2018 02:39:59: Process for pairing-model is terminated! cat: SRX3010341.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX3010341.05_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 `SRX3010341.20_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 `SRX3010341.20_*.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 `SRX3010341.20_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 pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3010341.05_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 `SRX3010341.05_*.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 `SRX3010341.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。