Job ID = 10937507 sra ファイルのダウンロード中... Completed: 389119K bytes transferred in 29 seconds (107172K 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 4110297 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010313/SRR5833306.sra Written 4110297 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010313/SRR5833306.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: 00:05:12 4110297 reads; of these: 4110297 (100.00%) were paired; of these: 292329 (7.11%) aligned concordantly 0 times 3049627 (74.19%) aligned concordantly exactly 1 time 768341 (18.69%) aligned concordantly >1 times ---- 292329 pairs aligned concordantly 0 times; of these: 33109 (11.33%) aligned discordantly 1 time ---- 259220 pairs aligned 0 times concordantly or discordantly; of these: 518440 mates make up the pairs; of these: 452132 (87.21%) aligned 0 times 38495 (7.43%) aligned exactly 1 time 27813 (5.36%) aligned >1 times 94.50% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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] 102725 / 3837782 = 0.0268 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 02:32:59: # Command line: callpeak -t SRX3010313.bam -f BAM -g 12100000 -n SRX3010313.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3010313.10 # format = BAM # ChIP-seq file = ['SRX3010313.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 02:32:59: # Command line: callpeak -t SRX3010313.bam -f BAM -g 12100000 -n SRX3010313.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3010313.05 # format = BAM # ChIP-seq file = ['SRX3010313.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 02:32:59: # Command line: callpeak -t SRX3010313.bam -f BAM -g 12100000 -n SRX3010313.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3010313.20 # format = BAM # ChIP-seq file = ['SRX3010313.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 02:32:59: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:32:59: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:32:59: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:32:59: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:32:59: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:32:59: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:33:07: 1000000 INFO @ Fri, 10 Aug 2018 02:33:08: 1000000 INFO @ Fri, 10 Aug 2018 02:33:08: 1000000 INFO @ Fri, 10 Aug 2018 02:33:14: 2000000 INFO @ Fri, 10 Aug 2018 02:33:16: 2000000 INFO @ Fri, 10 Aug 2018 02:33:16: 2000000 INFO @ Fri, 10 Aug 2018 02:33:21: 3000000 INFO @ Fri, 10 Aug 2018 02:33:24: 3000000 INFO @ Fri, 10 Aug 2018 02:33:24: 3000000 INFO @ Fri, 10 Aug 2018 02:33:29: 4000000 INFO @ Fri, 10 Aug 2018 02:33:32: 4000000 INFO @ Fri, 10 Aug 2018 02:33:32: 4000000 INFO @ Fri, 10 Aug 2018 02:33:36: 5000000 INFO @ Fri, 10 Aug 2018 02:33:40: 5000000 INFO @ Fri, 10 Aug 2018 02:33:40: 5000000 INFO @ Fri, 10 Aug 2018 02:33:44: 6000000 INFO @ Fri, 10 Aug 2018 02:33:48: 6000000 INFO @ Fri, 10 Aug 2018 02:33:48: 6000000 INFO @ Fri, 10 Aug 2018 02:33:51: 7000000 INFO @ Fri, 10 Aug 2018 02:33:55: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:33:55: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:33:55: #1 total tags in treatment: 3715339 INFO @ Fri, 10 Aug 2018 02:33:55: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:33:55: #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 02:33:55: #1 tags after filtering in treatment: 2994675 INFO @ Fri, 10 Aug 2018 02:33:55: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Aug 2018 02:33:55: #1 finished! INFO @ Fri, 10 Aug 2018 02:33:55: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:33:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:33:55: #2 number of paired peaks: 42 WARNING @ Fri, 10 Aug 2018 02:33:55: Too few paired peaks (42) 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 02:33:55: Process for pairing-model is terminated! cat: SRX3010313.10_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 `SRX3010313.10_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 `SRX3010313.10_*.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 `SRX3010313.10_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 02:33:57: 7000000 INFO @ Fri, 10 Aug 2018 02:33:57: 7000000 INFO @ Fri, 10 Aug 2018 02:34:01: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:34:01: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:34:01: #1 total tags in treatment: 3715339 INFO @ Fri, 10 Aug 2018 02:34:01: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:34:01: #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 02:34:01: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:34:01: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:34:01: #1 total tags in treatment: 3715339 INFO @ Fri, 10 Aug 2018 02:34:01: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:34:01: #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 02:34:01: #1 tags after filtering in treatment: 2994675 INFO @ Fri, 10 Aug 2018 02:34:01: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Aug 2018 02:34:01: #1 finished! INFO @ Fri, 10 Aug 2018 02:34:01: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:34:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:34:01: #1 tags after filtering in treatment: 2994675 INFO @ Fri, 10 Aug 2018 02:34:01: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Aug 2018 02:34:01: #1 finished! INFO @ Fri, 10 Aug 2018 02:34:01: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:34:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:34:01: #2 number of paired peaks: 42 WARNING @ Fri, 10 Aug 2018 02:34:01: Too few paired peaks (42) 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 02:34:01: Process for pairing-model is terminated! INFO @ Fri, 10 Aug 2018 02:34:01: #2 number of paired peaks: 42 WARNING @ Fri, 10 Aug 2018 02:34:01: Too few paired peaks (42) 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 02:34:01: Process for pairing-model is terminated! cat: SRX3010313.20_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: SRX3010313.05_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) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184)rm: cannot remove `SRX3010313.20_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 `SRX3010313.20_*.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 `SRX3010313.20_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 `SRX3010313.05_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 `SRX3010313.05_*.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 `SRX3010313.05_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。