Job ID = 9161940 sra ファイルのダウンロード中... Completed: 246034K bytes transferred in 5 seconds (365301K 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 3685747 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1419791/SRR2927540.sra Written 3685747 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: 00:04:06 3685747 reads; of these: 3685747 (100.00%) were paired; of these: 133112 (3.61%) aligned concordantly 0 times 3149145 (85.44%) aligned concordantly exactly 1 time 403490 (10.95%) aligned concordantly >1 times ---- 133112 pairs aligned concordantly 0 times; of these: 11431 (8.59%) aligned discordantly 1 time ---- 121681 pairs aligned 0 times concordantly or discordantly; of these: 243362 mates make up the pairs; of these: 213148 (87.58%) aligned 0 times 20712 (8.51%) aligned exactly 1 time 9502 (3.90%) aligned >1 times 97.11% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:06 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] 78036 / 3554710 = 0.0220 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 @ Wed, 28 Jun 2017 05:07:54: # Command line: callpeak -t SRX1419791.bam -f BAM -g 12100000 -n SRX1419791.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1419791.10 # format = BAM # ChIP-seq file = ['SRX1419791.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 @ Wed, 28 Jun 2017 05:07:54: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:07:54: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:07:54: # Command line: callpeak -t SRX1419791.bam -f BAM -g 12100000 -n SRX1419791.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1419791.20 # format = BAM # ChIP-seq file = ['SRX1419791.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 @ Wed, 28 Jun 2017 05:07:54: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:07:54: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:07:54: # Command line: callpeak -t SRX1419791.bam -f BAM -g 12100000 -n SRX1419791.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1419791.05 # format = BAM # ChIP-seq file = ['SRX1419791.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 @ Wed, 28 Jun 2017 05:07:54: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:07:54: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:08:00: 1000000 INFO @ Wed, 28 Jun 2017 05:08:01: 1000000 INFO @ Wed, 28 Jun 2017 05:08:01: 1000000 INFO @ Wed, 28 Jun 2017 05:08:07: 2000000 INFO @ Wed, 28 Jun 2017 05:08:08: 2000000 INFO @ Wed, 28 Jun 2017 05:08:08: 2000000 INFO @ Wed, 28 Jun 2017 05:08:14: 3000000 INFO @ Wed, 28 Jun 2017 05:08:15: 3000000 INFO @ Wed, 28 Jun 2017 05:08:16: 3000000 INFO @ Wed, 28 Jun 2017 05:08:22: 4000000 INFO @ Wed, 28 Jun 2017 05:08:24: 4000000 INFO @ Wed, 28 Jun 2017 05:08:25: 4000000 INFO @ Wed, 28 Jun 2017 05:08:30: 5000000 INFO @ Wed, 28 Jun 2017 05:08:32: 5000000 INFO @ Wed, 28 Jun 2017 05:08:33: 5000000 INFO @ Wed, 28 Jun 2017 05:08:38: 6000000 INFO @ Wed, 28 Jun 2017 05:08:40: 6000000 INFO @ Wed, 28 Jun 2017 05:08:41: 6000000 INFO @ Wed, 28 Jun 2017 05:08:46: 7000000 INFO @ Wed, 28 Jun 2017 05:08:46: #1 tag size is determined as 92 bps INFO @ Wed, 28 Jun 2017 05:08:46: #1 tag size = 92 INFO @ Wed, 28 Jun 2017 05:08:46: #1 total tags in treatment: 3474618 INFO @ Wed, 28 Jun 2017 05:08:46: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:08:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:08:47: #1 tags after filtering in treatment: 3069157 INFO @ Wed, 28 Jun 2017 05:08:47: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 28 Jun 2017 05:08:47: #1 finished! INFO @ Wed, 28 Jun 2017 05:08:47: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:08:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:08:47: #2 number of paired peaks: 30 WARNING @ Wed, 28 Jun 2017 05:08:47: Too few paired peaks (30) 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 @ Wed, 28 Jun 2017 05:08:47: Process for pairing-model is terminated! cat: SRX1419791.10_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 `SRX1419791.10_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 `SRX1419791.10_*.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 `SRX1419791.10_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 @ Wed, 28 Jun 2017 05:08:48: 7000000 INFO @ Wed, 28 Jun 2017 05:08:49: #1 tag size is determined as 92 bps INFO @ Wed, 28 Jun 2017 05:08:49: #1 tag size = 92 INFO @ Wed, 28 Jun 2017 05:08:49: #1 total tags in treatment: 3474618 INFO @ Wed, 28 Jun 2017 05:08:49: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:08:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:08:49: #1 tags after filtering in treatment: 3069157 INFO @ Wed, 28 Jun 2017 05:08:49: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 28 Jun 2017 05:08:49: #1 finished! INFO @ Wed, 28 Jun 2017 05:08:49: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:08:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:08:49: #2 number of paired peaks: 30 WARNING @ Wed, 28 Jun 2017 05:08:49: Too few paired peaks (30) 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 @ Wed, 28 Jun 2017 05:08:49: Process for pairing-model is terminated! cat: SRX1419791.05_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 `SRX1419791.05_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 `SRX1419791.05_*.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 `SRX1419791.05_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 @ Wed, 28 Jun 2017 05:08:50: 7000000 INFO @ Wed, 28 Jun 2017 05:08:50: #1 tag size is determined as 92 bps INFO @ Wed, 28 Jun 2017 05:08:50: #1 tag size = 92 INFO @ Wed, 28 Jun 2017 05:08:50: #1 total tags in treatment: 3474618 INFO @ Wed, 28 Jun 2017 05:08:50: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:08:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:08:50: #1 tags after filtering in treatment: 3069157 INFO @ Wed, 28 Jun 2017 05:08:50: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 28 Jun 2017 05:08:50: #1 finished! INFO @ Wed, 28 Jun 2017 05:08:50: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:08:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:08:50: #2 number of paired peaks: 30 WARNING @ Wed, 28 Jun 2017 05:08:50: Too few paired peaks (30) 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 @ Wed, 28 Jun 2017 05:08:50: Process for pairing-model is terminated! cat: SRX1419791.20_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 `SRX1419791.20_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 `SRX1419791.20_*.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 `SRX1419791.20_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。