Job ID = 10609007 sra ファイルのダウンロード中... Completed: 153045K bytes transferred in 17 seconds (73637K 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... Written 1794447 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3063095/SRR5901525.sra Written 1794447 spots total 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: 00:02:10 1794447 reads; of these: 1794447 (100.00%) were paired; of these: 68469 (3.82%) aligned concordantly 0 times 1498824 (83.53%) aligned concordantly exactly 1 time 227154 (12.66%) aligned concordantly >1 times ---- 68469 pairs aligned concordantly 0 times; of these: 21757 (31.78%) aligned discordantly 1 time ---- 46712 pairs aligned 0 times concordantly or discordantly; of these: 93424 mates make up the pairs; of these: 65304 (69.90%) aligned 0 times 17088 (18.29%) aligned exactly 1 time 11032 (11.81%) aligned >1 times 98.18% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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] 8572 / 1745076 = 0.0049 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 @ Thu, 03 May 2018 23:05:38: # Command line: callpeak -t SRX3063095.bam -f BAM -g 12100000 -n SRX3063095.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3063095.20 # format = BAM # ChIP-seq file = ['SRX3063095.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 @ Thu, 03 May 2018 23:05:38: # Command line: callpeak -t SRX3063095.bam -f BAM -g 12100000 -n SRX3063095.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3063095.05 # format = BAM # ChIP-seq file = ['SRX3063095.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 @ Thu, 03 May 2018 23:05:38: #1 read tag files... INFO @ Thu, 03 May 2018 23:05:38: #1 read tag files... INFO @ Thu, 03 May 2018 23:05:38: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:05:38: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:05:38: # Command line: callpeak -t SRX3063095.bam -f BAM -g 12100000 -n SRX3063095.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3063095.10 # format = BAM # ChIP-seq file = ['SRX3063095.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 @ Thu, 03 May 2018 23:05:38: #1 read tag files... INFO @ Thu, 03 May 2018 23:05:38: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:05:47: 1000000 INFO @ Thu, 03 May 2018 23:05:47: 1000000 INFO @ Thu, 03 May 2018 23:05:47: 1000000 INFO @ Thu, 03 May 2018 23:05:56: 2000000 INFO @ Thu, 03 May 2018 23:05:56: 2000000 INFO @ Thu, 03 May 2018 23:05:57: 2000000 INFO @ Thu, 03 May 2018 23:06:05: 3000000 INFO @ Thu, 03 May 2018 23:06:05: 3000000 INFO @ Thu, 03 May 2018 23:06:07: 3000000 INFO @ Thu, 03 May 2018 23:06:09: #1 tag size is determined as 79 bps INFO @ Thu, 03 May 2018 23:06:09: #1 tag size = 79 INFO @ Thu, 03 May 2018 23:06:09: #1 total tags in treatment: 1717437 INFO @ Thu, 03 May 2018 23:06:09: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:06:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:06:09: #1 tags after filtering in treatment: 1557651 INFO @ Thu, 03 May 2018 23:06:09: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 03 May 2018 23:06:09: #1 finished! INFO @ Thu, 03 May 2018 23:06:09: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:06:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:06:10: #1 tag size is determined as 79 bps INFO @ Thu, 03 May 2018 23:06:10: #1 tag size = 79 INFO @ Thu, 03 May 2018 23:06:10: #1 total tags in treatment: 1717437 INFO @ Thu, 03 May 2018 23:06:10: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:06:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:06:10: #1 tags after filtering in treatment: 1557651 INFO @ Thu, 03 May 2018 23:06:10: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 03 May 2018 23:06:10: #1 finished! INFO @ Thu, 03 May 2018 23:06:10: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:06:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:06:10: #2 number of paired peaks: 86 WARNING @ Thu, 03 May 2018 23:06:10: Too few paired peaks (86) 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 @ Thu, 03 May 2018 23:06:10: Process for pairing-model is terminated! cat: SRX3063095.05_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 `SRX3063095.05_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 `SRX3063095.05_*.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 `SRX3063095.05_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 @ Thu, 03 May 2018 23:06:10: #2 number of paired peaks: 86 WARNING @ Thu, 03 May 2018 23:06:10: Too few paired peaks (86) 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 @ Thu, 03 May 2018 23:06:10: Process for pairing-model is terminated! cat: SRX3063095.20_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3063095.20_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 `SRX3063095.20_*.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 `SRX3063095.20_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 @ Thu, 03 May 2018 23:06:11: #1 tag size is determined as 79 bps INFO @ Thu, 03 May 2018 23:06:11: #1 tag size = 79 INFO @ Thu, 03 May 2018 23:06:11: #1 total tags in treatment: 1717437 INFO @ Thu, 03 May 2018 23:06:11: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:06:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:06:11: #1 tags after filtering in treatment: 1557651 INFO @ Thu, 03 May 2018 23:06:11: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 03 May 2018 23:06:11: #1 finished! INFO @ Thu, 03 May 2018 23:06:11: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:06:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:06:12: #2 number of paired peaks: 86 WARNING @ Thu, 03 May 2018 23:06:12: Too few paired peaks (86) 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 @ Thu, 03 May 2018 23:06:12: Process for pairing-model is terminated! cat: SRX3063095.10_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 `SRX3063095.10_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 `SRX3063095.10_*.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 `SRX3063095.10_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。