Job ID = 9161681 sra ファイルのダウンロード中... Completed: 1706862K bytes transferred in 17 seconds (799768K bits/sec), in 2 files, 3 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 16734706 spots for /home/okishinya/chipatlas/results/sacCer3/SRX065610/SRR217314.sra Written 16734706 spots total Written 16969503 spots for /home/okishinya/chipatlas/results/sacCer3/SRX065610/SRR217313.sra Written 16969503 spots total 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: 00:17:08 33704209 reads; of these: 33704209 (100.00%) were paired; of these: 9550431 (28.34%) aligned concordantly 0 times 4447514 (13.20%) aligned concordantly exactly 1 time 19706264 (58.47%) aligned concordantly >1 times ---- 9550431 pairs aligned concordantly 0 times; of these: 5877 (0.06%) aligned discordantly 1 time ---- 9544554 pairs aligned 0 times concordantly or discordantly; of these: 19089108 mates make up the pairs; of these: 18509744 (96.96%) aligned 0 times 457849 (2.40%) aligned exactly 1 time 121515 (0.64%) aligned >1 times 72.54% overall alignment rate Time searching: 00:17:08 Overall time: 00:17:08 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_sort_core] merging from 16 files... [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] 20776639 / 24153546 = 0.8602 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 04:44:41: # Command line: callpeak -t SRX065610.bam -f BAM -g 12100000 -n SRX065610.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX065610.10 # format = BAM # ChIP-seq file = ['SRX065610.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 04:44:41: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:44:41: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:44:41: # Command line: callpeak -t SRX065610.bam -f BAM -g 12100000 -n SRX065610.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX065610.20 # format = BAM # ChIP-seq file = ['SRX065610.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 04:44:41: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:44:41: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:44:41: # Command line: callpeak -t SRX065610.bam -f BAM -g 12100000 -n SRX065610.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX065610.05 # format = BAM # ChIP-seq file = ['SRX065610.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 04:44:41: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:44:41: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:44:48: 1000000 INFO @ Wed, 28 Jun 2017 04:44:49: 1000000 INFO @ Wed, 28 Jun 2017 04:44:49: 1000000 INFO @ Wed, 28 Jun 2017 04:44:54: 2000000 INFO @ Wed, 28 Jun 2017 04:44:56: 2000000 INFO @ Wed, 28 Jun 2017 04:44:56: 2000000 INFO @ Wed, 28 Jun 2017 04:45:01: 3000000 INFO @ Wed, 28 Jun 2017 04:45:04: 3000000 INFO @ Wed, 28 Jun 2017 04:45:04: 3000000 INFO @ Wed, 28 Jun 2017 04:45:08: 4000000 INFO @ Wed, 28 Jun 2017 04:45:11: 4000000 INFO @ Wed, 28 Jun 2017 04:45:11: 4000000 INFO @ Wed, 28 Jun 2017 04:45:14: 5000000 INFO @ Wed, 28 Jun 2017 04:45:19: 5000000 INFO @ Wed, 28 Jun 2017 04:45:19: 5000000 INFO @ Wed, 28 Jun 2017 04:45:20: 6000000 INFO @ Wed, 28 Jun 2017 04:45:27: 6000000 INFO @ Wed, 28 Jun 2017 04:45:27: 6000000 INFO @ Wed, 28 Jun 2017 04:45:27: 7000000 INFO @ Wed, 28 Jun 2017 04:45:29: #1 tag size is determined as 36 bps INFO @ Wed, 28 Jun 2017 04:45:29: #1 tag size = 36 INFO @ Wed, 28 Jun 2017 04:45:29: #1 total tags in treatment: 3381677 INFO @ Wed, 28 Jun 2017 04:45:29: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:45:29: #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 04:45:29: #1 tags after filtering in treatment: 1529200 INFO @ Wed, 28 Jun 2017 04:45:29: #1 Redundant rate of treatment: 0.55 INFO @ Wed, 28 Jun 2017 04:45:29: #1 finished! INFO @ Wed, 28 Jun 2017 04:45:29: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:45:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:45:29: #2 number of paired peaks: 52 WARNING @ Wed, 28 Jun 2017 04:45:29: Too few paired peaks (52) 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 04:45:29: Process for pairing-model is terminated! cat: SRX065610.10_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 `SRX065610.10_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 `SRX065610.10_*.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 `SRX065610.10_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 04:45:34: 7000000 INFO @ Wed, 28 Jun 2017 04:45:34: 7000000 INFO @ Wed, 28 Jun 2017 04:45:37: #1 tag size is determined as 36 bps INFO @ Wed, 28 Jun 2017 04:45:37: #1 tag size is determined as 36 bps INFO @ Wed, 28 Jun 2017 04:45:37: #1 tag size = 36 INFO @ Wed, 28 Jun 2017 04:45:37: #1 tag size = 36 INFO @ Wed, 28 Jun 2017 04:45:37: #1 total tags in treatment: 3381677 INFO @ Wed, 28 Jun 2017 04:45:37: #1 total tags in treatment: 3381677 INFO @ Wed, 28 Jun 2017 04:45:37: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:45:37: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:45:37: #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 04:45:37: #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 04:45:37: #1 tags after filtering in treatment: 1529200 INFO @ Wed, 28 Jun 2017 04:45:37: #1 Redundant rate of treatment: 0.55 INFO @ Wed, 28 Jun 2017 04:45:37: #1 finished! INFO @ Wed, 28 Jun 2017 04:45:37: #1 tags after filtering in treatment: 1529200 INFO @ Wed, 28 Jun 2017 04:45:37: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:45:37: #1 Redundant rate of treatment: 0.55 INFO @ Wed, 28 Jun 2017 04:45:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:45:37: #1 finished! INFO @ Wed, 28 Jun 2017 04:45:37: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:45:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:45:37: #2 number of paired peaks: 52 WARNING @ Wed, 28 Jun 2017 04:45:37: Too few paired peaks (52) 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 04:45:37: Process for pairing-model is terminated! INFO @ Wed, 28 Jun 2017 04:45:37: #2 number of paired peaks: 52 WARNING @ Wed, 28 Jun 2017 04:45:37: Too few paired peaks (52) 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 04:45:37: Process for pairing-model is terminated! cat: SRX065610.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX065610.20_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX065610.20_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 `SRX065610.20_*.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 `SRX065610.05_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 `SRX065610.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `SRX065610.05_*.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 `SRX065610.05_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 CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。