Job ID = 9163655 sra ファイルのダウンロード中... Completed: 678169K bytes transferred in 10 seconds (532482K 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 10120768 spots for /home/okishinya/chipatlas/results/sacCer3/SRX997171/SRR1976203.sra Written 10120768 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: 00:06:57 10120768 reads; of these: 10120768 (100.00%) were paired; of these: 1451968 (14.35%) aligned concordantly 0 times 5444355 (53.79%) aligned concordantly exactly 1 time 3224445 (31.86%) aligned concordantly >1 times ---- 1451968 pairs aligned concordantly 0 times; of these: 46520 (3.20%) aligned discordantly 1 time ---- 1405448 pairs aligned 0 times concordantly or discordantly; of these: 2810896 mates make up the pairs; of these: 2497005 (88.83%) aligned 0 times 181727 (6.47%) aligned exactly 1 time 132164 (4.70%) aligned >1 times 87.66% overall alignment rate Time searching: 00:06:57 Overall time: 00:06:57 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 8 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] 2737934 / 8681429 = 0.3154 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 11:24:02: # Command line: callpeak -t SRX997171.bam -f BAM -g 12100000 -n SRX997171.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX997171.20 # format = BAM # ChIP-seq file = ['SRX997171.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 11:24:02: #1 read tag files... INFO @ Wed, 28 Jun 2017 11:24:02: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 11:24:02: # Command line: callpeak -t SRX997171.bam -f BAM -g 12100000 -n SRX997171.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX997171.05 # format = BAM # ChIP-seq file = ['SRX997171.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 11:24:02: #1 read tag files... INFO @ Wed, 28 Jun 2017 11:24:02: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 11:24:02: # Command line: callpeak -t SRX997171.bam -f BAM -g 12100000 -n SRX997171.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX997171.10 # format = BAM # ChIP-seq file = ['SRX997171.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 11:24:02: #1 read tag files... INFO @ Wed, 28 Jun 2017 11:24:02: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 11:24:07: 1000000 INFO @ Wed, 28 Jun 2017 11:24:07: 1000000 INFO @ Wed, 28 Jun 2017 11:24:07: 1000000 INFO @ Wed, 28 Jun 2017 11:24:13: 2000000 INFO @ Wed, 28 Jun 2017 11:24:13: 2000000 INFO @ Wed, 28 Jun 2017 11:24:13: 2000000 INFO @ Wed, 28 Jun 2017 11:24:18: 3000000 INFO @ Wed, 28 Jun 2017 11:24:19: 3000000 INFO @ Wed, 28 Jun 2017 11:24:19: 3000000 INFO @ Wed, 28 Jun 2017 11:24:24: 4000000 INFO @ Wed, 28 Jun 2017 11:24:24: 4000000 INFO @ Wed, 28 Jun 2017 11:24:24: 4000000 INFO @ Wed, 28 Jun 2017 11:24:30: 5000000 INFO @ Wed, 28 Jun 2017 11:24:30: 5000000 INFO @ Wed, 28 Jun 2017 11:24:30: 5000000 INFO @ Wed, 28 Jun 2017 11:24:35: 6000000 INFO @ Wed, 28 Jun 2017 11:24:36: 6000000 INFO @ Wed, 28 Jun 2017 11:24:36: 6000000 INFO @ Wed, 28 Jun 2017 11:24:41: 7000000 INFO @ Wed, 28 Jun 2017 11:24:41: 7000000 INFO @ Wed, 28 Jun 2017 11:24:42: 7000000 INFO @ Wed, 28 Jun 2017 11:24:46: 8000000 INFO @ Wed, 28 Jun 2017 11:24:47: 8000000 INFO @ Wed, 28 Jun 2017 11:24:48: 8000000 INFO @ Wed, 28 Jun 2017 11:24:51: 9000000 INFO @ Wed, 28 Jun 2017 11:24:52: 9000000 INFO @ Wed, 28 Jun 2017 11:24:53: 9000000 INFO @ Wed, 28 Jun 2017 11:24:57: 10000000 INFO @ Wed, 28 Jun 2017 11:24:58: 10000000 INFO @ Wed, 28 Jun 2017 11:24:59: 10000000 INFO @ Wed, 28 Jun 2017 11:25:02: 11000000 INFO @ Wed, 28 Jun 2017 11:25:04: 11000000 INFO @ Wed, 28 Jun 2017 11:25:05: 11000000 INFO @ Wed, 28 Jun 2017 11:25:08: 12000000 INFO @ Wed, 28 Jun 2017 11:25:09: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 11:25:09: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 11:25:09: #1 total tags in treatment: 5931089 INFO @ Wed, 28 Jun 2017 11:25:09: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 11:25:09: #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 11:25:09: #1 tags after filtering in treatment: 3501954 INFO @ Wed, 28 Jun 2017 11:25:09: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 28 Jun 2017 11:25:09: #1 finished! INFO @ Wed, 28 Jun 2017 11:25:09: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 11:25:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 11:25:10: #2 number of paired peaks: 28 WARNING @ Wed, 28 Jun 2017 11:25:10: Too few paired peaks (28) 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 11:25:10: Process for pairing-model is terminated! cat: SRX997171.10_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 `SRX997171.10_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 `SRX997171.10_*.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 `SRX997171.10_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 11:25:10: 12000000 INFO @ Wed, 28 Jun 2017 11:25:11: 12000000 INFO @ Wed, 28 Jun 2017 11:25:12: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 11:25:12: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 11:25:12: #1 total tags in treatment: 5931089 INFO @ Wed, 28 Jun 2017 11:25:12: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 11:25:12: #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 11:25:12: #1 tags after filtering in treatment: 3501954 INFO @ Wed, 28 Jun 2017 11:25:12: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 28 Jun 2017 11:25:12: #1 finished! INFO @ Wed, 28 Jun 2017 11:25:12: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 11:25:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 11:25:12: #2 number of paired peaks: 28 WARNING @ Wed, 28 Jun 2017 11:25:12: Too few paired peaks (28) 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 11:25:12: Process for pairing-model is terminated! cat: SRX997171.05_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 `SRX997171.05_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 `SRX997171.05_*.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 `SRX997171.05_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 11:25:12: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 11:25:12: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 11:25:12: #1 total tags in treatment: 5931089 INFO @ Wed, 28 Jun 2017 11:25:12: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 11:25:12: #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 11:25:12: #1 tags after filtering in treatment: 3501954 INFO @ Wed, 28 Jun 2017 11:25:12: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 28 Jun 2017 11:25:12: #1 finished! INFO @ Wed, 28 Jun 2017 11:25:12: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 11:25:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 11:25:13: #2 number of paired peaks: 28 WARNING @ Wed, 28 Jun 2017 11:25:13: Too few paired peaks (28) 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 11:25:13: Process for pairing-model is terminated! cat: SRX997171.20_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 `SRX997171.20_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 `SRX997171.20_*.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 `SRX997171.20_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。