Job ID = 9161732 sra ファイルのダウンロード中... Completed: 408164K bytes transferred in 6 seconds (482133K 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: SINGLE fastq に変換中... Written 12039758 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1004429/SRR1986247.sra Written 12039758 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: 00:02:16 12039758 reads; of these: 12039758 (100.00%) were unpaired; of these: 695356 (5.78%) aligned 0 times 10043308 (83.42%) aligned exactly 1 time 1301094 (10.81%) aligned >1 times 94.22% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 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_rmdupse_core] 5457153 / 11344402 = 0.4810 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 04:31:14: # Command line: callpeak -t SRX1004429.bam -f BAM -g 12100000 -n SRX1004429.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1004429.10 # format = BAM # ChIP-seq file = ['SRX1004429.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 04:31:14: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:31:14: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:31:14: # Command line: callpeak -t SRX1004429.bam -f BAM -g 12100000 -n SRX1004429.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1004429.05 # format = BAM # ChIP-seq file = ['SRX1004429.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 04:31:14: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:31:14: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:31:14: # Command line: callpeak -t SRX1004429.bam -f BAM -g 12100000 -n SRX1004429.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1004429.20 # format = BAM # ChIP-seq file = ['SRX1004429.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 04:31:14: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:31:14: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:31:21: 1000000 INFO @ Wed, 28 Jun 2017 04:31:21: 1000000 INFO @ Wed, 28 Jun 2017 04:31:21: 1000000 INFO @ Wed, 28 Jun 2017 04:31:28: 2000000 INFO @ Wed, 28 Jun 2017 04:31:28: 2000000 INFO @ Wed, 28 Jun 2017 04:31:28: 2000000 INFO @ Wed, 28 Jun 2017 04:31:35: 3000000 INFO @ Wed, 28 Jun 2017 04:31:35: 3000000 INFO @ Wed, 28 Jun 2017 04:31:35: 3000000 INFO @ Wed, 28 Jun 2017 04:31:42: 4000000 INFO @ Wed, 28 Jun 2017 04:31:42: 4000000 INFO @ Wed, 28 Jun 2017 04:31:42: 4000000 INFO @ Wed, 28 Jun 2017 04:31:49: 5000000 INFO @ Wed, 28 Jun 2017 04:31:49: 5000000 INFO @ Wed, 28 Jun 2017 04:31:49: 5000000 INFO @ Wed, 28 Jun 2017 04:31:55: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 04:31:55: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 04:31:55: #1 total tags in treatment: 5887249 INFO @ Wed, 28 Jun 2017 04:31:55: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:31:55: #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 04:31:55: #1 tags after filtering in treatment: 5887249 INFO @ Wed, 28 Jun 2017 04:31:55: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 04:31:55: #1 finished! INFO @ Wed, 28 Jun 2017 04:31:55: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:31:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:31:56: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:31:56: Too few paired peaks (0) 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 04:31:56: Process for pairing-model is terminated! cat: SRX1004429.10_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 `SRX1004429.10_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 `SRX1004429.10_*.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 `SRX1004429.10_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 04:31:56: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 04:31:56: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 04:31:56: #1 total tags in treatment: 5887249 INFO @ Wed, 28 Jun 2017 04:31:56: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:31:56: #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 04:31:56: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 04:31:56: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 04:31:56: #1 total tags in treatment: 5887249 INFO @ Wed, 28 Jun 2017 04:31:56: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:31:56: #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 04:31:56: #1 tags after filtering in treatment: 5887249 INFO @ Wed, 28 Jun 2017 04:31:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 04:31:56: #1 finished! INFO @ Wed, 28 Jun 2017 04:31:56: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:31:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:31:56: #1 tags after filtering in treatment: 5887249 INFO @ Wed, 28 Jun 2017 04:31:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 04:31:56: #1 finished! INFO @ Wed, 28 Jun 2017 04:31:56: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:31:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:31:56: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:31:56: Too few paired peaks (0) 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 04:31:56: Process for pairing-model is terminated! cat: SRX1004429.05_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 `SRX1004429.05_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 `SRX1004429.05_*.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 `SRX1004429.05_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 04:31:57: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:31:57: Too few paired peaks (0) 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 04:31:57: Process for pairing-model is terminated! cat: SRX1004429.20_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 `SRX1004429.20_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 `SRX1004429.20_*.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 `SRX1004429.20_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。