Job ID = 9161729 sra ファイルのダウンロード中... Completed: 409041K bytes transferred in 8 seconds (417968K 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 12149230 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1004425/SRR1986243.sra Written 12149230 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: 00:02:19 12149230 reads; of these: 12149230 (100.00%) were unpaired; of these: 759924 (6.25%) aligned 0 times 10318772 (84.93%) aligned exactly 1 time 1070534 (8.81%) aligned >1 times 93.75% overall alignment rate Time searching: 00:02:19 Overall time: 00:02:19 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] 5437074 / 11389306 = 0.4774 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 04:31:01: # Command line: callpeak -t SRX1004425.bam -f BAM -g 12100000 -n SRX1004425.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1004425.10 # format = BAM # ChIP-seq file = ['SRX1004425.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 04:31:01: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:31:01: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:31:01: # Command line: callpeak -t SRX1004425.bam -f BAM -g 12100000 -n SRX1004425.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1004425.20 # format = BAM # ChIP-seq file = ['SRX1004425.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 04:31:01: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:31:01: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:31:01: # Command line: callpeak -t SRX1004425.bam -f BAM -g 12100000 -n SRX1004425.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1004425.05 # format = BAM # ChIP-seq file = ['SRX1004425.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 04:31:01: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:31:01: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:31:09: 1000000 INFO @ Wed, 28 Jun 2017 04:31:09: 1000000 INFO @ Wed, 28 Jun 2017 04:31:10: 1000000 INFO @ Wed, 28 Jun 2017 04:31:17: 2000000 INFO @ Wed, 28 Jun 2017 04:31:17: 2000000 INFO @ Wed, 28 Jun 2017 04:31:18: 2000000 INFO @ Wed, 28 Jun 2017 04:31:25: 3000000 INFO @ Wed, 28 Jun 2017 04:31:25: 3000000 INFO @ Wed, 28 Jun 2017 04:31:27: 3000000 INFO @ Wed, 28 Jun 2017 04:31:33: 4000000 INFO @ Wed, 28 Jun 2017 04:31:33: 4000000 INFO @ Wed, 28 Jun 2017 04:31:35: 4000000 INFO @ Wed, 28 Jun 2017 04:31:40: 5000000 INFO @ Wed, 28 Jun 2017 04:31:40: 5000000 INFO @ Wed, 28 Jun 2017 04:31:44: 5000000 INFO @ Wed, 28 Jun 2017 04:31:48: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 04:31:48: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 04:31:48: #1 total tags in treatment: 5952232 INFO @ Wed, 28 Jun 2017 04:31:48: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:31:48: #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 04:31:48: #1 tags after filtering in treatment: 5952232 INFO @ Wed, 28 Jun 2017 04:31:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 04:31:48: #1 finished! INFO @ Wed, 28 Jun 2017 04:31:48: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:31:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:31:48: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 04:31:48: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 04:31:48: #1 total tags in treatment: 5952232 INFO @ Wed, 28 Jun 2017 04:31:48: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:31:48: #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 04:31:48: #1 tags after filtering in treatment: 5952232 INFO @ Wed, 28 Jun 2017 04:31:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 04:31:48: #1 finished! INFO @ Wed, 28 Jun 2017 04:31:48: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:31:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:31:48: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:31:48: 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 04:31:48: Process for pairing-model is terminated! cat: SRX1004425.20_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 `SRX1004425.20_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 `SRX1004425.20_*.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 `SRX1004425.20_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 @ Wed, 28 Jun 2017 04:31:49: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:31:49: 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 04:31:49: Process for pairing-model is terminated! cat: SRX1004425.05_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1004425.05_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 `SRX1004425.05_*.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 `SRX1004425.05_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 04:31:52: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 04:31:52: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 04:31:52: #1 total tags in treatment: 5952232 INFO @ Wed, 28 Jun 2017 04:31:52: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:31:52: #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 04:31:52: #1 tags after filtering in treatment: 5952232 INFO @ Wed, 28 Jun 2017 04:31:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 04:31:52: #1 finished! INFO @ Wed, 28 Jun 2017 04:31:52: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:31:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:31:52: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:31:52: 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 04:31:52: Process for pairing-model is terminated! cat: SRX1004425.10_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 `SRX1004425.10_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 `SRX1004425.10_*.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 `SRX1004425.10_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。