Job ID = 10254436 sra ファイルのダウンロード中... Completed: 89851K bytes transferred in 4 seconds (154625K 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: SINGLE fastq に変換中... Written 2780299 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3287337/SRR6176587.sra Written 2780299 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: 00:00:40 2780299 reads; of these: 2780299 (100.00%) were unpaired; of these: 823806 (29.63%) aligned 0 times 1646538 (59.22%) aligned exactly 1 time 309955 (11.15%) aligned >1 times 70.37% overall alignment rate Time searching: 00:00:40 Overall time: 00:00:40 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_rmdupse_core] 630879 / 1956493 = 0.3225 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, 06 Dec 2017 17:58:14: # Command line: callpeak -t SRX3287337.bam -f BAM -g 12100000 -n SRX3287337.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3287337.10 # format = BAM # ChIP-seq file = ['SRX3287337.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, 06 Dec 2017 17:58:14: #1 read tag files... INFO @ Wed, 06 Dec 2017 17:58:14: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 17:58:14: # Command line: callpeak -t SRX3287337.bam -f BAM -g 12100000 -n SRX3287337.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3287337.05 # format = BAM # ChIP-seq file = ['SRX3287337.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, 06 Dec 2017 17:58:14: #1 read tag files... INFO @ Wed, 06 Dec 2017 17:58:14: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 17:58:14: # Command line: callpeak -t SRX3287337.bam -f BAM -g 12100000 -n SRX3287337.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3287337.20 # format = BAM # ChIP-seq file = ['SRX3287337.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, 06 Dec 2017 17:58:14: #1 read tag files... INFO @ Wed, 06 Dec 2017 17:58:14: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 17:58:21: 1000000 INFO @ Wed, 06 Dec 2017 17:58:21: 1000000 INFO @ Wed, 06 Dec 2017 17:58:21: 1000000 INFO @ Wed, 06 Dec 2017 17:58:23: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 17:58:23: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 17:58:23: #1 total tags in treatment: 1325614 INFO @ Wed, 06 Dec 2017 17:58:23: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 17:58:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 17:58:23: #1 tags after filtering in treatment: 1325614 INFO @ Wed, 06 Dec 2017 17:58:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 17:58:23: #1 finished! INFO @ Wed, 06 Dec 2017 17:58:23: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 17:58:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 17:58:23: #2 number of paired peaks: 22 WARNING @ Wed, 06 Dec 2017 17:58:23: Too few paired peaks (22) 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, 06 Dec 2017 17:58:23: Process for pairing-model is terminated! cat: SRX3287337.10_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 `SRX3287337.10_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 `SRX3287337.10_*.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 `SRX3287337.10_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, 06 Dec 2017 17:58:23: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 17:58:23: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 17:58:23: #1 total tags in treatment: 1325614 INFO @ Wed, 06 Dec 2017 17:58:23: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 17:58:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 17:58:23: #1 tags after filtering in treatment: 1325614 INFO @ Wed, 06 Dec 2017 17:58:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 17:58:23: #1 finished! INFO @ Wed, 06 Dec 2017 17:58:23: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 17:58:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 17:58:23: #2 number of paired peaks: 22 WARNING @ Wed, 06 Dec 2017 17:58:23: Too few paired peaks (22) 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, 06 Dec 2017 17:58:23: Process for pairing-model is terminated! cat: SRX3287337.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Wed, 06 Dec 2017 17:58:23: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 17:58:23: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 17:58:23: #1 total tags in treatment: 1325614 INFO @ Wed, 06 Dec 2017 17:58:23: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 17:58:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3287337.05_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 `SRX3287337.05_*.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 `SRX3287337.05_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, 06 Dec 2017 17:58:23: #1 tags after filtering in treatment: 1325614 INFO @ Wed, 06 Dec 2017 17:58:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 17:58:23: #1 finished! INFO @ Wed, 06 Dec 2017 17:58:23: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 17:58:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 17:58:23: #2 number of paired peaks: 22 WARNING @ Wed, 06 Dec 2017 17:58:23: Too few paired peaks (22) 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, 06 Dec 2017 17:58:23: Process for pairing-model is terminated! cat: SRX3287337.20_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 `SRX3287337.20_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 `SRX3287337.20_*.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 `SRX3287337.20_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。