Job ID = 11296950 sra ファイルのダウンロード中... Completed: 245365K bytes transferred in 5 seconds (341811K 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... Read 11766454 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856372/SRR6908190.sra Written 11766454 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856372/SRR6908190.sra 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: 00:01:55 11766454 reads; of these: 11766454 (100.00%) were unpaired; of these: 801459 (6.81%) aligned 0 times 7810987 (66.38%) aligned exactly 1 time 3154008 (26.81%) aligned >1 times 93.19% overall alignment rate Time searching: 00:01:55 Overall time: 00:01:55 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] 7576980 / 10964995 = 0.6910 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 @ Mon, 05 Nov 2018 18:03:54: # Command line: callpeak -t SRX3856372.bam -f BAM -g 12100000 -n SRX3856372.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3856372.05 # format = BAM # ChIP-seq file = ['SRX3856372.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 @ Mon, 05 Nov 2018 18:03:54: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:03:54: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:03:54: # Command line: callpeak -t SRX3856372.bam -f BAM -g 12100000 -n SRX3856372.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3856372.20 # format = BAM # ChIP-seq file = ['SRX3856372.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 @ Mon, 05 Nov 2018 18:03:54: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:03:54: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:03:54: # Command line: callpeak -t SRX3856372.bam -f BAM -g 12100000 -n SRX3856372.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3856372.10 # format = BAM # ChIP-seq file = ['SRX3856372.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 @ Mon, 05 Nov 2018 18:03:54: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:03:54: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:04:00: 1000000 INFO @ Mon, 05 Nov 2018 18:04:01: 1000000 INFO @ Mon, 05 Nov 2018 18:04:01: 1000000 INFO @ Mon, 05 Nov 2018 18:04:06: 2000000 INFO @ Mon, 05 Nov 2018 18:04:07: 2000000 INFO @ Mon, 05 Nov 2018 18:04:08: 2000000 INFO @ Mon, 05 Nov 2018 18:04:12: 3000000 INFO @ Mon, 05 Nov 2018 18:04:14: 3000000 INFO @ Mon, 05 Nov 2018 18:04:14: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:04:14: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:04:14: #1 total tags in treatment: 3388015 INFO @ Mon, 05 Nov 2018 18:04:14: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:04:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:04:15: #1 tags after filtering in treatment: 3388015 INFO @ Mon, 05 Nov 2018 18:04:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:04:15: #1 finished! INFO @ Mon, 05 Nov 2018 18:04:15: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:04:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:04:15: 3000000 INFO @ Mon, 05 Nov 2018 18:04:15: #2 number of paired peaks: 30 WARNING @ Mon, 05 Nov 2018 18:04:15: Too few paired peaks (30) 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 @ Mon, 05 Nov 2018 18:04:15: Process for pairing-model is terminated! cat: SRX3856372.05_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 `SRX3856372.05_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 `SRX3856372.05_*.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 `SRX3856372.05_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 @ Mon, 05 Nov 2018 18:04:17: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:04:17: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:04:17: #1 total tags in treatment: 3388015 INFO @ Mon, 05 Nov 2018 18:04:17: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:04:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:04:17: #1 tags after filtering in treatment: 3388015 INFO @ Mon, 05 Nov 2018 18:04:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:04:17: #1 finished! INFO @ Mon, 05 Nov 2018 18:04:17: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:04:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:04:17: #2 number of paired peaks: 30 WARNING @ Mon, 05 Nov 2018 18:04:17: Too few paired peaks (30) 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 @ Mon, 05 Nov 2018 18:04:17: Process for pairing-model is terminated! cat: SRX3856372.10_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 `SRX3856372.10_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 `SRX3856372.10_*.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 `SRX3856372.10_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 @ Mon, 05 Nov 2018 18:04:17: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:04:17: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:04:17: #1 total tags in treatment: 3388015 INFO @ Mon, 05 Nov 2018 18:04:17: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:04:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:04:17: #1 tags after filtering in treatment: 3388015 INFO @ Mon, 05 Nov 2018 18:04:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:04:17: #1 finished! INFO @ Mon, 05 Nov 2018 18:04:17: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:04:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:04:17: #2 number of paired peaks: 30 WARNING @ Mon, 05 Nov 2018 18:04:17: Too few paired peaks (30) 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 @ Mon, 05 Nov 2018 18:04:17: Process for pairing-model is terminated! cat: SRX3856372.20_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 `SRX3856372.20_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 `SRX3856372.20_*.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 `SRX3856372.20_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。