Job ID = 11634697 sra ファイルのダウンロード中... Completed: 604771K bytes transferred in 9 seconds (535373K 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 17875267 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4940192/SRR8113811.sra Written 17875267 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4940192/SRR8113811.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: 00:04:19 17875267 reads; of these: 17875267 (100.00%) were unpaired; of these: 1594285 (8.92%) aligned 0 times 14568648 (81.50%) aligned exactly 1 time 1712334 (9.58%) aligned >1 times 91.08% overall alignment rate Time searching: 00:04:19 Overall time: 00:04:19 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] 10248087 / 16280982 = 0.6295 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 @ Fri, 15 Feb 2019 10:37:25: # Command line: callpeak -t SRX4940192.bam -f BAM -g 12100000 -n SRX4940192.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4940192.10 # format = BAM # ChIP-seq file = ['SRX4940192.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 @ Fri, 15 Feb 2019 10:37:25: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:37:25: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:37:25: # Command line: callpeak -t SRX4940192.bam -f BAM -g 12100000 -n SRX4940192.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4940192.05 # format = BAM # ChIP-seq file = ['SRX4940192.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 @ Fri, 15 Feb 2019 10:37:25: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:37:25: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:37:25: # Command line: callpeak -t SRX4940192.bam -f BAM -g 12100000 -n SRX4940192.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4940192.20 # format = BAM # ChIP-seq file = ['SRX4940192.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 @ Fri, 15 Feb 2019 10:37:25: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:37:25: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:37:31: 1000000 INFO @ Fri, 15 Feb 2019 10:37:31: 1000000 INFO @ Fri, 15 Feb 2019 10:37:31: 1000000 INFO @ Fri, 15 Feb 2019 10:37:37: 2000000 INFO @ Fri, 15 Feb 2019 10:37:38: 2000000 INFO @ Fri, 15 Feb 2019 10:37:38: 2000000 INFO @ Fri, 15 Feb 2019 10:37:44: 3000000 INFO @ Fri, 15 Feb 2019 10:37:44: 3000000 INFO @ Fri, 15 Feb 2019 10:37:45: 3000000 INFO @ Fri, 15 Feb 2019 10:37:50: 4000000 INFO @ Fri, 15 Feb 2019 10:37:51: 4000000 INFO @ Fri, 15 Feb 2019 10:37:52: 4000000 INFO @ Fri, 15 Feb 2019 10:37:56: 5000000 INFO @ Fri, 15 Feb 2019 10:37:57: 5000000 INFO @ Fri, 15 Feb 2019 10:38:00: 5000000 INFO @ Fri, 15 Feb 2019 10:38:03: 6000000 INFO @ Fri, 15 Feb 2019 10:38:03: #1 tag size is determined as 64 bps INFO @ Fri, 15 Feb 2019 10:38:03: #1 tag size = 64 INFO @ Fri, 15 Feb 2019 10:38:03: #1 total tags in treatment: 6032895 INFO @ Fri, 15 Feb 2019 10:38:03: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:38:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:38:03: #1 tags after filtering in treatment: 6032895 INFO @ Fri, 15 Feb 2019 10:38:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:38:03: #1 finished! INFO @ Fri, 15 Feb 2019 10:38:03: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:38:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:38:03: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:38:03: 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 @ Fri, 15 Feb 2019 10:38:03: Process for pairing-model is terminated! cat: SRX4940192.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4940192.10_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 `SRX4940192.10_*.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 `SRX4940192.10_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 @ Fri, 15 Feb 2019 10:38:04: 6000000 INFO @ Fri, 15 Feb 2019 10:38:04: #1 tag size is determined as 64 bps INFO @ Fri, 15 Feb 2019 10:38:04: #1 tag size = 64 INFO @ Fri, 15 Feb 2019 10:38:04: #1 total tags in treatment: 6032895 INFO @ Fri, 15 Feb 2019 10:38:04: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:38:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:38:04: #1 tags after filtering in treatment: 6032895 INFO @ Fri, 15 Feb 2019 10:38:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:38:04: #1 finished! INFO @ Fri, 15 Feb 2019 10:38:04: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:38:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:38:05: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:38:05: 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 @ Fri, 15 Feb 2019 10:38:05: Process for pairing-model is terminated! cat: SRX4940192.05_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4940192.05_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 `SRX4940192.05_*.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 `SRX4940192.05_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 @ Fri, 15 Feb 2019 10:38:06: 6000000 INFO @ Fri, 15 Feb 2019 10:38:07: #1 tag size is determined as 64 bps INFO @ Fri, 15 Feb 2019 10:38:07: #1 tag size = 64 INFO @ Fri, 15 Feb 2019 10:38:07: #1 total tags in treatment: 6032895 INFO @ Fri, 15 Feb 2019 10:38:07: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:38:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:38:07: #1 tags after filtering in treatment: 6032895 INFO @ Fri, 15 Feb 2019 10:38:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:38:07: #1 finished! INFO @ Fri, 15 Feb 2019 10:38:07: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:38:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:38:07: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:38:07: 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 @ Fri, 15 Feb 2019 10:38:07: Process for pairing-model is terminated! cat: SRX4940192.20_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4940192.20_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 `SRX4940192.20_*.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 `SRX4940192.20_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。