Job ID = 11634730 sra ファイルのダウンロード中... Completed: 480465K bytes transferred in 9 seconds (402040K 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 22282304 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5019429/SRR8200052.sra Written 22282304 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5019429/SRR8200052.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: 00:03:10 22282304 reads; of these: 22282304 (100.00%) were unpaired; of these: 6018389 (27.01%) aligned 0 times 12377050 (55.55%) aligned exactly 1 time 3886865 (17.44%) aligned >1 times 72.99% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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] 8361657 / 16263915 = 0.5141 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 10:39:33: # Command line: callpeak -t SRX5019429.bam -f BAM -g 12100000 -n SRX5019429.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5019429.10 # format = BAM # ChIP-seq file = ['SRX5019429.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 10:39:33: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:39:33: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:39:33: # Command line: callpeak -t SRX5019429.bam -f BAM -g 12100000 -n SRX5019429.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5019429.05 # format = BAM # ChIP-seq file = ['SRX5019429.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 10:39:33: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:39:33: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:39:33: # Command line: callpeak -t SRX5019429.bam -f BAM -g 12100000 -n SRX5019429.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5019429.20 # format = BAM # ChIP-seq file = ['SRX5019429.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 10:39:33: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:39:33: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:39:40: 1000000 INFO @ Fri, 15 Feb 2019 10:39:40: 1000000 INFO @ Fri, 15 Feb 2019 10:39:40: 1000000 INFO @ Fri, 15 Feb 2019 10:39:46: 2000000 INFO @ Fri, 15 Feb 2019 10:39:47: 2000000 INFO @ Fri, 15 Feb 2019 10:39:47: 2000000 INFO @ Fri, 15 Feb 2019 10:39:52: 3000000 INFO @ Fri, 15 Feb 2019 10:39:53: 3000000 INFO @ Fri, 15 Feb 2019 10:39:53: 3000000 INFO @ Fri, 15 Feb 2019 10:39:58: 4000000 INFO @ Fri, 15 Feb 2019 10:40:00: 4000000 INFO @ Fri, 15 Feb 2019 10:40:00: 4000000 INFO @ Fri, 15 Feb 2019 10:40:04: 5000000 INFO @ Fri, 15 Feb 2019 10:40:06: 5000000 INFO @ Fri, 15 Feb 2019 10:40:07: 5000000 INFO @ Fri, 15 Feb 2019 10:40:10: 6000000 INFO @ Fri, 15 Feb 2019 10:40:12: 6000000 INFO @ Fri, 15 Feb 2019 10:40:13: 6000000 INFO @ Fri, 15 Feb 2019 10:40:16: 7000000 INFO @ Fri, 15 Feb 2019 10:40:18: 7000000 INFO @ Fri, 15 Feb 2019 10:40:19: 7000000 INFO @ Fri, 15 Feb 2019 10:40:21: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:40:21: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:40:21: #1 total tags in treatment: 7902258 INFO @ Fri, 15 Feb 2019 10:40:21: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:40:21: #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 10:40:21: #1 tags after filtering in treatment: 7902258 INFO @ Fri, 15 Feb 2019 10:40:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:40:21: #1 finished! INFO @ Fri, 15 Feb 2019 10:40:21: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:40:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:40:22: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:40:22: 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 10:40:22: Process for pairing-model is terminated! cat: SRX5019429.10_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 `SRX5019429.10_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 `SRX5019429.10_*.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 `SRX5019429.10_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 10:40:24: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:40:24: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:40:24: #1 total tags in treatment: 7902258 INFO @ Fri, 15 Feb 2019 10:40:24: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:40:24: #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 10:40:24: #1 tags after filtering in treatment: 7902258 INFO @ Fri, 15 Feb 2019 10:40:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:40:24: #1 finished! INFO @ Fri, 15 Feb 2019 10:40:24: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:40:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:40:24: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:40:24: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:40:24: #1 total tags in treatment: 7902258 INFO @ Fri, 15 Feb 2019 10:40:24: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:40:24: #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 10:40:24: #1 tags after filtering in treatment: 7902258 INFO @ Fri, 15 Feb 2019 10:40:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:40:24: #1 finished! INFO @ Fri, 15 Feb 2019 10:40:24: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:40:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:40:24: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:40:24: 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 10:40:24: Process for pairing-model is terminated! cat: SRX5019429.20_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 `SRX5019429.20_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 `SRX5019429.20_*.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 `SRX5019429.20_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 @ Fri, 15 Feb 2019 10:40:25: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:40:25: 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 10:40:25: Process for pairing-model is terminated! cat: SRX5019429.05_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 `SRX5019429.05_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 `SRX5019429.05_*.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 `SRX5019429.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。