Job ID = 11634729 sra ファイルのダウンロード中... Completed: 486660K bytes transferred in 8 seconds (447903K 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 23581655 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5019428/SRR8200051.sra Written 23581655 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5019428/SRR8200051.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: 00:03:52 23581655 reads; of these: 23581655 (100.00%) were unpaired; of these: 1118033 (4.74%) aligned 0 times 15886251 (67.37%) aligned exactly 1 time 6577371 (27.89%) aligned >1 times 95.26% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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 12 files... [bam_rmdupse_core] 11087765 / 22463622 = 0.4936 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 10:40:45: # Command line: callpeak -t SRX5019428.bam -f BAM -g 12100000 -n SRX5019428.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5019428.05 # format = BAM # ChIP-seq file = ['SRX5019428.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 10:40:45: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:40:45: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:40:45: # Command line: callpeak -t SRX5019428.bam -f BAM -g 12100000 -n SRX5019428.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5019428.20 # format = BAM # ChIP-seq file = ['SRX5019428.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 10:40:45: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:40:45: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:40:45: # Command line: callpeak -t SRX5019428.bam -f BAM -g 12100000 -n SRX5019428.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5019428.10 # format = BAM # ChIP-seq file = ['SRX5019428.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 10:40:45: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:40:45: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:40:51: 1000000 INFO @ Fri, 15 Feb 2019 10:40:51: 1000000 INFO @ Fri, 15 Feb 2019 10:40:52: 1000000 INFO @ Fri, 15 Feb 2019 10:40:58: 2000000 INFO @ Fri, 15 Feb 2019 10:40:58: 2000000 INFO @ Fri, 15 Feb 2019 10:41:00: 2000000 INFO @ Fri, 15 Feb 2019 10:41:04: 3000000 INFO @ Fri, 15 Feb 2019 10:41:04: 3000000 INFO @ Fri, 15 Feb 2019 10:41:07: 3000000 INFO @ Fri, 15 Feb 2019 10:41:11: 4000000 INFO @ Fri, 15 Feb 2019 10:41:11: 4000000 INFO @ Fri, 15 Feb 2019 10:41:13: 4000000 INFO @ Fri, 15 Feb 2019 10:41:17: 5000000 INFO @ Fri, 15 Feb 2019 10:41:17: 5000000 INFO @ Fri, 15 Feb 2019 10:41:20: 5000000 INFO @ Fri, 15 Feb 2019 10:41:24: 6000000 INFO @ Fri, 15 Feb 2019 10:41:24: 6000000 INFO @ Fri, 15 Feb 2019 10:41:27: 6000000 INFO @ Fri, 15 Feb 2019 10:41:30: 7000000 INFO @ Fri, 15 Feb 2019 10:41:30: 7000000 INFO @ Fri, 15 Feb 2019 10:41:33: 7000000 INFO @ Fri, 15 Feb 2019 10:41:37: 8000000 INFO @ Fri, 15 Feb 2019 10:41:37: 8000000 INFO @ Fri, 15 Feb 2019 10:41:40: 8000000 INFO @ Fri, 15 Feb 2019 10:41:43: 9000000 INFO @ Fri, 15 Feb 2019 10:41:43: 9000000 INFO @ Fri, 15 Feb 2019 10:41:47: 9000000 INFO @ Fri, 15 Feb 2019 10:41:50: 10000000 INFO @ Fri, 15 Feb 2019 10:41:50: 10000000 INFO @ Fri, 15 Feb 2019 10:41:53: 10000000 INFO @ Fri, 15 Feb 2019 10:41:56: 11000000 INFO @ Fri, 15 Feb 2019 10:41:56: 11000000 INFO @ Fri, 15 Feb 2019 10:41:59: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:41:59: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:41:59: #1 total tags in treatment: 11375857 INFO @ Fri, 15 Feb 2019 10:41:59: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:41:59: #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 10:41:59: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:41:59: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:41:59: #1 total tags in treatment: 11375857 INFO @ Fri, 15 Feb 2019 10:41:59: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:41:59: #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 10:41:59: #1 tags after filtering in treatment: 11375857 INFO @ Fri, 15 Feb 2019 10:41:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:41:59: #1 finished! INFO @ Fri, 15 Feb 2019 10:41:59: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:41:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:41:59: #1 tags after filtering in treatment: 11375857 INFO @ Fri, 15 Feb 2019 10:41:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:41:59: #1 finished! INFO @ Fri, 15 Feb 2019 10:41:59: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:41:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:42:00: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:42:00: 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 10:42:00: Process for pairing-model is terminated! cat: SRX5019428.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Fri, 15 Feb 2019 10:42:00: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:42:00: 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 10:42:00: Process for pairing-model is terminated! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5019428.20_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 `SRX5019428.20_*.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 `SRX5019428.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません cat: SRX5019428.05_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 pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5019428.05_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 `SRX5019428.05_*.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 `SRX5019428.05_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 10:42:00: 11000000 INFO @ Fri, 15 Feb 2019 10:42:02: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:42:02: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:42:02: #1 total tags in treatment: 11375857 INFO @ Fri, 15 Feb 2019 10:42:02: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:42:02: #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 10:42:03: #1 tags after filtering in treatment: 11375857 INFO @ Fri, 15 Feb 2019 10:42:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:42:03: #1 finished! INFO @ Fri, 15 Feb 2019 10:42:03: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:42:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:42:03: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:42:03: 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 10:42:03: Process for pairing-model is terminated! cat: SRX5019428.10_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 `SRX5019428.10_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 `SRX5019428.10_*.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 `SRX5019428.10_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。