Job ID = 11245224 sra ファイルのダウンロード中... Completed: 569017K bytes transferred in 8 seconds (551761K 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 20699016 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4717368/SRR7878691.sra Written 20699016 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4717368/SRR7878691.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: 00:04:16 20699016 reads; of these: 20699016 (100.00%) were unpaired; of these: 744495 (3.60%) aligned 0 times 13045190 (63.02%) aligned exactly 1 time 6909331 (33.38%) aligned >1 times 96.40% overall alignment rate Time searching: 00:04:16 Overall time: 00:04:16 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] 12521972 / 19954521 = 0.6275 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, 10 Oct 2018 00:02:31: # Command line: callpeak -t SRX4717368.bam -f BAM -g 12100000 -n SRX4717368.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4717368.10 # format = BAM # ChIP-seq file = ['SRX4717368.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, 10 Oct 2018 00:02:31: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:02:31: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:02:31: # Command line: callpeak -t SRX4717368.bam -f BAM -g 12100000 -n SRX4717368.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4717368.05 # format = BAM # ChIP-seq file = ['SRX4717368.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, 10 Oct 2018 00:02:31: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:02:31: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:02:31: # Command line: callpeak -t SRX4717368.bam -f BAM -g 12100000 -n SRX4717368.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4717368.20 # format = BAM # ChIP-seq file = ['SRX4717368.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, 10 Oct 2018 00:02:31: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:02:31: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:02:39: 1000000 INFO @ Wed, 10 Oct 2018 00:02:40: 1000000 INFO @ Wed, 10 Oct 2018 00:02:40: 1000000 INFO @ Wed, 10 Oct 2018 00:02:47: 2000000 INFO @ Wed, 10 Oct 2018 00:02:49: 2000000 INFO @ Wed, 10 Oct 2018 00:02:49: 2000000 INFO @ Wed, 10 Oct 2018 00:02:55: 3000000 INFO @ Wed, 10 Oct 2018 00:02:59: 3000000 INFO @ Wed, 10 Oct 2018 00:02:59: 3000000 INFO @ Wed, 10 Oct 2018 00:03:03: 4000000 INFO @ Wed, 10 Oct 2018 00:03:08: 4000000 INFO @ Wed, 10 Oct 2018 00:03:08: 4000000 INFO @ Wed, 10 Oct 2018 00:03:11: 5000000 INFO @ Wed, 10 Oct 2018 00:03:17: 5000000 INFO @ Wed, 10 Oct 2018 00:03:17: 5000000 INFO @ Wed, 10 Oct 2018 00:03:19: 6000000 INFO @ Wed, 10 Oct 2018 00:03:26: 6000000 INFO @ Wed, 10 Oct 2018 00:03:26: 6000000 INFO @ Wed, 10 Oct 2018 00:03:27: 7000000 INFO @ Wed, 10 Oct 2018 00:03:30: #1 tag size is determined as 76 bps INFO @ Wed, 10 Oct 2018 00:03:30: #1 tag size = 76 INFO @ Wed, 10 Oct 2018 00:03:30: #1 total tags in treatment: 7432549 INFO @ Wed, 10 Oct 2018 00:03:30: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:03:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:03:30: #1 tags after filtering in treatment: 7432549 INFO @ Wed, 10 Oct 2018 00:03:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:03:30: #1 finished! INFO @ Wed, 10 Oct 2018 00:03:30: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:03:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:03:30: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:03:30: 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 @ Wed, 10 Oct 2018 00:03:30: Process for pairing-model is terminated! cat: SRX4717368.20_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 `SRX4717368.20_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 `SRX4717368.20_*.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 `SRX4717368.20_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 @ Wed, 10 Oct 2018 00:03:34: 7000000 INFO @ Wed, 10 Oct 2018 00:03:34: 7000000 INFO @ Wed, 10 Oct 2018 00:03:37: #1 tag size is determined as 76 bps INFO @ Wed, 10 Oct 2018 00:03:37: #1 tag size = 76 INFO @ Wed, 10 Oct 2018 00:03:37: #1 total tags in treatment: 7432549 INFO @ Wed, 10 Oct 2018 00:03:37: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:03:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:03:37: #1 tag size is determined as 76 bps INFO @ Wed, 10 Oct 2018 00:03:37: #1 tag size = 76 INFO @ Wed, 10 Oct 2018 00:03:37: #1 total tags in treatment: 7432549 INFO @ Wed, 10 Oct 2018 00:03:37: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:03:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:03:38: #1 tags after filtering in treatment: 7432549 INFO @ Wed, 10 Oct 2018 00:03:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:03:38: #1 finished! INFO @ Wed, 10 Oct 2018 00:03:38: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:03:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:03:38: #1 tags after filtering in treatment: 7432549 INFO @ Wed, 10 Oct 2018 00:03:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:03:38: #1 finished! INFO @ Wed, 10 Oct 2018 00:03:38: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:03:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:03:38: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:03:38: 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 @ Wed, 10 Oct 2018 00:03:38: Process for pairing-model is terminated! INFO @ Wed, 10 Oct 2018 00:03:38: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:03:38: 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 @ Wed, 10 Oct 2018 00:03:38: Process for pairing-model is terminated! cat: SRX4717368.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX4717368.05_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 `SRX4717368.10_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 `SRX4717368.10_*.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 `SRX4717368.10_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4717368.05_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 `SRX4717368.05_*.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 `SRX4717368.05_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。