Job ID = 11245098 sra ファイルのダウンロード中... Completed: 405284K bytes transferred in 8 seconds (412083K 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 23909732 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4590916/SRR7734557.sra Written 23909732 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4590916/SRR7734557.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: 00:04:08 23909732 reads; of these: 23909732 (100.00%) were unpaired; of these: 1736083 (7.26%) aligned 0 times 19596349 (81.96%) aligned exactly 1 time 2577300 (10.78%) aligned >1 times 92.74% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 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] 11755382 / 22173649 = 0.5302 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 @ Tue, 09 Oct 2018 23:31:04: # Command line: callpeak -t SRX4590916.bam -f BAM -g 12100000 -n SRX4590916.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4590916.10 # format = BAM # ChIP-seq file = ['SRX4590916.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 @ Tue, 09 Oct 2018 23:31:04: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:31:04: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:31:04: # Command line: callpeak -t SRX4590916.bam -f BAM -g 12100000 -n SRX4590916.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4590916.20 # format = BAM # ChIP-seq file = ['SRX4590916.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 @ Tue, 09 Oct 2018 23:31:04: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:31:04: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:31:04: # Command line: callpeak -t SRX4590916.bam -f BAM -g 12100000 -n SRX4590916.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4590916.05 # format = BAM # ChIP-seq file = ['SRX4590916.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 @ Tue, 09 Oct 2018 23:31:04: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:31:04: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:31:11: 1000000 INFO @ Tue, 09 Oct 2018 23:31:11: 1000000 INFO @ Tue, 09 Oct 2018 23:31:11: 1000000 INFO @ Tue, 09 Oct 2018 23:31:17: 2000000 INFO @ Tue, 09 Oct 2018 23:31:18: 2000000 INFO @ Tue, 09 Oct 2018 23:31:18: 2000000 INFO @ Tue, 09 Oct 2018 23:31:24: 3000000 INFO @ Tue, 09 Oct 2018 23:31:25: 3000000 INFO @ Tue, 09 Oct 2018 23:31:25: 3000000 INFO @ Tue, 09 Oct 2018 23:31:31: 4000000 INFO @ Tue, 09 Oct 2018 23:31:32: 4000000 INFO @ Tue, 09 Oct 2018 23:31:32: 4000000 INFO @ Tue, 09 Oct 2018 23:31:38: 5000000 INFO @ Tue, 09 Oct 2018 23:31:39: 5000000 INFO @ Tue, 09 Oct 2018 23:31:40: 5000000 INFO @ Tue, 09 Oct 2018 23:31:44: 6000000 INFO @ Tue, 09 Oct 2018 23:31:46: 6000000 INFO @ Tue, 09 Oct 2018 23:31:47: 6000000 INFO @ Tue, 09 Oct 2018 23:31:51: 7000000 INFO @ Tue, 09 Oct 2018 23:31:53: 7000000 INFO @ Tue, 09 Oct 2018 23:31:54: 7000000 INFO @ Tue, 09 Oct 2018 23:31:58: 8000000 INFO @ Tue, 09 Oct 2018 23:32:00: 8000000 INFO @ Tue, 09 Oct 2018 23:32:02: 8000000 INFO @ Tue, 09 Oct 2018 23:32:05: 9000000 INFO @ Tue, 09 Oct 2018 23:32:08: 9000000 INFO @ Tue, 09 Oct 2018 23:32:10: 9000000 INFO @ Tue, 09 Oct 2018 23:32:12: 10000000 INFO @ Tue, 09 Oct 2018 23:32:15: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:32:15: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:32:15: #1 total tags in treatment: 10418267 INFO @ Tue, 09 Oct 2018 23:32:15: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:32:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:32:15: 10000000 INFO @ Tue, 09 Oct 2018 23:32:15: #1 tags after filtering in treatment: 10418267 INFO @ Tue, 09 Oct 2018 23:32:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 23:32:15: #1 finished! INFO @ Tue, 09 Oct 2018 23:32:15: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:32:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:32:16: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:32:16: 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 @ Tue, 09 Oct 2018 23:32:16: Process for pairing-model is terminated! cat: SRX4590916.05_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 `SRX4590916.05_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 `SRX4590916.05_*.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 `SRX4590916.05_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 @ Tue, 09 Oct 2018 23:32:17: 10000000 INFO @ Tue, 09 Oct 2018 23:32:18: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:32:18: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:32:18: #1 total tags in treatment: 10418267 INFO @ Tue, 09 Oct 2018 23:32:18: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:32:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:32:18: #1 tags after filtering in treatment: 10418267 INFO @ Tue, 09 Oct 2018 23:32:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 23:32:18: #1 finished! INFO @ Tue, 09 Oct 2018 23:32:18: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:32:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:32:19: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:32:19: 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 @ Tue, 09 Oct 2018 23:32:19: Process for pairing-model is terminated! cat: SRX4590916.10_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 `SRX4590916.10_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 `SRX4590916.10_*.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 `SRX4590916.10_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 @ Tue, 09 Oct 2018 23:32:20: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:32:20: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:32:20: #1 total tags in treatment: 10418267 INFO @ Tue, 09 Oct 2018 23:32:20: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:32:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:32:20: #1 tags after filtering in treatment: 10418267 INFO @ Tue, 09 Oct 2018 23:32:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 23:32:20: #1 finished! INFO @ Tue, 09 Oct 2018 23:32:20: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:32:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:32:21: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:32:21: 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 @ Tue, 09 Oct 2018 23:32:21: Process for pairing-model is terminated! cat: SRX4590916.20_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 `SRX4590916.20_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 `SRX4590916.20_*.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 `SRX4590916.20_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。