Job ID = 11244866 sra ファイルのダウンロード中... Completed: 611959K bytes transferred in 9 seconds (524920K 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: PAIRED fastq に変換中... Read 6331224 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765658/SRR6807381.sra Written 6331224 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765658/SRR6807381.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: 00:08:50 6331224 reads; of these: 6331224 (100.00%) were paired; of these: 225919 (3.57%) aligned concordantly 0 times 5591495 (88.32%) aligned concordantly exactly 1 time 513810 (8.12%) aligned concordantly >1 times ---- 225919 pairs aligned concordantly 0 times; of these: 101505 (44.93%) aligned discordantly 1 time ---- 124414 pairs aligned 0 times concordantly or discordantly; of these: 248828 mates make up the pairs; of these: 154653 (62.15%) aligned 0 times 66763 (26.83%) aligned exactly 1 time 27412 (11.02%) aligned >1 times 98.78% overall alignment rate Time searching: 00:08:50 Overall time: 00:08:50 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 528970 / 6143355 = 0.0861 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 22:28:05: # Command line: callpeak -t SRX3765658.bam -f BAM -g 12100000 -n SRX3765658.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3765658.10 # format = BAM # ChIP-seq file = ['SRX3765658.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 22:28:05: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:28:05: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:28:05: # Command line: callpeak -t SRX3765658.bam -f BAM -g 12100000 -n SRX3765658.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3765658.20 # format = BAM # ChIP-seq file = ['SRX3765658.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 22:28:05: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:28:05: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:28:05: # Command line: callpeak -t SRX3765658.bam -f BAM -g 12100000 -n SRX3765658.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3765658.05 # format = BAM # ChIP-seq file = ['SRX3765658.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 22:28:05: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:28:05: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:28:17: 1000000 INFO @ Tue, 09 Oct 2018 22:28:17: 1000000 INFO @ Tue, 09 Oct 2018 22:28:19: 1000000 INFO @ Tue, 09 Oct 2018 22:28:29: 2000000 INFO @ Tue, 09 Oct 2018 22:28:29: 2000000 INFO @ Tue, 09 Oct 2018 22:28:34: 2000000 INFO @ Tue, 09 Oct 2018 22:28:41: 3000000 INFO @ Tue, 09 Oct 2018 22:28:42: 3000000 INFO @ Tue, 09 Oct 2018 22:28:48: 3000000 INFO @ Tue, 09 Oct 2018 22:28:53: 4000000 INFO @ Tue, 09 Oct 2018 22:28:53: 4000000 INFO @ Tue, 09 Oct 2018 22:29:03: 4000000 INFO @ Tue, 09 Oct 2018 22:29:04: 5000000 INFO @ Tue, 09 Oct 2018 22:29:05: 5000000 INFO @ Tue, 09 Oct 2018 22:29:15: 6000000 INFO @ Tue, 09 Oct 2018 22:29:16: 6000000 INFO @ Tue, 09 Oct 2018 22:29:17: 5000000 INFO @ Tue, 09 Oct 2018 22:29:26: 7000000 INFO @ Tue, 09 Oct 2018 22:29:28: 7000000 INFO @ Tue, 09 Oct 2018 22:29:31: 6000000 INFO @ Tue, 09 Oct 2018 22:29:36: 8000000 INFO @ Tue, 09 Oct 2018 22:29:39: 8000000 INFO @ Tue, 09 Oct 2018 22:29:43: 7000000 INFO @ Tue, 09 Oct 2018 22:29:46: 9000000 INFO @ Tue, 09 Oct 2018 22:29:49: 9000000 INFO @ Tue, 09 Oct 2018 22:29:54: 8000000 INFO @ Tue, 09 Oct 2018 22:29:56: 10000000 INFO @ Tue, 09 Oct 2018 22:30:00: 10000000 INFO @ Tue, 09 Oct 2018 22:30:05: 11000000 INFO @ Tue, 09 Oct 2018 22:30:07: 9000000 INFO @ Tue, 09 Oct 2018 22:30:10: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:30:10: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:30:10: #1 total tags in treatment: 5576896 INFO @ Tue, 09 Oct 2018 22:30:10: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:30:10: #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 22:30:10: #1 tags after filtering in treatment: 3591491 INFO @ Tue, 09 Oct 2018 22:30:10: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 09 Oct 2018 22:30:10: #1 finished! INFO @ Tue, 09 Oct 2018 22:30:10: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:30:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:30:10: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:30:10: 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 22:30:10: Process for pairing-model is terminated! cat: SRX3765658.05_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 `SRX3765658.05_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 `SRX3765658.05_*.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 `SRX3765658.05_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 22:30:10: 11000000 INFO @ Tue, 09 Oct 2018 22:30:15: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:30:15: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:30:15: #1 total tags in treatment: 5576896 INFO @ Tue, 09 Oct 2018 22:30:15: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:30:15: #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 22:30:15: #1 tags after filtering in treatment: 3591491 INFO @ Tue, 09 Oct 2018 22:30:15: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 09 Oct 2018 22:30:15: #1 finished! INFO @ Tue, 09 Oct 2018 22:30:15: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:30:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:30:16: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:30:16: 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 22:30:16: Process for pairing-model is terminated! cat: SRX3765658.10_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 `SRX3765658.10_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 `SRX3765658.10_*.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 `SRX3765658.10_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 22:30:18: 10000000 INFO @ Tue, 09 Oct 2018 22:30:28: 11000000 INFO @ Tue, 09 Oct 2018 22:30:33: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:30:33: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:30:33: #1 total tags in treatment: 5576896 INFO @ Tue, 09 Oct 2018 22:30:33: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:30:33: #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 22:30:33: #1 tags after filtering in treatment: 3591491 INFO @ Tue, 09 Oct 2018 22:30:33: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 09 Oct 2018 22:30:33: #1 finished! INFO @ Tue, 09 Oct 2018 22:30:33: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:30:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:30:33: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:30:33: 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 22:30:33: Process for pairing-model is terminated! cat: SRX3765658.20_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 `SRX3765658.20_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 `SRX3765658.20_*.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 `SRX3765658.20_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。