Job ID = 11244902 sra ファイルのダウンロード中... Completed: 481278K bytes transferred in 12 seconds (316877K 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 14806290 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554650/SRR7696323.sra Written 14806290 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554650/SRR7696323.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:45 14806290 reads; of these: 14806290 (100.00%) were paired; of these: 2516856 (17.00%) aligned concordantly 0 times 10354438 (69.93%) aligned concordantly exactly 1 time 1934996 (13.07%) aligned concordantly >1 times ---- 2516856 pairs aligned concordantly 0 times; of these: 346574 (13.77%) aligned discordantly 1 time ---- 2170282 pairs aligned 0 times concordantly or discordantly; of these: 4340564 mates make up the pairs; of these: 3804812 (87.66%) aligned 0 times 319168 (7.35%) aligned exactly 1 time 216584 (4.99%) aligned >1 times 87.15% overall alignment rate Time searching: 00:08:46 Overall time: 00:08:46 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] 537273 / 12564857 = 0.0428 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 22:57:14: # Command line: callpeak -t SRX4554650.bam -f BAM -g 12100000 -n SRX4554650.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554650.20 # format = BAM # ChIP-seq file = ['SRX4554650.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 22:57:14: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:57:14: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:57:14: # Command line: callpeak -t SRX4554650.bam -f BAM -g 12100000 -n SRX4554650.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554650.05 # format = BAM # ChIP-seq file = ['SRX4554650.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 22:57:14: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:57:14: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:57:14: # Command line: callpeak -t SRX4554650.bam -f BAM -g 12100000 -n SRX4554650.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554650.10 # format = BAM # ChIP-seq file = ['SRX4554650.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 22:57:14: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:57:14: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:57:20: 1000000 INFO @ Tue, 09 Oct 2018 22:57:20: 1000000 INFO @ Tue, 09 Oct 2018 22:57:20: 1000000 INFO @ Tue, 09 Oct 2018 22:57:25: 2000000 INFO @ Tue, 09 Oct 2018 22:57:25: 2000000 INFO @ Tue, 09 Oct 2018 22:57:25: 2000000 INFO @ Tue, 09 Oct 2018 22:57:30: 3000000 INFO @ Tue, 09 Oct 2018 22:57:30: 3000000 INFO @ Tue, 09 Oct 2018 22:57:30: 3000000 INFO @ Tue, 09 Oct 2018 22:57:35: 4000000 INFO @ Tue, 09 Oct 2018 22:57:36: 4000000 INFO @ Tue, 09 Oct 2018 22:57:36: 4000000 INFO @ Tue, 09 Oct 2018 22:57:41: 5000000 INFO @ Tue, 09 Oct 2018 22:57:41: 5000000 INFO @ Tue, 09 Oct 2018 22:57:41: 5000000 INFO @ Tue, 09 Oct 2018 22:57:46: 6000000 INFO @ Tue, 09 Oct 2018 22:57:46: 6000000 INFO @ Tue, 09 Oct 2018 22:57:46: 6000000 INFO @ Tue, 09 Oct 2018 22:57:51: 7000000 INFO @ Tue, 09 Oct 2018 22:57:51: 7000000 INFO @ Tue, 09 Oct 2018 22:57:52: 7000000 INFO @ Tue, 09 Oct 2018 22:57:56: 8000000 INFO @ Tue, 09 Oct 2018 22:57:56: 8000000 INFO @ Tue, 09 Oct 2018 22:57:57: 8000000 INFO @ Tue, 09 Oct 2018 22:58:02: 9000000 INFO @ Tue, 09 Oct 2018 22:58:02: 9000000 INFO @ Tue, 09 Oct 2018 22:58:02: 9000000 INFO @ Tue, 09 Oct 2018 22:58:07: 10000000 INFO @ Tue, 09 Oct 2018 22:58:07: 10000000 INFO @ Tue, 09 Oct 2018 22:58:08: 10000000 INFO @ Tue, 09 Oct 2018 22:58:12: 11000000 INFO @ Tue, 09 Oct 2018 22:58:12: 11000000 INFO @ Tue, 09 Oct 2018 22:58:13: 11000000 INFO @ Tue, 09 Oct 2018 22:58:17: 12000000 INFO @ Tue, 09 Oct 2018 22:58:18: 12000000 INFO @ Tue, 09 Oct 2018 22:58:18: 12000000 INFO @ Tue, 09 Oct 2018 22:58:23: 13000000 INFO @ Tue, 09 Oct 2018 22:58:23: 13000000 INFO @ Tue, 09 Oct 2018 22:58:24: 13000000 INFO @ Tue, 09 Oct 2018 22:58:28: 14000000 INFO @ Tue, 09 Oct 2018 22:58:28: 14000000 INFO @ Tue, 09 Oct 2018 22:58:29: 14000000 INFO @ Tue, 09 Oct 2018 22:58:33: 15000000 INFO @ Tue, 09 Oct 2018 22:58:34: 15000000 INFO @ Tue, 09 Oct 2018 22:58:34: 15000000 INFO @ Tue, 09 Oct 2018 22:58:38: 16000000 INFO @ Tue, 09 Oct 2018 22:58:39: 16000000 INFO @ Tue, 09 Oct 2018 22:58:40: 16000000 INFO @ Tue, 09 Oct 2018 22:58:43: 17000000 INFO @ Tue, 09 Oct 2018 22:58:44: 17000000 INFO @ Tue, 09 Oct 2018 22:58:45: 17000000 INFO @ Tue, 09 Oct 2018 22:58:49: 18000000 INFO @ Tue, 09 Oct 2018 22:58:49: 18000000 INFO @ Tue, 09 Oct 2018 22:58:50: 18000000 INFO @ Tue, 09 Oct 2018 22:58:54: 19000000 INFO @ Tue, 09 Oct 2018 22:58:55: 19000000 INFO @ Tue, 09 Oct 2018 22:58:56: 19000000 INFO @ Tue, 09 Oct 2018 22:58:59: 20000000 INFO @ Tue, 09 Oct 2018 22:59:00: 20000000 INFO @ Tue, 09 Oct 2018 22:59:02: 20000000 INFO @ Tue, 09 Oct 2018 22:59:05: 21000000 INFO @ Tue, 09 Oct 2018 22:59:06: 21000000 INFO @ Tue, 09 Oct 2018 22:59:07: 21000000 INFO @ Tue, 09 Oct 2018 22:59:10: 22000000 INFO @ Tue, 09 Oct 2018 22:59:11: 22000000 INFO @ Tue, 09 Oct 2018 22:59:13: 22000000 INFO @ Tue, 09 Oct 2018 22:59:15: 23000000 INFO @ Tue, 09 Oct 2018 22:59:16: 23000000 INFO @ Tue, 09 Oct 2018 22:59:18: 23000000 INFO @ Tue, 09 Oct 2018 22:59:20: 24000000 INFO @ Tue, 09 Oct 2018 22:59:22: 24000000 INFO @ Tue, 09 Oct 2018 22:59:24: 24000000 INFO @ Tue, 09 Oct 2018 22:59:24: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:59:24: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:59:24: #1 total tags in treatment: 11763607 INFO @ Tue, 09 Oct 2018 22:59:24: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:59:24: #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 22:59:24: #1 tags after filtering in treatment: 7481203 INFO @ Tue, 09 Oct 2018 22:59:24: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 09 Oct 2018 22:59:24: #1 finished! INFO @ Tue, 09 Oct 2018 22:59:24: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:59:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:59:25: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:59:25: 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 @ Tue, 09 Oct 2018 22:59:25: Process for pairing-model is terminated! cat: SRX4554650.20_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 `SRX4554650.20_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 `SRX4554650.20_*.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 `SRX4554650.20_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 @ Tue, 09 Oct 2018 22:59:26: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:59:26: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:59:26: #1 total tags in treatment: 11763607 INFO @ Tue, 09 Oct 2018 22:59:26: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:59:26: #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 22:59:26: #1 tags after filtering in treatment: 7481203 INFO @ Tue, 09 Oct 2018 22:59:26: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 09 Oct 2018 22:59:26: #1 finished! INFO @ Tue, 09 Oct 2018 22:59:26: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:59:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:59:26: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:59:26: 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 22:59:26: Process for pairing-model is terminated! cat: SRX4554650.10_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 `SRX4554650.10_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 `SRX4554650.10_*.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 `SRX4554650.10_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 22:59:28: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:59:28: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:59:28: #1 total tags in treatment: 11763607 INFO @ Tue, 09 Oct 2018 22:59:28: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:59:28: #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 22:59:28: #1 tags after filtering in treatment: 7481203 INFO @ Tue, 09 Oct 2018 22:59:28: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 09 Oct 2018 22:59:28: #1 finished! INFO @ Tue, 09 Oct 2018 22:59:28: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:59:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:59:28: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:59:28: 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 22:59:28: Process for pairing-model is terminated! cat: SRX4554650.05_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 `SRX4554650.05_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 `SRX4554650.05_*.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 `SRX4554650.05_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。