Job ID = 11244860 sra ファイルのダウンロード中... Completed: 926685K bytes transferred in 11 seconds (650116K 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 9566683 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765653/SRR6807376.sra Written 9566683 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765653/SRR6807376.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: 00:14:23 9566683 reads; of these: 9566683 (100.00%) were paired; of these: 227765 (2.38%) aligned concordantly 0 times 8452443 (88.35%) aligned concordantly exactly 1 time 886475 (9.27%) aligned concordantly >1 times ---- 227765 pairs aligned concordantly 0 times; of these: 58497 (25.68%) aligned discordantly 1 time ---- 169268 pairs aligned 0 times concordantly or discordantly; of these: 338536 mates make up the pairs; of these: 231931 (68.51%) aligned 0 times 82942 (24.50%) aligned exactly 1 time 23663 (6.99%) aligned >1 times 98.79% overall alignment rate Time searching: 00:14:23 Overall time: 00:14:23 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] 848036 / 9307403 = 0.0911 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 22:35:33: # Command line: callpeak -t SRX3765653.bam -f BAM -g 12100000 -n SRX3765653.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3765653.05 # format = BAM # ChIP-seq file = ['SRX3765653.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 22:35:33: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:35:33: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:35:33: # Command line: callpeak -t SRX3765653.bam -f BAM -g 12100000 -n SRX3765653.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3765653.20 # format = BAM # ChIP-seq file = ['SRX3765653.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 22:35:33: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:35:33: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:35:33: # Command line: callpeak -t SRX3765653.bam -f BAM -g 12100000 -n SRX3765653.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3765653.10 # format = BAM # ChIP-seq file = ['SRX3765653.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 22:35:33: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:35:33: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:35:41: 1000000 INFO @ Tue, 09 Oct 2018 22:35:43: 1000000 INFO @ Tue, 09 Oct 2018 22:35:43: 1000000 INFO @ Tue, 09 Oct 2018 22:35:50: 2000000 INFO @ Tue, 09 Oct 2018 22:35:53: 2000000 INFO @ Tue, 09 Oct 2018 22:35:53: 2000000 INFO @ Tue, 09 Oct 2018 22:35:58: 3000000 INFO @ Tue, 09 Oct 2018 22:36:02: 3000000 INFO @ Tue, 09 Oct 2018 22:36:02: 3000000 INFO @ Tue, 09 Oct 2018 22:36:06: 4000000 INFO @ Tue, 09 Oct 2018 22:36:12: 4000000 INFO @ Tue, 09 Oct 2018 22:36:12: 4000000 INFO @ Tue, 09 Oct 2018 22:36:15: 5000000 INFO @ Tue, 09 Oct 2018 22:36:21: 5000000 INFO @ Tue, 09 Oct 2018 22:36:21: 5000000 INFO @ Tue, 09 Oct 2018 22:36:23: 6000000 INFO @ Tue, 09 Oct 2018 22:36:31: 6000000 INFO @ Tue, 09 Oct 2018 22:36:31: 6000000 INFO @ Tue, 09 Oct 2018 22:36:32: 7000000 INFO @ Tue, 09 Oct 2018 22:36:40: 8000000 INFO @ Tue, 09 Oct 2018 22:36:40: 7000000 INFO @ Tue, 09 Oct 2018 22:36:40: 7000000 INFO @ Tue, 09 Oct 2018 22:36:48: 9000000 INFO @ Tue, 09 Oct 2018 22:36:50: 8000000 INFO @ Tue, 09 Oct 2018 22:36:50: 8000000 INFO @ Tue, 09 Oct 2018 22:36:56: 10000000 INFO @ Tue, 09 Oct 2018 22:36:59: 9000000 INFO @ Tue, 09 Oct 2018 22:36:59: 9000000 INFO @ Tue, 09 Oct 2018 22:37:05: 11000000 INFO @ Tue, 09 Oct 2018 22:37:09: 10000000 INFO @ Tue, 09 Oct 2018 22:37:09: 10000000 INFO @ Tue, 09 Oct 2018 22:37:13: 12000000 INFO @ Tue, 09 Oct 2018 22:37:18: 11000000 INFO @ Tue, 09 Oct 2018 22:37:18: 11000000 INFO @ Tue, 09 Oct 2018 22:37:21: 13000000 INFO @ Tue, 09 Oct 2018 22:37:28: 12000000 INFO @ Tue, 09 Oct 2018 22:37:28: 12000000 INFO @ Tue, 09 Oct 2018 22:37:30: 14000000 INFO @ Tue, 09 Oct 2018 22:37:37: 13000000 INFO @ Tue, 09 Oct 2018 22:37:37: 13000000 INFO @ Tue, 09 Oct 2018 22:37:38: 15000000 INFO @ Tue, 09 Oct 2018 22:37:46: 16000000 INFO @ Tue, 09 Oct 2018 22:37:47: 14000000 INFO @ Tue, 09 Oct 2018 22:37:47: 14000000 INFO @ Tue, 09 Oct 2018 22:37:55: 17000000 INFO @ Tue, 09 Oct 2018 22:37:56: 15000000 INFO @ Tue, 09 Oct 2018 22:37:56: 15000000 INFO @ Tue, 09 Oct 2018 22:37:57: #1 tag size is determined as 101 bps INFO @ Tue, 09 Oct 2018 22:37:57: #1 tag size = 101 INFO @ Tue, 09 Oct 2018 22:37:57: #1 total tags in treatment: 8491671 INFO @ Tue, 09 Oct 2018 22:37:57: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:37:57: #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 22:37:57: #1 tags after filtering in treatment: 5064860 INFO @ Tue, 09 Oct 2018 22:37:57: #1 Redundant rate of treatment: 0.40 INFO @ Tue, 09 Oct 2018 22:37:57: #1 finished! INFO @ Tue, 09 Oct 2018 22:37:57: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:37:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:37:57: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:37:57: 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 22:37:57: Process for pairing-model is terminated! cat: SRX3765653.05_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 `SRX3765653.05_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 `SRX3765653.05_*.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 `SRX3765653.05_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 22:38:05: 16000000 INFO @ Tue, 09 Oct 2018 22:38:05: 16000000 INFO @ Tue, 09 Oct 2018 22:38:15: 17000000 INFO @ Tue, 09 Oct 2018 22:38:15: 17000000 INFO @ Tue, 09 Oct 2018 22:38:17: #1 tag size is determined as 101 bps INFO @ Tue, 09 Oct 2018 22:38:17: #1 tag size is determined as 101 bps INFO @ Tue, 09 Oct 2018 22:38:17: #1 tag size = 101 INFO @ Tue, 09 Oct 2018 22:38:17: #1 tag size = 101 INFO @ Tue, 09 Oct 2018 22:38:17: #1 total tags in treatment: 8491671 INFO @ Tue, 09 Oct 2018 22:38:17: #1 total tags in treatment: 8491671 INFO @ Tue, 09 Oct 2018 22:38:17: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:38:17: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:38:17: #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 22:38:17: #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 22:38:17: #1 tags after filtering in treatment: 5064860 INFO @ Tue, 09 Oct 2018 22:38:17: #1 tags after filtering in treatment: 5064860 INFO @ Tue, 09 Oct 2018 22:38:17: #1 Redundant rate of treatment: 0.40 INFO @ Tue, 09 Oct 2018 22:38:17: #1 Redundant rate of treatment: 0.40 INFO @ Tue, 09 Oct 2018 22:38:17: #1 finished! INFO @ Tue, 09 Oct 2018 22:38:17: #1 finished! INFO @ Tue, 09 Oct 2018 22:38:17: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:38:17: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:38:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:38:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:38:17: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:38:17: 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 22:38:17: Process for pairing-model is terminated! INFO @ Tue, 09 Oct 2018 22:38:17: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:38:17: 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 22:38:17: Process for pairing-model is terminated! cat: SRX3765653.10_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: SRX3765653.20_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 `SRX3765653.10_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 `SRX3765653.10_*.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 `SRX3765653.10_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 `SRX3765653.20_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 `SRX3765653.20_*.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 `SRX3765653.20_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。