Job ID = 11388940 sra ファイルのダウンロード中... Completed: 756241K bytes transferred in 13 seconds (444284K 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 13236547 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017459/SRR8198082.sra Written 13236547 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017459/SRR8198082.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: 00:22:58 13236547 reads; of these: 13236547 (100.00%) were paired; of these: 3149988 (23.80%) aligned concordantly 0 times 8763775 (66.21%) aligned concordantly exactly 1 time 1322784 (9.99%) aligned concordantly >1 times ---- 3149988 pairs aligned concordantly 0 times; of these: 455834 (14.47%) aligned discordantly 1 time ---- 2694154 pairs aligned 0 times concordantly or discordantly; of these: 5388308 mates make up the pairs; of these: 4825105 (89.55%) aligned 0 times 359943 (6.68%) aligned exactly 1 time 203260 (3.77%) aligned >1 times 81.77% overall alignment rate Time searching: 00:22:58 Overall time: 00:22:58 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_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] 1475001 / 10277118 = 0.1435 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 @ Thu, 13 Dec 2018 00:51:49: # Command line: callpeak -t SRX5017459.bam -f BAM -g 12100000 -n SRX5017459.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5017459.05 # format = BAM # ChIP-seq file = ['SRX5017459.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 @ Thu, 13 Dec 2018 00:51:49: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:51:49: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:51:49: # Command line: callpeak -t SRX5017459.bam -f BAM -g 12100000 -n SRX5017459.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5017459.10 # format = BAM # ChIP-seq file = ['SRX5017459.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 @ Thu, 13 Dec 2018 00:51:49: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:51:49: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:51:49: # Command line: callpeak -t SRX5017459.bam -f BAM -g 12100000 -n SRX5017459.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5017459.20 # format = BAM # ChIP-seq file = ['SRX5017459.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 @ Thu, 13 Dec 2018 00:51:49: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:51:49: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:52:00: 1000000 INFO @ Thu, 13 Dec 2018 00:52:00: 1000000 INFO @ Thu, 13 Dec 2018 00:52:00: 1000000 INFO @ Thu, 13 Dec 2018 00:52:12: 2000000 INFO @ Thu, 13 Dec 2018 00:52:13: 2000000 INFO @ Thu, 13 Dec 2018 00:52:13: 2000000 INFO @ Thu, 13 Dec 2018 00:52:25: 3000000 INFO @ Thu, 13 Dec 2018 00:52:25: 3000000 INFO @ Thu, 13 Dec 2018 00:52:28: 3000000 INFO @ Thu, 13 Dec 2018 00:52:38: 4000000 INFO @ Thu, 13 Dec 2018 00:52:38: 4000000 INFO @ Thu, 13 Dec 2018 00:52:42: 4000000 INFO @ Thu, 13 Dec 2018 00:52:50: 5000000 INFO @ Thu, 13 Dec 2018 00:52:51: 5000000 INFO @ Thu, 13 Dec 2018 00:52:56: 5000000 INFO @ Thu, 13 Dec 2018 00:53:00: 6000000 INFO @ Thu, 13 Dec 2018 00:53:05: 6000000 INFO @ Thu, 13 Dec 2018 00:53:09: 7000000 INFO @ Thu, 13 Dec 2018 00:53:09: 6000000 INFO @ Thu, 13 Dec 2018 00:53:17: 7000000 INFO @ Thu, 13 Dec 2018 00:53:17: 8000000 INFO @ Thu, 13 Dec 2018 00:53:20: 7000000 INFO @ Thu, 13 Dec 2018 00:53:25: 9000000 INFO @ Thu, 13 Dec 2018 00:53:29: 8000000 INFO @ Thu, 13 Dec 2018 00:53:31: 8000000 INFO @ Thu, 13 Dec 2018 00:53:34: 10000000 INFO @ Thu, 13 Dec 2018 00:53:41: 9000000 INFO @ Thu, 13 Dec 2018 00:53:42: 9000000 INFO @ Thu, 13 Dec 2018 00:53:42: 11000000 INFO @ Thu, 13 Dec 2018 00:53:50: 12000000 INFO @ Thu, 13 Dec 2018 00:53:53: 10000000 INFO @ Thu, 13 Dec 2018 00:53:54: 10000000 INFO @ Thu, 13 Dec 2018 00:53:59: 13000000 INFO @ Thu, 13 Dec 2018 00:54:05: 11000000 INFO @ Thu, 13 Dec 2018 00:54:08: 11000000 INFO @ Thu, 13 Dec 2018 00:54:08: 14000000 INFO @ Thu, 13 Dec 2018 00:54:16: 12000000 INFO @ Thu, 13 Dec 2018 00:54:17: 15000000 INFO @ Thu, 13 Dec 2018 00:54:20: 12000000 INFO @ Thu, 13 Dec 2018 00:54:26: 16000000 INFO @ Thu, 13 Dec 2018 00:54:28: 13000000 INFO @ Thu, 13 Dec 2018 00:54:32: 13000000 INFO @ Thu, 13 Dec 2018 00:54:35: 17000000 INFO @ Thu, 13 Dec 2018 00:54:40: 14000000 INFO @ Thu, 13 Dec 2018 00:54:44: 18000000 INFO @ Thu, 13 Dec 2018 00:54:44: 14000000 INFO @ Thu, 13 Dec 2018 00:54:49: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:54:49: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:54:49: #1 total tags in treatment: 8624634 INFO @ Thu, 13 Dec 2018 00:54:49: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:54:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:54:50: #1 tags after filtering in treatment: 5568991 INFO @ Thu, 13 Dec 2018 00:54:50: #1 Redundant rate of treatment: 0.35 INFO @ Thu, 13 Dec 2018 00:54:50: #1 finished! INFO @ Thu, 13 Dec 2018 00:54:50: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:54:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:54:50: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 00:54:50: 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 @ Thu, 13 Dec 2018 00:54:50: Process for pairing-model is terminated! cat: SRX5017459.20_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): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017459.20_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 `SRX5017459.20_*.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 `SRX5017459.20_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 @ Thu, 13 Dec 2018 00:54:52: 15000000 INFO @ Thu, 13 Dec 2018 00:54:56: 15000000 INFO @ Thu, 13 Dec 2018 00:55:04: 16000000 INFO @ Thu, 13 Dec 2018 00:55:09: 16000000 INFO @ Thu, 13 Dec 2018 00:55:15: 17000000 INFO @ Thu, 13 Dec 2018 00:55:20: 17000000 INFO @ Thu, 13 Dec 2018 00:55:27: 18000000 INFO @ Thu, 13 Dec 2018 00:55:33: 18000000 INFO @ Thu, 13 Dec 2018 00:55:36: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:55:36: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:55:36: #1 total tags in treatment: 8624634 INFO @ Thu, 13 Dec 2018 00:55:36: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:55:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:55:36: #1 tags after filtering in treatment: 5568991 INFO @ Thu, 13 Dec 2018 00:55:36: #1 Redundant rate of treatment: 0.35 INFO @ Thu, 13 Dec 2018 00:55:36: #1 finished! INFO @ Thu, 13 Dec 2018 00:55:36: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:55:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:55:36: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 00:55:36: 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 @ Thu, 13 Dec 2018 00:55:36: Process for pairing-model is terminated! cat: SRX5017459.10_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017459.10_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 `SRX5017459.10_*.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 `SRX5017459.10_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 @ Thu, 13 Dec 2018 00:55:41: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:55:41: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:55:41: #1 total tags in treatment: 8624634 INFO @ Thu, 13 Dec 2018 00:55:41: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:55:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:55:41: #1 tags after filtering in treatment: 5568991 INFO @ Thu, 13 Dec 2018 00:55:41: #1 Redundant rate of treatment: 0.35 INFO @ Thu, 13 Dec 2018 00:55:41: #1 finished! INFO @ Thu, 13 Dec 2018 00:55:41: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:55:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:55:41: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 00:55:41: 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 @ Thu, 13 Dec 2018 00:55:41: Process for pairing-model is terminated! cat: SRX5017459.05_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): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017459.05_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 `SRX5017459.05_*.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 `SRX5017459.05_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。