Job ID = 9161792 sra ファイルのダウンロード中... Completed: 634343K bytes transferred in 8 seconds (580816K bits/sec), in 1 file, 2 directories. 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... Written 14430529 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1044178/SRR2045659.sra Written 14430529 spots total 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: 00:11:57 14430529 reads; of these: 14430529 (100.00%) were paired; of these: 1421431 (9.85%) aligned concordantly 0 times 11182727 (77.49%) aligned concordantly exactly 1 time 1826371 (12.66%) aligned concordantly >1 times ---- 1421431 pairs aligned concordantly 0 times; of these: 583541 (41.05%) aligned discordantly 1 time ---- 837890 pairs aligned 0 times concordantly or discordantly; of these: 1675780 mates make up the pairs; of these: 1120026 (66.84%) aligned 0 times 272892 (16.28%) aligned exactly 1 time 282862 (16.88%) aligned >1 times 96.12% overall alignment rate Time searching: 00:11:57 Overall time: 00:11:57 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] 633715 / 13237775 = 0.0479 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 @ Wed, 28 Jun 2017 04:54:02: # Command line: callpeak -t SRX1044178.bam -f BAM -g 12100000 -n SRX1044178.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1044178.10 # format = BAM # ChIP-seq file = ['SRX1044178.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 @ Wed, 28 Jun 2017 04:54:02: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:54:02: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:54:02: # Command line: callpeak -t SRX1044178.bam -f BAM -g 12100000 -n SRX1044178.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1044178.05 # format = BAM # ChIP-seq file = ['SRX1044178.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 @ Wed, 28 Jun 2017 04:54:02: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:54:02: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:54:02: # Command line: callpeak -t SRX1044178.bam -f BAM -g 12100000 -n SRX1044178.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1044178.20 # format = BAM # ChIP-seq file = ['SRX1044178.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 @ Wed, 28 Jun 2017 04:54:02: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:54:02: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:54:09: 1000000 INFO @ Wed, 28 Jun 2017 04:54:09: 1000000 INFO @ Wed, 28 Jun 2017 04:54:09: 1000000 INFO @ Wed, 28 Jun 2017 04:54:15: 2000000 INFO @ Wed, 28 Jun 2017 04:54:15: 2000000 INFO @ Wed, 28 Jun 2017 04:54:15: 2000000 INFO @ Wed, 28 Jun 2017 04:54:22: 3000000 INFO @ Wed, 28 Jun 2017 04:54:22: 3000000 INFO @ Wed, 28 Jun 2017 04:54:22: 3000000 INFO @ Wed, 28 Jun 2017 04:54:28: 4000000 INFO @ Wed, 28 Jun 2017 04:54:29: 4000000 INFO @ Wed, 28 Jun 2017 04:54:29: 4000000 INFO @ Wed, 28 Jun 2017 04:54:34: 5000000 INFO @ Wed, 28 Jun 2017 04:54:36: 5000000 INFO @ Wed, 28 Jun 2017 04:54:36: 5000000 INFO @ Wed, 28 Jun 2017 04:54:40: 6000000 INFO @ Wed, 28 Jun 2017 04:54:43: 6000000 INFO @ Wed, 28 Jun 2017 04:54:43: 6000000 INFO @ Wed, 28 Jun 2017 04:54:46: 7000000 INFO @ Wed, 28 Jun 2017 04:54:50: 7000000 INFO @ Wed, 28 Jun 2017 04:54:50: 7000000 INFO @ Wed, 28 Jun 2017 04:54:53: 8000000 INFO @ Wed, 28 Jun 2017 04:54:57: 8000000 INFO @ Wed, 28 Jun 2017 04:54:57: 8000000 INFO @ Wed, 28 Jun 2017 04:54:59: 9000000 INFO @ Wed, 28 Jun 2017 04:55:04: 9000000 INFO @ Wed, 28 Jun 2017 04:55:04: 9000000 INFO @ Wed, 28 Jun 2017 04:55:05: 10000000 INFO @ Wed, 28 Jun 2017 04:55:11: 10000000 INFO @ Wed, 28 Jun 2017 04:55:11: 10000000 INFO @ Wed, 28 Jun 2017 04:55:11: 11000000 INFO @ Wed, 28 Jun 2017 04:55:17: 11000000 INFO @ Wed, 28 Jun 2017 04:55:17: 11000000 INFO @ Wed, 28 Jun 2017 04:55:17: 12000000 INFO @ Wed, 28 Jun 2017 04:55:24: 13000000 INFO @ Wed, 28 Jun 2017 04:55:24: 12000000 INFO @ Wed, 28 Jun 2017 04:55:24: 12000000 INFO @ Wed, 28 Jun 2017 04:55:30: 14000000 INFO @ Wed, 28 Jun 2017 04:55:31: 13000000 INFO @ Wed, 28 Jun 2017 04:55:31: 13000000 INFO @ Wed, 28 Jun 2017 04:55:36: 15000000 INFO @ Wed, 28 Jun 2017 04:55:38: 14000000 INFO @ Wed, 28 Jun 2017 04:55:38: 14000000 INFO @ Wed, 28 Jun 2017 04:55:42: 16000000 INFO @ Wed, 28 Jun 2017 04:55:45: 15000000 INFO @ Wed, 28 Jun 2017 04:55:45: 15000000 INFO @ Wed, 28 Jun 2017 04:55:49: 17000000 INFO @ Wed, 28 Jun 2017 04:55:51: 16000000 INFO @ Wed, 28 Jun 2017 04:55:53: 16000000 INFO @ Wed, 28 Jun 2017 04:55:56: 18000000 INFO @ Wed, 28 Jun 2017 04:55:59: 17000000 INFO @ Wed, 28 Jun 2017 04:56:00: 17000000 INFO @ Wed, 28 Jun 2017 04:56:02: 19000000 INFO @ Wed, 28 Jun 2017 04:56:06: 18000000 INFO @ Wed, 28 Jun 2017 04:56:07: 18000000 INFO @ Wed, 28 Jun 2017 04:56:08: 20000000 INFO @ Wed, 28 Jun 2017 04:56:13: 19000000 INFO @ Wed, 28 Jun 2017 04:56:14: 19000000 INFO @ Wed, 28 Jun 2017 04:56:15: 21000000 INFO @ Wed, 28 Jun 2017 04:56:20: 20000000 INFO @ Wed, 28 Jun 2017 04:56:21: 22000000 INFO @ Wed, 28 Jun 2017 04:56:21: 20000000 INFO @ Wed, 28 Jun 2017 04:56:27: 23000000 INFO @ Wed, 28 Jun 2017 04:56:28: 21000000 INFO @ Wed, 28 Jun 2017 04:56:28: 21000000 INFO @ Wed, 28 Jun 2017 04:56:33: 24000000 INFO @ Wed, 28 Jun 2017 04:56:35: 22000000 INFO @ Wed, 28 Jun 2017 04:56:35: 22000000 INFO @ Wed, 28 Jun 2017 04:56:40: 25000000 INFO @ Wed, 28 Jun 2017 04:56:42: 23000000 INFO @ Wed, 28 Jun 2017 04:56:42: 23000000 INFO @ Wed, 28 Jun 2017 04:56:46: 26000000 INFO @ Wed, 28 Jun 2017 04:56:49: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 04:56:49: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 04:56:49: #1 total tags in treatment: 12382443 INFO @ Wed, 28 Jun 2017 04:56:49: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:56:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 04:56:49: 24000000 INFO @ Wed, 28 Jun 2017 04:56:49: 24000000 INFO @ Wed, 28 Jun 2017 04:56:49: #1 tags after filtering in treatment: 8322711 INFO @ Wed, 28 Jun 2017 04:56:49: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 28 Jun 2017 04:56:49: #1 finished! INFO @ Wed, 28 Jun 2017 04:56:49: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:56:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:56:50: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:56:50: 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 @ Wed, 28 Jun 2017 04:56:50: Process for pairing-model is terminated! cat: SRX1044178.10_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 `SRX1044178.10_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 `SRX1044178.10_*.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 `SRX1044178.10_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 @ Wed, 28 Jun 2017 04:56:56: 25000000 INFO @ Wed, 28 Jun 2017 04:56:56: 25000000 INFO @ Wed, 28 Jun 2017 04:57:03: 26000000 INFO @ Wed, 28 Jun 2017 04:57:03: 26000000 INFO @ Wed, 28 Jun 2017 04:57:07: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 04:57:07: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 04:57:07: #1 total tags in treatment: 12382443 INFO @ Wed, 28 Jun 2017 04:57:07: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:57:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 04:57:07: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 04:57:07: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 04:57:07: #1 total tags in treatment: 12382443 INFO @ Wed, 28 Jun 2017 04:57:07: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:57:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 04:57:07: #1 tags after filtering in treatment: 8322711 INFO @ Wed, 28 Jun 2017 04:57:07: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 28 Jun 2017 04:57:07: #1 finished! INFO @ Wed, 28 Jun 2017 04:57:07: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:57:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:57:07: #1 tags after filtering in treatment: 8322711 INFO @ Wed, 28 Jun 2017 04:57:07: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 28 Jun 2017 04:57:07: #1 finished! INFO @ Wed, 28 Jun 2017 04:57:07: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:57:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:57:07: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:57:07: 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 @ Wed, 28 Jun 2017 04:57:07: Process for pairing-model is terminated! cat: SRX1044178.05_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 `SRX1044178.05_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 `SRX1044178.05_*.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 `SRX1044178.05_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 @ Wed, 28 Jun 2017 04:57:07: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:57:07: 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 @ Wed, 28 Jun 2017 04:57:07: Process for pairing-model is terminated! cat: SRX1044178.20_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 `SRX1044178.20_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 `SRX1044178.20_*.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 `SRX1044178.20_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。