Job ID = 9162947 sra ファイルのダウンロード中... Completed: 828959K bytes transferred in 9 seconds (734657K 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 13683651 spots for /home/okishinya/chipatlas/results/sacCer3/SRX404647/SRR1068587.sra Written 13683651 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: 00:10:20 13683651 reads; of these: 13683651 (100.00%) were paired; of these: 2816932 (20.59%) aligned concordantly 0 times 8414092 (61.49%) aligned concordantly exactly 1 time 2452627 (17.92%) aligned concordantly >1 times ---- 2816932 pairs aligned concordantly 0 times; of these: 12482 (0.44%) aligned discordantly 1 time ---- 2804450 pairs aligned 0 times concordantly or discordantly; of these: 5608900 mates make up the pairs; of these: 5363209 (95.62%) aligned 0 times 150498 (2.68%) aligned exactly 1 time 95193 (1.70%) aligned >1 times 80.40% overall alignment rate Time searching: 00:10:20 Overall time: 00:10:20 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] 487479 / 10873943 = 0.0448 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 09:42:13: # Command line: callpeak -t SRX404647.bam -f BAM -g 12100000 -n SRX404647.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX404647.20 # format = BAM # ChIP-seq file = ['SRX404647.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 09:42:13: #1 read tag files... INFO @ Wed, 28 Jun 2017 09:42:13: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 09:42:13: # Command line: callpeak -t SRX404647.bam -f BAM -g 12100000 -n SRX404647.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX404647.10 # format = BAM # ChIP-seq file = ['SRX404647.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 09:42:13: #1 read tag files... INFO @ Wed, 28 Jun 2017 09:42:13: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 09:42:13: # Command line: callpeak -t SRX404647.bam -f BAM -g 12100000 -n SRX404647.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX404647.05 # format = BAM # ChIP-seq file = ['SRX404647.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 09:42:13: #1 read tag files... INFO @ Wed, 28 Jun 2017 09:42:13: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 09:42:18: 1000000 INFO @ Wed, 28 Jun 2017 09:42:18: 1000000 INFO @ Wed, 28 Jun 2017 09:42:19: 1000000 INFO @ Wed, 28 Jun 2017 09:42:24: 2000000 INFO @ Wed, 28 Jun 2017 09:42:24: 2000000 INFO @ Wed, 28 Jun 2017 09:42:25: 2000000 INFO @ Wed, 28 Jun 2017 09:42:29: 3000000 INFO @ Wed, 28 Jun 2017 09:42:30: 3000000 INFO @ Wed, 28 Jun 2017 09:42:31: 3000000 INFO @ Wed, 28 Jun 2017 09:42:35: 4000000 INFO @ Wed, 28 Jun 2017 09:42:35: 4000000 INFO @ Wed, 28 Jun 2017 09:42:37: 4000000 INFO @ Wed, 28 Jun 2017 09:42:41: 5000000 INFO @ Wed, 28 Jun 2017 09:42:41: 5000000 INFO @ Wed, 28 Jun 2017 09:42:43: 5000000 INFO @ Wed, 28 Jun 2017 09:42:46: 6000000 INFO @ Wed, 28 Jun 2017 09:42:47: 6000000 INFO @ Wed, 28 Jun 2017 09:42:48: 6000000 INFO @ Wed, 28 Jun 2017 09:42:52: 7000000 INFO @ Wed, 28 Jun 2017 09:42:52: 7000000 INFO @ Wed, 28 Jun 2017 09:42:54: 7000000 INFO @ Wed, 28 Jun 2017 09:42:58: 8000000 INFO @ Wed, 28 Jun 2017 09:42:58: 8000000 INFO @ Wed, 28 Jun 2017 09:43:00: 8000000 INFO @ Wed, 28 Jun 2017 09:43:03: 9000000 INFO @ Wed, 28 Jun 2017 09:43:04: 9000000 INFO @ Wed, 28 Jun 2017 09:43:06: 9000000 INFO @ Wed, 28 Jun 2017 09:43:09: 10000000 INFO @ Wed, 28 Jun 2017 09:43:09: 10000000 INFO @ Wed, 28 Jun 2017 09:43:12: 10000000 INFO @ Wed, 28 Jun 2017 09:43:15: 11000000 INFO @ Wed, 28 Jun 2017 09:43:15: 11000000 INFO @ Wed, 28 Jun 2017 09:43:18: 11000000 INFO @ Wed, 28 Jun 2017 09:43:20: 12000000 INFO @ Wed, 28 Jun 2017 09:43:20: 12000000 INFO @ Wed, 28 Jun 2017 09:43:24: 12000000 INFO @ Wed, 28 Jun 2017 09:43:25: 13000000 INFO @ Wed, 28 Jun 2017 09:43:25: 13000000 INFO @ Wed, 28 Jun 2017 09:43:29: 13000000 INFO @ Wed, 28 Jun 2017 09:43:31: 14000000 INFO @ Wed, 28 Jun 2017 09:43:31: 14000000 INFO @ Wed, 28 Jun 2017 09:43:35: 14000000 INFO @ Wed, 28 Jun 2017 09:43:36: 15000000 INFO @ Wed, 28 Jun 2017 09:43:36: 15000000 INFO @ Wed, 28 Jun 2017 09:43:41: 15000000 INFO @ Wed, 28 Jun 2017 09:43:42: 16000000 INFO @ Wed, 28 Jun 2017 09:43:42: 16000000 INFO @ Wed, 28 Jun 2017 09:43:47: 16000000 INFO @ Wed, 28 Jun 2017 09:43:47: 17000000 INFO @ Wed, 28 Jun 2017 09:43:47: 17000000 INFO @ Wed, 28 Jun 2017 09:43:53: 18000000 INFO @ Wed, 28 Jun 2017 09:43:53: 18000000 INFO @ Wed, 28 Jun 2017 09:43:53: 17000000 INFO @ Wed, 28 Jun 2017 09:43:58: 19000000 INFO @ Wed, 28 Jun 2017 09:43:58: 19000000 INFO @ Wed, 28 Jun 2017 09:43:59: 18000000 INFO @ Wed, 28 Jun 2017 09:44:03: 20000000 INFO @ Wed, 28 Jun 2017 09:44:03: 20000000 INFO @ Wed, 28 Jun 2017 09:44:05: 19000000 INFO @ Wed, 28 Jun 2017 09:44:09: 21000000 INFO @ Wed, 28 Jun 2017 09:44:09: 21000000 INFO @ Wed, 28 Jun 2017 09:44:09: #1 tag size is determined as 45 bps INFO @ Wed, 28 Jun 2017 09:44:09: #1 tag size = 45 INFO @ Wed, 28 Jun 2017 09:44:09: #1 total tags in treatment: 10379379 INFO @ Wed, 28 Jun 2017 09:44:09: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 09:44:09: #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 09:44:09: #1 tag size is determined as 45 bps INFO @ Wed, 28 Jun 2017 09:44:09: #1 tag size = 45 INFO @ Wed, 28 Jun 2017 09:44:09: #1 total tags in treatment: 10379379 INFO @ Wed, 28 Jun 2017 09:44:09: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 09:44:09: #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 09:44:09: #1 tags after filtering in treatment: 6835310 INFO @ Wed, 28 Jun 2017 09:44:09: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 28 Jun 2017 09:44:09: #1 finished! INFO @ Wed, 28 Jun 2017 09:44:09: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 09:44:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 09:44:09: #1 tags after filtering in treatment: 6835310 INFO @ Wed, 28 Jun 2017 09:44:09: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 28 Jun 2017 09:44:09: #1 finished! INFO @ Wed, 28 Jun 2017 09:44:09: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 09:44:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 09:44:10: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 09:44:10: 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 @ Wed, 28 Jun 2017 09:44:10: Process for pairing-model is terminated! cat: SRX404647.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Wed, 28 Jun 2017 09:44:10: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 09:44:10: 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 @ Wed, 28 Jun 2017 09:44:10: Process for pairing-model is terminated! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX404647.05_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 `SRX404647.05_*.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 `SRX404647.05_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 cat: SRX404647.20_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 `SRX404647.20_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 `SRX404647.20_*.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 `SRX404647.20_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 @ Wed, 28 Jun 2017 09:44:10: 20000000 INFO @ Wed, 28 Jun 2017 09:44:16: 21000000 INFO @ Wed, 28 Jun 2017 09:44:16: #1 tag size is determined as 45 bps INFO @ Wed, 28 Jun 2017 09:44:16: #1 tag size = 45 INFO @ Wed, 28 Jun 2017 09:44:16: #1 total tags in treatment: 10379379 INFO @ Wed, 28 Jun 2017 09:44:16: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 09:44:16: #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 09:44:17: #1 tags after filtering in treatment: 6835310 INFO @ Wed, 28 Jun 2017 09:44:17: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 28 Jun 2017 09:44:17: #1 finished! INFO @ Wed, 28 Jun 2017 09:44:17: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 09:44:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 09:44:17: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 09:44:17: 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 @ Wed, 28 Jun 2017 09:44:17: Process for pairing-model is terminated! cat: SRX404647.10_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 `SRX404647.10_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 `SRX404647.10_*.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 `SRX404647.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。