Job ID = 9302972 sra ファイルのダウンロード中... Completed: 743606K bytes transferred in 17 seconds (347263K 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 13714360 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2961329/SRR5761578.sra Written 13714360 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: 00:10:12 13714360 reads; of these: 13714360 (100.00%) were paired; of these: 1498595 (10.93%) aligned concordantly 0 times 11322691 (82.56%) aligned concordantly exactly 1 time 893074 (6.51%) aligned concordantly >1 times ---- 1498595 pairs aligned concordantly 0 times; of these: 86820 (5.79%) aligned discordantly 1 time ---- 1411775 pairs aligned 0 times concordantly or discordantly; of these: 2823550 mates make up the pairs; of these: 2539892 (89.95%) aligned 0 times 181674 (6.43%) aligned exactly 1 time 101984 (3.61%) aligned >1 times 90.74% overall alignment rate Time searching: 00:10:12 Overall time: 00:10:12 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] 1531428 / 12229688 = 0.1252 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 @ Fri, 28 Jul 2017 11:57:07: # Command line: callpeak -t SRX2961329.bam -f BAM -g 12100000 -n SRX2961329.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2961329.20 # format = BAM # ChIP-seq file = ['SRX2961329.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 @ Fri, 28 Jul 2017 11:57:07: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:57:07: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:57:07: # Command line: callpeak -t SRX2961329.bam -f BAM -g 12100000 -n SRX2961329.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2961329.05 # format = BAM # ChIP-seq file = ['SRX2961329.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 @ Fri, 28 Jul 2017 11:57:07: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:57:07: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:57:07: # Command line: callpeak -t SRX2961329.bam -f BAM -g 12100000 -n SRX2961329.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2961329.10 # format = BAM # ChIP-seq file = ['SRX2961329.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 @ Fri, 28 Jul 2017 11:57:07: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:57:07: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:57:15: 1000000 INFO @ Fri, 28 Jul 2017 11:57:15: 1000000 INFO @ Fri, 28 Jul 2017 11:57:15: 1000000 INFO @ Fri, 28 Jul 2017 11:57:21: 2000000 INFO @ Fri, 28 Jul 2017 11:57:21: 2000000 INFO @ Fri, 28 Jul 2017 11:57:23: 2000000 INFO @ Fri, 28 Jul 2017 11:57:27: 3000000 INFO @ Fri, 28 Jul 2017 11:57:27: 3000000 INFO @ Fri, 28 Jul 2017 11:57:31: 3000000 INFO @ Fri, 28 Jul 2017 11:57:34: 4000000 INFO @ Fri, 28 Jul 2017 11:57:34: 4000000 INFO @ Fri, 28 Jul 2017 11:57:38: 4000000 INFO @ Fri, 28 Jul 2017 11:57:40: 5000000 INFO @ Fri, 28 Jul 2017 11:57:40: 5000000 INFO @ Fri, 28 Jul 2017 11:57:44: 5000000 INFO @ Fri, 28 Jul 2017 11:57:46: 6000000 INFO @ Fri, 28 Jul 2017 11:57:46: 6000000 INFO @ Fri, 28 Jul 2017 11:57:50: 6000000 INFO @ Fri, 28 Jul 2017 11:57:52: 7000000 INFO @ Fri, 28 Jul 2017 11:57:52: 7000000 INFO @ Fri, 28 Jul 2017 11:57:56: 7000000 INFO @ Fri, 28 Jul 2017 11:57:58: 8000000 INFO @ Fri, 28 Jul 2017 11:57:58: 8000000 INFO @ Fri, 28 Jul 2017 11:58:02: 8000000 INFO @ Fri, 28 Jul 2017 11:58:05: 9000000 INFO @ Fri, 28 Jul 2017 11:58:05: 9000000 INFO @ Fri, 28 Jul 2017 11:58:08: 9000000 INFO @ Fri, 28 Jul 2017 11:58:11: 10000000 INFO @ Fri, 28 Jul 2017 11:58:11: 10000000 INFO @ Fri, 28 Jul 2017 11:58:14: 10000000 INFO @ Fri, 28 Jul 2017 11:58:17: 11000000 INFO @ Fri, 28 Jul 2017 11:58:17: 11000000 INFO @ Fri, 28 Jul 2017 11:58:21: 11000000 INFO @ Fri, 28 Jul 2017 11:58:23: 12000000 INFO @ Fri, 28 Jul 2017 11:58:23: 12000000 INFO @ Fri, 28 Jul 2017 11:58:27: 12000000 INFO @ Fri, 28 Jul 2017 11:58:29: 13000000 INFO @ Fri, 28 Jul 2017 11:58:29: 13000000 INFO @ Fri, 28 Jul 2017 11:58:33: 13000000 INFO @ Fri, 28 Jul 2017 11:58:36: 14000000 INFO @ Fri, 28 Jul 2017 11:58:36: 14000000 INFO @ Fri, 28 Jul 2017 11:58:39: 14000000 INFO @ Fri, 28 Jul 2017 11:58:42: 15000000 INFO @ Fri, 28 Jul 2017 11:58:42: 15000000 INFO @ Fri, 28 Jul 2017 11:58:45: 15000000 INFO @ Fri, 28 Jul 2017 11:58:48: 16000000 INFO @ Fri, 28 Jul 2017 11:58:48: 16000000 INFO @ Fri, 28 Jul 2017 11:58:51: 16000000 INFO @ Fri, 28 Jul 2017 11:58:54: 17000000 INFO @ Fri, 28 Jul 2017 11:58:54: 17000000 INFO @ Fri, 28 Jul 2017 11:58:57: 17000000 INFO @ Fri, 28 Jul 2017 11:59:00: 18000000 INFO @ Fri, 28 Jul 2017 11:59:00: 18000000 INFO @ Fri, 28 Jul 2017 11:59:03: 18000000 INFO @ Fri, 28 Jul 2017 11:59:06: 19000000 INFO @ Fri, 28 Jul 2017 11:59:06: 19000000 INFO @ Fri, 28 Jul 2017 11:59:09: 19000000 INFO @ Fri, 28 Jul 2017 11:59:13: 20000000 INFO @ Fri, 28 Jul 2017 11:59:13: 20000000 INFO @ Fri, 28 Jul 2017 11:59:15: 20000000 INFO @ Fri, 28 Jul 2017 11:59:19: 21000000 INFO @ Fri, 28 Jul 2017 11:59:19: 21000000 INFO @ Fri, 28 Jul 2017 11:59:21: 21000000 INFO @ Fri, 28 Jul 2017 11:59:24: #1 tag size is determined as 50 bps INFO @ Fri, 28 Jul 2017 11:59:24: #1 tag size is determined as 50 bps INFO @ Fri, 28 Jul 2017 11:59:24: #1 tag size = 50 INFO @ Fri, 28 Jul 2017 11:59:24: #1 tag size = 50 INFO @ Fri, 28 Jul 2017 11:59:24: #1 total tags in treatment: 10684985 INFO @ Fri, 28 Jul 2017 11:59:24: #1 total tags in treatment: 10684985 INFO @ Fri, 28 Jul 2017 11:59:24: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:59:24: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:59:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 28 Jul 2017 11:59:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 28 Jul 2017 11:59:24: #1 tags after filtering in treatment: 5381770 INFO @ Fri, 28 Jul 2017 11:59:24: #1 Redundant rate of treatment: 0.50 INFO @ Fri, 28 Jul 2017 11:59:24: #1 tags after filtering in treatment: 5381770 INFO @ Fri, 28 Jul 2017 11:59:24: #1 finished! INFO @ Fri, 28 Jul 2017 11:59:24: #1 Redundant rate of treatment: 0.50 INFO @ Fri, 28 Jul 2017 11:59:24: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:59:24: #1 finished! INFO @ Fri, 28 Jul 2017 11:59:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:59:24: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:59:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:59:24: #2 number of paired peaks: 0 WARNING @ Fri, 28 Jul 2017 11:59:24: 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 @ Fri, 28 Jul 2017 11:59:24: Process for pairing-model is terminated! INFO @ Fri, 28 Jul 2017 11:59:24: #2 number of paired peaks: 0 WARNING @ Fri, 28 Jul 2017 11:59:24: 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 @ Fri, 28 Jul 2017 11:59:24: Process for pairing-model is terminated! cat: SRX2961329.20_peaks.narrowPeakcat: SRX2961329.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません : 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): 0 millis pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2961329.05_model.r'rm: cannot remove `SRX2961329.20_model.r': そのようなファイルやディレクトリはありません : 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 `SRX2961329.05_*.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 `SRX2961329.20_*.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 `SRX2961329.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `SRX2961329.20_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 CompletedMACS2peakCalling INFO @ Fri, 28 Jul 2017 11:59:26: #1 tag size is determined as 50 bps INFO @ Fri, 28 Jul 2017 11:59:26: #1 tag size = 50 INFO @ Fri, 28 Jul 2017 11:59:26: #1 total tags in treatment: 10684985 INFO @ Fri, 28 Jul 2017 11:59:26: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:59:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 28 Jul 2017 11:59:26: #1 tags after filtering in treatment: 5381770 INFO @ Fri, 28 Jul 2017 11:59:26: #1 Redundant rate of treatment: 0.50 INFO @ Fri, 28 Jul 2017 11:59:26: #1 finished! INFO @ Fri, 28 Jul 2017 11:59:26: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:59:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:59:26: #2 number of paired peaks: 0 WARNING @ Fri, 28 Jul 2017 11:59:26: 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 @ Fri, 28 Jul 2017 11:59:26: Process for pairing-model is terminated! cat: SRX2961329.10_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 `SRX2961329.10_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 `SRX2961329.10_*.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 `SRX2961329.10_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。