Job ID = 9160014 sra ファイルのダウンロード中... Completed: 1003001K bytes transferred in 12 seconds (650695K 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 9686704 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2402739/SRR5085184.sra Written 9686704 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: 00:08:57 9686704 reads; of these: 9686704 (100.00%) were paired; of these: 336589 (3.47%) aligned concordantly 0 times 8797177 (90.82%) aligned concordantly exactly 1 time 552938 (5.71%) aligned concordantly >1 times ---- 336589 pairs aligned concordantly 0 times; of these: 45642 (13.56%) aligned discordantly 1 time ---- 290947 pairs aligned 0 times concordantly or discordantly; of these: 581894 mates make up the pairs; of these: 534714 (91.89%) aligned 0 times 38897 (6.68%) aligned exactly 1 time 8283 (1.42%) aligned >1 times 97.24% overall alignment rate Time searching: 00:08:57 Overall time: 00:08:57 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 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] 230601 / 9389509 = 0.0246 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 01:54:40: # Command line: callpeak -t SRX2402739.bam -f BAM -g 12100000 -n SRX2402739.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2402739.05 # format = BAM # ChIP-seq file = ['SRX2402739.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 01:54:40: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:54:40: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:54:40: # Command line: callpeak -t SRX2402739.bam -f BAM -g 12100000 -n SRX2402739.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2402739.20 # format = BAM # ChIP-seq file = ['SRX2402739.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 01:54:40: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:54:40: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:54:40: # Command line: callpeak -t SRX2402739.bam -f BAM -g 12100000 -n SRX2402739.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2402739.10 # format = BAM # ChIP-seq file = ['SRX2402739.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 01:54:40: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:54:40: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:54:48: 1000000 INFO @ Wed, 28 Jun 2017 01:54:48: 1000000 INFO @ Wed, 28 Jun 2017 01:54:48: 1000000 INFO @ Wed, 28 Jun 2017 01:54:56: 2000000 INFO @ Wed, 28 Jun 2017 01:54:56: 2000000 INFO @ Wed, 28 Jun 2017 01:54:57: 2000000 INFO @ Wed, 28 Jun 2017 01:55:04: 3000000 INFO @ Wed, 28 Jun 2017 01:55:04: 3000000 INFO @ Wed, 28 Jun 2017 01:55:06: 3000000 INFO @ Wed, 28 Jun 2017 01:55:13: 4000000 INFO @ Wed, 28 Jun 2017 01:55:13: 4000000 INFO @ Wed, 28 Jun 2017 01:55:14: 4000000 INFO @ Wed, 28 Jun 2017 01:55:20: 5000000 INFO @ Wed, 28 Jun 2017 01:55:20: 5000000 INFO @ Wed, 28 Jun 2017 01:55:22: 5000000 INFO @ Wed, 28 Jun 2017 01:55:28: 6000000 INFO @ Wed, 28 Jun 2017 01:55:28: 6000000 INFO @ Wed, 28 Jun 2017 01:55:30: 6000000 INFO @ Wed, 28 Jun 2017 01:55:35: 7000000 INFO @ Wed, 28 Jun 2017 01:55:35: 7000000 INFO @ Wed, 28 Jun 2017 01:55:38: 7000000 INFO @ Wed, 28 Jun 2017 01:55:42: 8000000 INFO @ Wed, 28 Jun 2017 01:55:42: 8000000 INFO @ Wed, 28 Jun 2017 01:55:46: 8000000 INFO @ Wed, 28 Jun 2017 01:55:49: 9000000 INFO @ Wed, 28 Jun 2017 01:55:49: 9000000 INFO @ Wed, 28 Jun 2017 01:55:53: 9000000 INFO @ Wed, 28 Jun 2017 01:55:56: 10000000 INFO @ Wed, 28 Jun 2017 01:55:56: 10000000 INFO @ Wed, 28 Jun 2017 01:56:01: 10000000 INFO @ Wed, 28 Jun 2017 01:56:02: 11000000 INFO @ Wed, 28 Jun 2017 01:56:03: 11000000 INFO @ Wed, 28 Jun 2017 01:56:07: 11000000 INFO @ Wed, 28 Jun 2017 01:56:09: 12000000 INFO @ Wed, 28 Jun 2017 01:56:09: 12000000 INFO @ Wed, 28 Jun 2017 01:56:14: 12000000 INFO @ Wed, 28 Jun 2017 01:56:15: 13000000 INFO @ Wed, 28 Jun 2017 01:56:15: 13000000 INFO @ Wed, 28 Jun 2017 01:56:20: 13000000 INFO @ Wed, 28 Jun 2017 01:56:22: 14000000 INFO @ Wed, 28 Jun 2017 01:56:22: 14000000 INFO @ Wed, 28 Jun 2017 01:56:27: 14000000 INFO @ Wed, 28 Jun 2017 01:56:28: 15000000 INFO @ Wed, 28 Jun 2017 01:56:29: 15000000 INFO @ Wed, 28 Jun 2017 01:56:33: 15000000 INFO @ Wed, 28 Jun 2017 01:56:34: 16000000 INFO @ Wed, 28 Jun 2017 01:56:35: 16000000 INFO @ Wed, 28 Jun 2017 01:56:40: 16000000 INFO @ Wed, 28 Jun 2017 01:56:41: 17000000 INFO @ Wed, 28 Jun 2017 01:56:42: 17000000 INFO @ Wed, 28 Jun 2017 01:56:46: 17000000 INFO @ Wed, 28 Jun 2017 01:56:47: 18000000 INFO @ Wed, 28 Jun 2017 01:56:48: 18000000 INFO @ Wed, 28 Jun 2017 01:56:50: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 01:56:50: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 01:56:50: #1 total tags in treatment: 9119854 INFO @ Wed, 28 Jun 2017 01:56:50: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:56:50: #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 01:56:50: #1 tags after filtering in treatment: 5043308 INFO @ Wed, 28 Jun 2017 01:56:50: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 28 Jun 2017 01:56:50: #1 finished! INFO @ Wed, 28 Jun 2017 01:56:50: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:56:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:56:50: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 01:56:50: 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 01:56:50: Process for pairing-model is terminated! cat: SRX2402739.20_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 `SRX2402739.20_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 `SRX2402739.20_*.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 `SRX2402739.20_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 01:56:51: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 01:56:51: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 01:56:51: #1 total tags in treatment: 9119854 INFO @ Wed, 28 Jun 2017 01:56:51: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:56:51: #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 01:56:51: #1 tags after filtering in treatment: 5043308 INFO @ Wed, 28 Jun 2017 01:56:51: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 28 Jun 2017 01:56:51: #1 finished! INFO @ Wed, 28 Jun 2017 01:56:51: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:56:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:56:51: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 01:56:51: 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 01:56:51: Process for pairing-model is terminated! cat: SRX2402739.05_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 `SRX2402739.05_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 `SRX2402739.05_*.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 `SRX2402739.05_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 01:56:53: 18000000 INFO @ Wed, 28 Jun 2017 01:56:55: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 01:56:55: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 01:56:55: #1 total tags in treatment: 9119854 INFO @ Wed, 28 Jun 2017 01:56:55: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:56:55: #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 01:56:56: #1 tags after filtering in treatment: 5043308 INFO @ Wed, 28 Jun 2017 01:56:56: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 28 Jun 2017 01:56:56: #1 finished! INFO @ Wed, 28 Jun 2017 01:56:56: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:56:56: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 01:56:56: 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 01:56:56: Process for pairing-model is terminated! cat: SRX2402739.10_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 `SRX2402739.10_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 `SRX2402739.10_*.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 `SRX2402739.10_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。