Job ID = 9161919 sra ファイルのダウンロード中... Completed: 2035893K bytes transferred in 16 seconds (1034963K 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 15475838 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1406641/SRR2889314.sra Written 15475838 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: 00:16:07 15475838 reads; of these: 15475838 (100.00%) were paired; of these: 5244555 (33.89%) aligned concordantly 0 times 8444054 (54.56%) aligned concordantly exactly 1 time 1787229 (11.55%) aligned concordantly >1 times ---- 5244555 pairs aligned concordantly 0 times; of these: 723508 (13.80%) aligned discordantly 1 time ---- 4521047 pairs aligned 0 times concordantly or discordantly; of these: 9042094 mates make up the pairs; of these: 8466195 (93.63%) aligned 0 times 187420 (2.07%) aligned exactly 1 time 388479 (4.30%) aligned >1 times 72.65% overall alignment rate Time searching: 00:16:07 Overall time: 00:16:07 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] 342110 / 10886633 = 0.0314 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 05:25:55: # Command line: callpeak -t SRX1406641.bam -f BAM -g 12100000 -n SRX1406641.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1406641.20 # format = BAM # ChIP-seq file = ['SRX1406641.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 05:25:55: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:25:55: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:25:55: # Command line: callpeak -t SRX1406641.bam -f BAM -g 12100000 -n SRX1406641.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1406641.10 # format = BAM # ChIP-seq file = ['SRX1406641.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 05:25:55: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:25:55: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:25:55: # Command line: callpeak -t SRX1406641.bam -f BAM -g 12100000 -n SRX1406641.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1406641.05 # format = BAM # ChIP-seq file = ['SRX1406641.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 05:25:55: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:25:55: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:26:03: 1000000 INFO @ Wed, 28 Jun 2017 05:26:04: 1000000 INFO @ Wed, 28 Jun 2017 05:26:04: 1000000 INFO @ Wed, 28 Jun 2017 05:26:12: 2000000 INFO @ Wed, 28 Jun 2017 05:26:13: 2000000 INFO @ Wed, 28 Jun 2017 05:26:13: 2000000 INFO @ Wed, 28 Jun 2017 05:26:20: 3000000 INFO @ Wed, 28 Jun 2017 05:26:23: 3000000 INFO @ Wed, 28 Jun 2017 05:26:23: 3000000 INFO @ Wed, 28 Jun 2017 05:26:29: 4000000 INFO @ Wed, 28 Jun 2017 05:26:33: 4000000 INFO @ Wed, 28 Jun 2017 05:26:33: 4000000 INFO @ Wed, 28 Jun 2017 05:26:37: 5000000 INFO @ Wed, 28 Jun 2017 05:26:44: 5000000 INFO @ Wed, 28 Jun 2017 05:26:44: 5000000 INFO @ Wed, 28 Jun 2017 05:26:46: 6000000 INFO @ Wed, 28 Jun 2017 05:26:54: 7000000 INFO @ Wed, 28 Jun 2017 05:26:56: 6000000 INFO @ Wed, 28 Jun 2017 05:26:56: 6000000 INFO @ Wed, 28 Jun 2017 05:27:03: 8000000 INFO @ Wed, 28 Jun 2017 05:27:07: 7000000 INFO @ Wed, 28 Jun 2017 05:27:07: 7000000 INFO @ Wed, 28 Jun 2017 05:27:12: 9000000 INFO @ Wed, 28 Jun 2017 05:27:16: 8000000 INFO @ Wed, 28 Jun 2017 05:27:16: 8000000 INFO @ Wed, 28 Jun 2017 05:27:22: 10000000 INFO @ Wed, 28 Jun 2017 05:27:26: 9000000 INFO @ Wed, 28 Jun 2017 05:27:26: 9000000 INFO @ Wed, 28 Jun 2017 05:27:31: 11000000 INFO @ Wed, 28 Jun 2017 05:27:35: 10000000 INFO @ Wed, 28 Jun 2017 05:27:35: 10000000 INFO @ Wed, 28 Jun 2017 05:27:39: 12000000 INFO @ Wed, 28 Jun 2017 05:27:45: 11000000 INFO @ Wed, 28 Jun 2017 05:27:45: 11000000 INFO @ Wed, 28 Jun 2017 05:27:48: 13000000 INFO @ Wed, 28 Jun 2017 05:27:54: 12000000 INFO @ Wed, 28 Jun 2017 05:27:54: 12000000 INFO @ Wed, 28 Jun 2017 05:27:56: 14000000 INFO @ Wed, 28 Jun 2017 05:28:04: 13000000 INFO @ Wed, 28 Jun 2017 05:28:04: 13000000 INFO @ Wed, 28 Jun 2017 05:28:04: 15000000 INFO @ Wed, 28 Jun 2017 05:28:13: 16000000 INFO @ Wed, 28 Jun 2017 05:28:13: 14000000 INFO @ Wed, 28 Jun 2017 05:28:13: 14000000 INFO @ Wed, 28 Jun 2017 05:28:21: 17000000 INFO @ Wed, 28 Jun 2017 05:28:22: 15000000 INFO @ Wed, 28 Jun 2017 05:28:22: 15000000 INFO @ Wed, 28 Jun 2017 05:28:30: 18000000 INFO @ Wed, 28 Jun 2017 05:28:32: 16000000 INFO @ Wed, 28 Jun 2017 05:28:32: 16000000 INFO @ Wed, 28 Jun 2017 05:28:38: 19000000 INFO @ Wed, 28 Jun 2017 05:28:42: 17000000 INFO @ Wed, 28 Jun 2017 05:28:42: 17000000 INFO @ Wed, 28 Jun 2017 05:28:46: 20000000 INFO @ Wed, 28 Jun 2017 05:28:51: 18000000 INFO @ Wed, 28 Jun 2017 05:28:51: 18000000 INFO @ Wed, 28 Jun 2017 05:28:55: 21000000 INFO @ Wed, 28 Jun 2017 05:29:00: 19000000 INFO @ Wed, 28 Jun 2017 05:29:00: 19000000 INFO @ Wed, 28 Jun 2017 05:29:01: #1 tag size is determined as 100 bps INFO @ Wed, 28 Jun 2017 05:29:01: #1 tag size = 100 INFO @ Wed, 28 Jun 2017 05:29:01: #1 total tags in treatment: 9902461 INFO @ Wed, 28 Jun 2017 05:29:01: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:29:01: #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 05:29:01: #1 tags after filtering in treatment: 7236381 INFO @ Wed, 28 Jun 2017 05:29:01: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 28 Jun 2017 05:29:01: #1 finished! INFO @ Wed, 28 Jun 2017 05:29:01: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:29:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:29:02: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:29:02: 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 05:29:02: Process for pairing-model is terminated! cat: SRX1406641.05_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 `SRX1406641.05_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 `SRX1406641.05_*.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 `SRX1406641.05_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 05:29:10: 20000000 INFO @ Wed, 28 Jun 2017 05:29:10: 20000000 INFO @ Wed, 28 Jun 2017 05:29:19: 21000000 INFO @ Wed, 28 Jun 2017 05:29:19: 21000000 INFO @ Wed, 28 Jun 2017 05:29:26: #1 tag size is determined as 100 bps INFO @ Wed, 28 Jun 2017 05:29:26: #1 tag size = 100 INFO @ Wed, 28 Jun 2017 05:29:26: #1 total tags in treatment: 9902461 INFO @ Wed, 28 Jun 2017 05:29:26: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:29:26: #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 05:29:26: #1 tag size is determined as 100 bps INFO @ Wed, 28 Jun 2017 05:29:26: #1 tag size = 100 INFO @ Wed, 28 Jun 2017 05:29:26: #1 total tags in treatment: 9902461 INFO @ Wed, 28 Jun 2017 05:29:26: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:29:26: #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 05:29:26: #1 tags after filtering in treatment: 7236381 INFO @ Wed, 28 Jun 2017 05:29:26: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 28 Jun 2017 05:29:26: #1 finished! INFO @ Wed, 28 Jun 2017 05:29:26: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:29:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:29:26: #1 tags after filtering in treatment: 7236381 INFO @ Wed, 28 Jun 2017 05:29:26: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 28 Jun 2017 05:29:26: #1 finished! INFO @ Wed, 28 Jun 2017 05:29:26: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:29:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:29:27: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:29:27: 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 05:29:27: Process for pairing-model is terminated! INFO @ Wed, 28 Jun 2017 05:29:27: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:29:27: 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 05:29:27: Process for pairing-model is terminated! cat: SRX1406641.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX1406641.10_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) pass1 - making usageList (0 chroms): 1 millis rm: cannot remove `SRX1406641.20_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: needLargeMem: trying to allocate 0 bytes (limit: 17179869184)cannot remove `SRX1406641.20_*.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 `SRX1406641.20_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 rm: cannot remove `SRX1406641.10_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 `SRX1406641.10_*.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 `SRX1406641.10_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。