Job ID = 9161976 sra ファイルのダウンロード中... Completed: 1635041K bytes transferred in 18 seconds (732534K 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 27714859 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423708/SRR2930997.sra Written 27714859 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: 00:12:06 27714859 reads; of these: 27714859 (100.00%) were paired; of these: 14204890 (51.25%) aligned concordantly 0 times 12470536 (45.00%) aligned concordantly exactly 1 time 1039433 (3.75%) aligned concordantly >1 times ---- 14204890 pairs aligned concordantly 0 times; of these: 233409 (1.64%) aligned discordantly 1 time ---- 13971481 pairs aligned 0 times concordantly or discordantly; of these: 27942962 mates make up the pairs; of these: 27441029 (98.20%) aligned 0 times 408788 (1.46%) aligned exactly 1 time 93145 (0.33%) aligned >1 times 50.49% overall alignment rate Time searching: 00:12:06 Overall time: 00:12:06 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] 5387020 / 13722236 = 0.3926 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 05:30:28: # Command line: callpeak -t SRX1423708.bam -f BAM -g 12100000 -n SRX1423708.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423708.10 # format = BAM # ChIP-seq file = ['SRX1423708.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 05:30:28: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:30:28: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:30:28: # Command line: callpeak -t SRX1423708.bam -f BAM -g 12100000 -n SRX1423708.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423708.05 # format = BAM # ChIP-seq file = ['SRX1423708.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 05:30:28: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:30:28: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:30:28: # Command line: callpeak -t SRX1423708.bam -f BAM -g 12100000 -n SRX1423708.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423708.20 # format = BAM # ChIP-seq file = ['SRX1423708.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 05:30:28: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:30:28: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:30:34: 1000000 INFO @ Wed, 28 Jun 2017 05:30:35: 1000000 INFO @ Wed, 28 Jun 2017 05:30:35: 1000000 INFO @ Wed, 28 Jun 2017 05:30:40: 2000000 INFO @ Wed, 28 Jun 2017 05:30:41: 2000000 INFO @ Wed, 28 Jun 2017 05:30:41: 2000000 INFO @ Wed, 28 Jun 2017 05:30:46: 3000000 INFO @ Wed, 28 Jun 2017 05:30:47: 3000000 INFO @ Wed, 28 Jun 2017 05:30:47: 3000000 INFO @ Wed, 28 Jun 2017 05:30:52: 4000000 INFO @ Wed, 28 Jun 2017 05:30:53: 4000000 INFO @ Wed, 28 Jun 2017 05:30:54: 4000000 INFO @ Wed, 28 Jun 2017 05:30:59: 5000000 INFO @ Wed, 28 Jun 2017 05:30:59: 5000000 INFO @ Wed, 28 Jun 2017 05:31:00: 5000000 INFO @ Wed, 28 Jun 2017 05:31:05: 6000000 INFO @ Wed, 28 Jun 2017 05:31:05: 6000000 INFO @ Wed, 28 Jun 2017 05:31:06: 6000000 INFO @ Wed, 28 Jun 2017 05:31:11: 7000000 INFO @ Wed, 28 Jun 2017 05:31:12: 7000000 INFO @ Wed, 28 Jun 2017 05:31:13: 7000000 INFO @ Wed, 28 Jun 2017 05:31:17: 8000000 INFO @ Wed, 28 Jun 2017 05:31:18: 8000000 INFO @ Wed, 28 Jun 2017 05:31:19: 8000000 INFO @ Wed, 28 Jun 2017 05:31:24: 9000000 INFO @ Wed, 28 Jun 2017 05:31:24: 9000000 INFO @ Wed, 28 Jun 2017 05:31:25: 9000000 INFO @ Wed, 28 Jun 2017 05:31:30: 10000000 INFO @ Wed, 28 Jun 2017 05:31:31: 10000000 INFO @ Wed, 28 Jun 2017 05:31:32: 10000000 INFO @ Wed, 28 Jun 2017 05:31:36: 11000000 INFO @ Wed, 28 Jun 2017 05:31:37: 11000000 INFO @ Wed, 28 Jun 2017 05:31:39: 11000000 INFO @ Wed, 28 Jun 2017 05:31:42: 12000000 INFO @ Wed, 28 Jun 2017 05:31:43: 12000000 INFO @ Wed, 28 Jun 2017 05:31:45: 12000000 INFO @ Wed, 28 Jun 2017 05:31:49: 13000000 INFO @ Wed, 28 Jun 2017 05:31:50: 13000000 INFO @ Wed, 28 Jun 2017 05:31:52: 13000000 INFO @ Wed, 28 Jun 2017 05:31:55: 14000000 INFO @ Wed, 28 Jun 2017 05:31:56: 14000000 INFO @ Wed, 28 Jun 2017 05:31:58: 14000000 INFO @ Wed, 28 Jun 2017 05:32:01: 15000000 INFO @ Wed, 28 Jun 2017 05:32:02: 15000000 INFO @ Wed, 28 Jun 2017 05:32:04: 15000000 INFO @ Wed, 28 Jun 2017 05:32:07: 16000000 INFO @ Wed, 28 Jun 2017 05:32:09: 16000000 INFO @ Wed, 28 Jun 2017 05:32:11: 16000000 INFO @ Wed, 28 Jun 2017 05:32:14: 17000000 INFO @ Wed, 28 Jun 2017 05:32:15: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:32:15: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:32:15: #1 total tags in treatment: 8155653 INFO @ Wed, 28 Jun 2017 05:32:15: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:32:15: #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 05:32:15: 17000000 INFO @ Wed, 28 Jun 2017 05:32:15: #1 tags after filtering in treatment: 5856554 INFO @ Wed, 28 Jun 2017 05:32:15: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 28 Jun 2017 05:32:15: #1 finished! INFO @ Wed, 28 Jun 2017 05:32:15: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:32:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:32:16: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:32:16: 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 05:32:16: Process for pairing-model is terminated! cat: SRX1423708.20_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 `SRX1423708.20_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 `SRX1423708.20_*.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 `SRX1423708.20_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 05:32:16: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:32:16: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:32:16: #1 total tags in treatment: 8155653 INFO @ Wed, 28 Jun 2017 05:32:16: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:32:16: #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 05:32:17: #1 tags after filtering in treatment: 5856554 INFO @ Wed, 28 Jun 2017 05:32:17: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 28 Jun 2017 05:32:17: #1 finished! INFO @ Wed, 28 Jun 2017 05:32:17: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:32:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:32:17: 17000000 INFO @ Wed, 28 Jun 2017 05:32:17: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:32:17: 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 05:32:17: Process for pairing-model is terminated! cat: SRX1423708.05_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 `SRX1423708.05_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 `SRX1423708.05_*.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 `SRX1423708.05_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 05:32:18: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:32:18: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:32:18: #1 total tags in treatment: 8155653 INFO @ Wed, 28 Jun 2017 05:32:18: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:32:18: #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 05:32:18: #1 tags after filtering in treatment: 5856554 INFO @ Wed, 28 Jun 2017 05:32:18: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 28 Jun 2017 05:32:18: #1 finished! INFO @ Wed, 28 Jun 2017 05:32:18: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:32:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:32:19: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:32:19: 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 05:32:19: Process for pairing-model is terminated! cat: SRX1423708.10_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 `SRX1423708.10_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 `SRX1423708.10_*.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 `SRX1423708.10_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。