Job ID = 10254444 sra ファイルのダウンロード中... Completed: 297981K bytes transferred in 9 seconds (251620K bits/sec), in 1 file. Completed: 340194K bytes transferred in 21 seconds (131947K bits/sec), in 1 file. 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 4657243 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3353382/SRR6246238.sra Written 4657243 spots total Written 5462699 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3353382/SRR6246239.sra Written 5462699 spots total rm: cannot remove `[DSE]RX*': 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: 00:08:37 10119942 reads; of these: 10119942 (100.00%) were paired; of these: 2254590 (22.28%) aligned concordantly 0 times 6735977 (66.56%) aligned concordantly exactly 1 time 1129375 (11.16%) aligned concordantly >1 times ---- 2254590 pairs aligned concordantly 0 times; of these: 996809 (44.21%) aligned discordantly 1 time ---- 1257781 pairs aligned 0 times concordantly or discordantly; of these: 2515562 mates make up the pairs; of these: 1441747 (57.31%) aligned 0 times 626488 (24.90%) aligned exactly 1 time 447327 (17.78%) aligned >1 times 92.88% overall alignment rate Time searching: 00:08:37 Overall time: 00:08:37 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] 85767 / 8662979 = 0.0099 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, 06 Dec 2017 18:17:07: # Command line: callpeak -t SRX3353382.bam -f BAM -g 12100000 -n SRX3353382.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3353382.20 # format = BAM # ChIP-seq file = ['SRX3353382.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, 06 Dec 2017 18:17:07: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:17:07: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:17:07: # Command line: callpeak -t SRX3353382.bam -f BAM -g 12100000 -n SRX3353382.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3353382.10 # format = BAM # ChIP-seq file = ['SRX3353382.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, 06 Dec 2017 18:17:07: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:17:07: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:17:07: # Command line: callpeak -t SRX3353382.bam -f BAM -g 12100000 -n SRX3353382.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3353382.05 # format = BAM # ChIP-seq file = ['SRX3353382.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, 06 Dec 2017 18:17:07: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:17:07: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:17:14: 1000000 INFO @ Wed, 06 Dec 2017 18:17:14: 1000000 INFO @ Wed, 06 Dec 2017 18:17:14: 1000000 INFO @ Wed, 06 Dec 2017 18:17:21: 2000000 INFO @ Wed, 06 Dec 2017 18:17:21: 2000000 INFO @ Wed, 06 Dec 2017 18:17:21: 2000000 INFO @ Wed, 06 Dec 2017 18:17:27: 3000000 INFO @ Wed, 06 Dec 2017 18:17:27: 3000000 INFO @ Wed, 06 Dec 2017 18:17:27: 3000000 INFO @ Wed, 06 Dec 2017 18:17:33: 4000000 INFO @ Wed, 06 Dec 2017 18:17:33: 4000000 INFO @ Wed, 06 Dec 2017 18:17:33: 4000000 INFO @ Wed, 06 Dec 2017 18:17:40: 5000000 INFO @ Wed, 06 Dec 2017 18:17:40: 5000000 INFO @ Wed, 06 Dec 2017 18:17:40: 5000000 INFO @ Wed, 06 Dec 2017 18:17:46: 6000000 INFO @ Wed, 06 Dec 2017 18:17:46: 6000000 INFO @ Wed, 06 Dec 2017 18:17:46: 6000000 INFO @ Wed, 06 Dec 2017 18:17:52: 7000000 INFO @ Wed, 06 Dec 2017 18:17:52: 7000000 INFO @ Wed, 06 Dec 2017 18:17:53: 7000000 INFO @ Wed, 06 Dec 2017 18:17:59: 8000000 INFO @ Wed, 06 Dec 2017 18:17:59: 8000000 INFO @ Wed, 06 Dec 2017 18:17:59: 8000000 INFO @ Wed, 06 Dec 2017 18:18:05: 9000000 INFO @ Wed, 06 Dec 2017 18:18:05: 9000000 INFO @ Wed, 06 Dec 2017 18:18:06: 9000000 INFO @ Wed, 06 Dec 2017 18:18:11: 10000000 INFO @ Wed, 06 Dec 2017 18:18:12: 10000000 INFO @ Wed, 06 Dec 2017 18:18:13: 10000000 INFO @ Wed, 06 Dec 2017 18:18:17: 11000000 INFO @ Wed, 06 Dec 2017 18:18:19: 11000000 INFO @ Wed, 06 Dec 2017 18:18:20: 11000000 INFO @ Wed, 06 Dec 2017 18:18:23: 12000000 INFO @ Wed, 06 Dec 2017 18:18:25: 12000000 INFO @ Wed, 06 Dec 2017 18:18:26: 12000000 INFO @ Wed, 06 Dec 2017 18:18:30: 13000000 INFO @ Wed, 06 Dec 2017 18:18:32: 13000000 INFO @ Wed, 06 Dec 2017 18:18:33: 13000000 INFO @ Wed, 06 Dec 2017 18:18:36: 14000000 INFO @ Wed, 06 Dec 2017 18:18:39: 14000000 INFO @ Wed, 06 Dec 2017 18:18:39: 14000000 INFO @ Wed, 06 Dec 2017 18:18:42: 15000000 INFO @ Wed, 06 Dec 2017 18:18:46: 15000000 INFO @ Wed, 06 Dec 2017 18:18:47: 15000000 INFO @ Wed, 06 Dec 2017 18:18:49: 16000000 INFO @ Wed, 06 Dec 2017 18:18:53: 16000000 INFO @ Wed, 06 Dec 2017 18:18:54: 16000000 INFO @ Wed, 06 Dec 2017 18:18:55: 17000000 INFO @ Wed, 06 Dec 2017 18:19:00: 17000000 INFO @ Wed, 06 Dec 2017 18:19:01: 17000000 INFO @ Wed, 06 Dec 2017 18:19:02: 18000000 INFO @ Wed, 06 Dec 2017 18:19:06: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:19:06: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:19:06: #1 total tags in treatment: 7781978 INFO @ Wed, 06 Dec 2017 18:19:06: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:19:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:19:06: #1 tags after filtering in treatment: 5968972 INFO @ Wed, 06 Dec 2017 18:19:06: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 06 Dec 2017 18:19:06: #1 finished! INFO @ Wed, 06 Dec 2017 18:19:06: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:19:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:19:07: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 18:19:07: 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, 06 Dec 2017 18:19:07: Process for pairing-model is terminated! cat: SRX3353382.05_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 `SRX3353382.05_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 `SRX3353382.05_*.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 `SRX3353382.05_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, 06 Dec 2017 18:19:07: 18000000 INFO @ Wed, 06 Dec 2017 18:19:08: 18000000 INFO @ Wed, 06 Dec 2017 18:19:12: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:19:12: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:19:12: #1 total tags in treatment: 7781978 INFO @ Wed, 06 Dec 2017 18:19:12: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:19:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:19:12: #1 tags after filtering in treatment: 5968972 INFO @ Wed, 06 Dec 2017 18:19:12: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 06 Dec 2017 18:19:12: #1 finished! INFO @ Wed, 06 Dec 2017 18:19:12: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:19:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:19:12: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 18:19:12: 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, 06 Dec 2017 18:19:12: Process for pairing-model is terminated! cat: SRX3353382.20_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 `SRX3353382.20_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 `SRX3353382.20_*.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 `SRX3353382.20_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, 06 Dec 2017 18:19:13: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:19:13: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:19:13: #1 total tags in treatment: 7781978 INFO @ Wed, 06 Dec 2017 18:19:13: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:19:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:19:13: #1 tags after filtering in treatment: 5968972 INFO @ Wed, 06 Dec 2017 18:19:13: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 06 Dec 2017 18:19:13: #1 finished! INFO @ Wed, 06 Dec 2017 18:19:13: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:19:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:19:13: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 18:19:13: 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, 06 Dec 2017 18:19:13: Process for pairing-model is terminated! cat: SRX3353382.10_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 `SRX3353382.10_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 `SRX3353382.10_*.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 `SRX3353382.10_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。