Job ID = 10254442 sra ファイルのダウンロード中... Completed: 515190K bytes transferred in 15 seconds (266732K bits/sec), in 1 file. Completed: 368995K bytes transferred in 13 seconds (227646K 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 5964497 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3353380/SRR6246235.sra Written 5964497 spots total Written 8289966 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3353380/SRR6246234.sra Written 8289966 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: 00:12:34 14254463 reads; of these: 14254463 (100.00%) were paired; of these: 4756578 (33.37%) aligned concordantly 0 times 6952038 (48.77%) aligned concordantly exactly 1 time 2545847 (17.86%) aligned concordantly >1 times ---- 4756578 pairs aligned concordantly 0 times; of these: 2302990 (48.42%) aligned discordantly 1 time ---- 2453588 pairs aligned 0 times concordantly or discordantly; of these: 4907176 mates make up the pairs; of these: 2198339 (44.80%) aligned 0 times 1757229 (35.81%) aligned exactly 1 time 951608 (19.39%) aligned >1 times 92.29% overall alignment rate Time searching: 00:12:34 Overall time: 00:12:34 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] 468419 / 9945361 = 0.0471 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 18:22:15: # Command line: callpeak -t SRX3353380.bam -f BAM -g 12100000 -n SRX3353380.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3353380.20 # format = BAM # ChIP-seq file = ['SRX3353380.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 18:22:15: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:22:15: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:22:15: # Command line: callpeak -t SRX3353380.bam -f BAM -g 12100000 -n SRX3353380.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3353380.10 # format = BAM # ChIP-seq file = ['SRX3353380.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 18:22:15: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:22:15: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:22:15: # Command line: callpeak -t SRX3353380.bam -f BAM -g 12100000 -n SRX3353380.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3353380.05 # format = BAM # ChIP-seq file = ['SRX3353380.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 18:22:15: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:22:15: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:22:21: 1000000 INFO @ Wed, 06 Dec 2017 18:22:21: 1000000 INFO @ Wed, 06 Dec 2017 18:22:21: 1000000 INFO @ Wed, 06 Dec 2017 18:22:26: 2000000 INFO @ Wed, 06 Dec 2017 18:22:26: 2000000 INFO @ Wed, 06 Dec 2017 18:22:27: 2000000 INFO @ Wed, 06 Dec 2017 18:22:32: 3000000 INFO @ Wed, 06 Dec 2017 18:22:32: 3000000 INFO @ Wed, 06 Dec 2017 18:22:33: 3000000 INFO @ Wed, 06 Dec 2017 18:22:38: 4000000 INFO @ Wed, 06 Dec 2017 18:22:38: 4000000 INFO @ Wed, 06 Dec 2017 18:22:39: 4000000 INFO @ Wed, 06 Dec 2017 18:22:44: 5000000 INFO @ Wed, 06 Dec 2017 18:22:44: 5000000 INFO @ Wed, 06 Dec 2017 18:22:46: 5000000 INFO @ Wed, 06 Dec 2017 18:22:50: 6000000 INFO @ Wed, 06 Dec 2017 18:22:50: 6000000 INFO @ Wed, 06 Dec 2017 18:22:52: 6000000 INFO @ Wed, 06 Dec 2017 18:22:56: 7000000 INFO @ Wed, 06 Dec 2017 18:22:56: 7000000 INFO @ Wed, 06 Dec 2017 18:22:59: 7000000 INFO @ Wed, 06 Dec 2017 18:23:03: 8000000 INFO @ Wed, 06 Dec 2017 18:23:03: 8000000 INFO @ Wed, 06 Dec 2017 18:23:05: 8000000 INFO @ Wed, 06 Dec 2017 18:23:09: 9000000 INFO @ Wed, 06 Dec 2017 18:23:09: 9000000 INFO @ Wed, 06 Dec 2017 18:23:12: 9000000 INFO @ Wed, 06 Dec 2017 18:23:15: 10000000 INFO @ Wed, 06 Dec 2017 18:23:15: 10000000 INFO @ Wed, 06 Dec 2017 18:23:19: 10000000 INFO @ Wed, 06 Dec 2017 18:23:21: 11000000 INFO @ Wed, 06 Dec 2017 18:23:22: 11000000 INFO @ Wed, 06 Dec 2017 18:23:25: 11000000 INFO @ Wed, 06 Dec 2017 18:23:28: 12000000 INFO @ Wed, 06 Dec 2017 18:23:28: 12000000 INFO @ Wed, 06 Dec 2017 18:23:32: 12000000 INFO @ Wed, 06 Dec 2017 18:23:34: 13000000 INFO @ Wed, 06 Dec 2017 18:23:34: 13000000 INFO @ Wed, 06 Dec 2017 18:23:39: 13000000 INFO @ Wed, 06 Dec 2017 18:23:40: 14000000 INFO @ Wed, 06 Dec 2017 18:23:40: 14000000 INFO @ Wed, 06 Dec 2017 18:23:45: 14000000 INFO @ Wed, 06 Dec 2017 18:23:46: 15000000 INFO @ Wed, 06 Dec 2017 18:23:47: 15000000 INFO @ Wed, 06 Dec 2017 18:23:52: 15000000 INFO @ Wed, 06 Dec 2017 18:23:53: 16000000 INFO @ Wed, 06 Dec 2017 18:23:53: 16000000 INFO @ Wed, 06 Dec 2017 18:23:58: 16000000 INFO @ Wed, 06 Dec 2017 18:23:59: 17000000 INFO @ Wed, 06 Dec 2017 18:23:59: 17000000 INFO @ Wed, 06 Dec 2017 18:24:05: 17000000 INFO @ Wed, 06 Dec 2017 18:24:05: 18000000 INFO @ Wed, 06 Dec 2017 18:24:06: 18000000 INFO @ Wed, 06 Dec 2017 18:24:12: 18000000 INFO @ Wed, 06 Dec 2017 18:24:12: 19000000 INFO @ Wed, 06 Dec 2017 18:24:12: 19000000 INFO @ Wed, 06 Dec 2017 18:24:18: 20000000 INFO @ Wed, 06 Dec 2017 18:24:18: 19000000 INFO @ Wed, 06 Dec 2017 18:24:19: 20000000 INFO @ Wed, 06 Dec 2017 18:24:25: 21000000 INFO @ Wed, 06 Dec 2017 18:24:25: 20000000 INFO @ Wed, 06 Dec 2017 18:24:26: 21000000 INFO @ Wed, 06 Dec 2017 18:24:31: 22000000 INFO @ Wed, 06 Dec 2017 18:24:32: 21000000 INFO @ Wed, 06 Dec 2017 18:24:32: 22000000 INFO @ Wed, 06 Dec 2017 18:24:38: 23000000 INFO @ Wed, 06 Dec 2017 18:24:38: 22000000 INFO @ Wed, 06 Dec 2017 18:24:39: 23000000 INFO @ Wed, 06 Dec 2017 18:24:44: 24000000 INFO @ Wed, 06 Dec 2017 18:24:45: 23000000 INFO @ Wed, 06 Dec 2017 18:24:45: 24000000 INFO @ Wed, 06 Dec 2017 18:24:50: 25000000 INFO @ Wed, 06 Dec 2017 18:24:51: 24000000 INFO @ Wed, 06 Dec 2017 18:24:52: 25000000 INFO @ Wed, 06 Dec 2017 18:24:53: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:24:53: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:24:53: #1 total tags in treatment: 9030489 INFO @ Wed, 06 Dec 2017 18:24:53: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:24:53: #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 18:24:53: #1 tags after filtering in treatment: 6161336 INFO @ Wed, 06 Dec 2017 18:24:53: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 06 Dec 2017 18:24:53: #1 finished! INFO @ Wed, 06 Dec 2017 18:24:53: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:24:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:24:54: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 18:24:54: 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 18:24:54: Process for pairing-model is terminated! cat: SRX3353380.10_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 `SRX3353380.10_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 `SRX3353380.10_*.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 `SRX3353380.10_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 INFO @ Wed, 06 Dec 2017 18:24:54: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:24:54: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:24:54: #1 total tags in treatment: 9030489 INFO @ Wed, 06 Dec 2017 18:24:54: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:24:54: #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 18:24:54: #1 tags after filtering in treatment: 6161336 INFO @ Wed, 06 Dec 2017 18:24:54: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 06 Dec 2017 18:24:54: #1 finished! INFO @ Wed, 06 Dec 2017 18:24:54: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:24:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:24:55: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 18:24:55: 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 18:24:55: Process for pairing-model is terminated! cat: SRX3353380.05_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3353380.05_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 `SRX3353380.05_*.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 `SRX3353380.05_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 18:24:57: 25000000 INFO @ Wed, 06 Dec 2017 18:24:59: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:24:59: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:24:59: #1 total tags in treatment: 9030489 INFO @ Wed, 06 Dec 2017 18:24:59: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:24:59: #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 18:24:59: #1 tags after filtering in treatment: 6161336 INFO @ Wed, 06 Dec 2017 18:24:59: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 06 Dec 2017 18:24:59: #1 finished! INFO @ Wed, 06 Dec 2017 18:24:59: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:24:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:25:00: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 18:25:00: 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 18:25:00: Process for pairing-model is terminated! cat: SRX3353380.20_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 `SRX3353380.20_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 `SRX3353380.20_*.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 `SRX3353380.20_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。