Job ID = 10536381 sra ファイルのダウンロード中... Completed: 1295868K bytes transferred in 36 seconds (289033K 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 32493685 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671140/SRR6696892.sra Written 32493685 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 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: 00:22:35 32493685 reads; of these: 32493685 (100.00%) were paired; of these: 6185265 (19.04%) aligned concordantly 0 times 23202260 (71.41%) aligned concordantly exactly 1 time 3106160 (9.56%) aligned concordantly >1 times ---- 6185265 pairs aligned concordantly 0 times; of these: 63360 (1.02%) aligned discordantly 1 time ---- 6121905 pairs aligned 0 times concordantly or discordantly; of these: 12243810 mates make up the pairs; of these: 11857674 (96.85%) aligned 0 times 319880 (2.61%) aligned exactly 1 time 66256 (0.54%) aligned >1 times 81.75% overall alignment rate Time searching: 00:22:35 Overall time: 00:22:36 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 24 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] 9486558 / 26326691 = 0.3603 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 @ Thu, 05 Apr 2018 09:45:53: # Command line: callpeak -t SRX3671140.bam -f BAM -g 12100000 -n SRX3671140.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671140.20 # format = BAM # ChIP-seq file = ['SRX3671140.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 @ Thu, 05 Apr 2018 09:45:53: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:45:53: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:45:53: # Command line: callpeak -t SRX3671140.bam -f BAM -g 12100000 -n SRX3671140.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671140.10 # format = BAM # ChIP-seq file = ['SRX3671140.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 @ Thu, 05 Apr 2018 09:45:53: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:45:53: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:45:53: # Command line: callpeak -t SRX3671140.bam -f BAM -g 12100000 -n SRX3671140.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671140.05 # format = BAM # ChIP-seq file = ['SRX3671140.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 @ Thu, 05 Apr 2018 09:45:53: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:45:53: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:45:59: 1000000 INFO @ Thu, 05 Apr 2018 09:45:59: 1000000 INFO @ Thu, 05 Apr 2018 09:45:59: 1000000 INFO @ Thu, 05 Apr 2018 09:46:06: 2000000 INFO @ Thu, 05 Apr 2018 09:46:06: 2000000 INFO @ Thu, 05 Apr 2018 09:46:06: 2000000 INFO @ Thu, 05 Apr 2018 09:46:12: 3000000 INFO @ Thu, 05 Apr 2018 09:46:12: 3000000 INFO @ Thu, 05 Apr 2018 09:46:12: 3000000 INFO @ Thu, 05 Apr 2018 09:46:18: 4000000 INFO @ Thu, 05 Apr 2018 09:46:18: 4000000 INFO @ Thu, 05 Apr 2018 09:46:18: 4000000 INFO @ Thu, 05 Apr 2018 09:46:24: 5000000 INFO @ Thu, 05 Apr 2018 09:46:24: 5000000 INFO @ Thu, 05 Apr 2018 09:46:24: 5000000 INFO @ Thu, 05 Apr 2018 09:46:30: 6000000 INFO @ Thu, 05 Apr 2018 09:46:30: 6000000 INFO @ Thu, 05 Apr 2018 09:46:30: 6000000 INFO @ Thu, 05 Apr 2018 09:46:36: 7000000 INFO @ Thu, 05 Apr 2018 09:46:36: 7000000 INFO @ Thu, 05 Apr 2018 09:46:36: 7000000 INFO @ Thu, 05 Apr 2018 09:46:41: 8000000 INFO @ Thu, 05 Apr 2018 09:46:41: 8000000 INFO @ Thu, 05 Apr 2018 09:46:41: 8000000 INFO @ Thu, 05 Apr 2018 09:46:47: 9000000 INFO @ Thu, 05 Apr 2018 09:46:47: 9000000 INFO @ Thu, 05 Apr 2018 09:46:47: 9000000 INFO @ Thu, 05 Apr 2018 09:46:53: 10000000 INFO @ Thu, 05 Apr 2018 09:46:53: 10000000 INFO @ Thu, 05 Apr 2018 09:46:53: 10000000 INFO @ Thu, 05 Apr 2018 09:46:59: 11000000 INFO @ Thu, 05 Apr 2018 09:46:59: 11000000 INFO @ Thu, 05 Apr 2018 09:46:59: 11000000 INFO @ Thu, 05 Apr 2018 09:47:05: 12000000 INFO @ Thu, 05 Apr 2018 09:47:05: 12000000 INFO @ Thu, 05 Apr 2018 09:47:05: 12000000 INFO @ Thu, 05 Apr 2018 09:47:11: 13000000 INFO @ Thu, 05 Apr 2018 09:47:11: 13000000 INFO @ Thu, 05 Apr 2018 09:47:11: 13000000 INFO @ Thu, 05 Apr 2018 09:47:16: 14000000 INFO @ Thu, 05 Apr 2018 09:47:17: 14000000 INFO @ Thu, 05 Apr 2018 09:47:17: 14000000 INFO @ Thu, 05 Apr 2018 09:47:22: 15000000 INFO @ Thu, 05 Apr 2018 09:47:22: 15000000 INFO @ Thu, 05 Apr 2018 09:47:22: 15000000 INFO @ Thu, 05 Apr 2018 09:47:28: 16000000 INFO @ Thu, 05 Apr 2018 09:47:29: 16000000 INFO @ Thu, 05 Apr 2018 09:47:29: 16000000 INFO @ Thu, 05 Apr 2018 09:47:36: 17000000 INFO @ Thu, 05 Apr 2018 09:47:37: 17000000 INFO @ Thu, 05 Apr 2018 09:47:37: 17000000 INFO @ Thu, 05 Apr 2018 09:47:43: 18000000 INFO @ Thu, 05 Apr 2018 09:47:44: 18000000 INFO @ Thu, 05 Apr 2018 09:47:44: 18000000 INFO @ Thu, 05 Apr 2018 09:47:51: 19000000 INFO @ Thu, 05 Apr 2018 09:47:52: 19000000 INFO @ Thu, 05 Apr 2018 09:47:52: 19000000 INFO @ Thu, 05 Apr 2018 09:47:59: 20000000 INFO @ Thu, 05 Apr 2018 09:48:00: 20000000 INFO @ Thu, 05 Apr 2018 09:48:00: 20000000 INFO @ Thu, 05 Apr 2018 09:48:06: 21000000 INFO @ Thu, 05 Apr 2018 09:48:07: 21000000 INFO @ Thu, 05 Apr 2018 09:48:07: 21000000 INFO @ Thu, 05 Apr 2018 09:48:14: 22000000 INFO @ Thu, 05 Apr 2018 09:48:15: 22000000 INFO @ Thu, 05 Apr 2018 09:48:15: 22000000 INFO @ Thu, 05 Apr 2018 09:48:21: 23000000 INFO @ Thu, 05 Apr 2018 09:48:23: 23000000 INFO @ Thu, 05 Apr 2018 09:48:23: 23000000 INFO @ Thu, 05 Apr 2018 09:48:29: 24000000 INFO @ Thu, 05 Apr 2018 09:48:31: 24000000 INFO @ Thu, 05 Apr 2018 09:48:31: 24000000 INFO @ Thu, 05 Apr 2018 09:48:37: 25000000 INFO @ Thu, 05 Apr 2018 09:48:39: 25000000 INFO @ Thu, 05 Apr 2018 09:48:39: 25000000 INFO @ Thu, 05 Apr 2018 09:48:44: 26000000 INFO @ Thu, 05 Apr 2018 09:48:47: 26000000 INFO @ Thu, 05 Apr 2018 09:48:47: 26000000 INFO @ Thu, 05 Apr 2018 09:48:52: 27000000 INFO @ Thu, 05 Apr 2018 09:48:55: 27000000 INFO @ Thu, 05 Apr 2018 09:48:55: 27000000 INFO @ Thu, 05 Apr 2018 09:48:59: 28000000 INFO @ Thu, 05 Apr 2018 09:49:03: 28000000 INFO @ Thu, 05 Apr 2018 09:49:03: 28000000 INFO @ Thu, 05 Apr 2018 09:49:06: 29000000 INFO @ Thu, 05 Apr 2018 09:49:11: 29000000 INFO @ Thu, 05 Apr 2018 09:49:11: 29000000 INFO @ Thu, 05 Apr 2018 09:49:14: 30000000 INFO @ Thu, 05 Apr 2018 09:49:19: 30000000 INFO @ Thu, 05 Apr 2018 09:49:19: 30000000 INFO @ Thu, 05 Apr 2018 09:49:21: 31000000 INFO @ Thu, 05 Apr 2018 09:49:27: 31000000 INFO @ Thu, 05 Apr 2018 09:49:27: 31000000 INFO @ Thu, 05 Apr 2018 09:49:29: 32000000 INFO @ Thu, 05 Apr 2018 09:49:35: 32000000 INFO @ Thu, 05 Apr 2018 09:49:35: 32000000 INFO @ Thu, 05 Apr 2018 09:49:36: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 09:49:43: 33000000 INFO @ Thu, 05 Apr 2018 09:49:43: 33000000 INFO @ Thu, 05 Apr 2018 09:49:44: 34000000 INFO @ Thu, 05 Apr 2018 09:49:45: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:49:45: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:49:45: #1 total tags in treatment: 16825074 INFO @ Thu, 05 Apr 2018 09:49:45: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:49:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:49:46: #1 tags after filtering in treatment: 11096768 INFO @ Thu, 05 Apr 2018 09:49:46: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 05 Apr 2018 09:49:46: #1 finished! INFO @ Thu, 05 Apr 2018 09:49:46: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:49:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:49:46: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:49:46: 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 @ Thu, 05 Apr 2018 09:49:46: Process for pairing-model is terminated! cat: SRX3671140.20_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 `SRX3671140.20_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 `SRX3671140.20_*.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 `SRX3671140.20_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 @ Thu, 05 Apr 2018 09:49:51: 34000000 INFO @ Thu, 05 Apr 2018 09:49:51: 34000000 INFO @ Thu, 05 Apr 2018 09:49:52: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:49:52: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:49:52: #1 total tags in treatment: 16825074 INFO @ Thu, 05 Apr 2018 09:49:52: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:49:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:49:52: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:49:52: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:49:52: #1 total tags in treatment: 16825074 INFO @ Thu, 05 Apr 2018 09:49:52: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:49:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:49:52: #1 tags after filtering in treatment: 11096768 INFO @ Thu, 05 Apr 2018 09:49:52: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 05 Apr 2018 09:49:52: #1 finished! INFO @ Thu, 05 Apr 2018 09:49:52: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:49:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:49:52: #1 tags after filtering in treatment: 11096768 INFO @ Thu, 05 Apr 2018 09:49:52: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 05 Apr 2018 09:49:52: #1 finished! INFO @ Thu, 05 Apr 2018 09:49:52: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:49:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:49:53: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:49:53: 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 @ Thu, 05 Apr 2018 09:49:53: Process for pairing-model is terminated! INFO @ Thu, 05 Apr 2018 09:49:53: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:49:53: 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 @ Thu, 05 Apr 2018 09:49:53: Process for pairing-model is terminated! cat: SRX3671140.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX3671140.10_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 `SRX3671140.05_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 `SRX3671140.05_*.xls': そのようなファイルやディレクトリはありません needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671140.05_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 rm: cannot remove `SRX3671140.10_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 `SRX3671140.10_*.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 `SRX3671140.10_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 BigWig に変換しました。