Job ID = 10937456 sra ファイルのダウンロード中... Completed: 566120K bytes transferred in 10 seconds (453138K 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... Read 10493636 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198736/SRR4304466.sra Written 10493636 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198736/SRR4304466.sra 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: 00:07:00 10493636 reads; of these: 10493636 (100.00%) were paired; of these: 529560 (5.05%) aligned concordantly 0 times 8780561 (83.68%) aligned concordantly exactly 1 time 1183515 (11.28%) aligned concordantly >1 times ---- 529560 pairs aligned concordantly 0 times; of these: 151951 (28.69%) aligned discordantly 1 time ---- 377609 pairs aligned 0 times concordantly or discordantly; of these: 755218 mates make up the pairs; of these: 552333 (73.14%) aligned 0 times 129248 (17.11%) aligned exactly 1 time 73637 (9.75%) aligned >1 times 97.37% overall alignment rate Time searching: 00:07:00 Overall time: 00:07:00 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] 261736 / 10015592 = 0.0261 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 @ Fri, 10 Aug 2018 02:26:59: # Command line: callpeak -t SRX2198736.bam -f BAM -g 12100000 -n SRX2198736.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2198736.10 # format = BAM # ChIP-seq file = ['SRX2198736.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 @ Fri, 10 Aug 2018 02:26:59: # Command line: callpeak -t SRX2198736.bam -f BAM -g 12100000 -n SRX2198736.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2198736.20 # format = BAM # ChIP-seq file = ['SRX2198736.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 @ Fri, 10 Aug 2018 02:26:59: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:26:59: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:26:59: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:26:59: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:26:59: # Command line: callpeak -t SRX2198736.bam -f BAM -g 12100000 -n SRX2198736.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2198736.05 # format = BAM # ChIP-seq file = ['SRX2198736.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 @ Fri, 10 Aug 2018 02:26:59: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:26:59: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:27:05: 1000000 INFO @ Fri, 10 Aug 2018 02:27:05: 1000000 INFO @ Fri, 10 Aug 2018 02:27:05: 1000000 INFO @ Fri, 10 Aug 2018 02:27:11: 2000000 INFO @ Fri, 10 Aug 2018 02:27:11: 2000000 INFO @ Fri, 10 Aug 2018 02:27:11: 2000000 INFO @ Fri, 10 Aug 2018 02:27:16: 3000000 INFO @ Fri, 10 Aug 2018 02:27:17: 3000000 INFO @ Fri, 10 Aug 2018 02:27:17: 3000000 INFO @ Fri, 10 Aug 2018 02:27:21: 4000000 INFO @ Fri, 10 Aug 2018 02:27:23: 4000000 INFO @ Fri, 10 Aug 2018 02:27:23: 4000000 INFO @ Fri, 10 Aug 2018 02:27:27: 5000000 INFO @ Fri, 10 Aug 2018 02:27:29: 5000000 INFO @ Fri, 10 Aug 2018 02:27:29: 5000000 INFO @ Fri, 10 Aug 2018 02:27:32: 6000000 INFO @ Fri, 10 Aug 2018 02:27:35: 6000000 INFO @ Fri, 10 Aug 2018 02:27:35: 6000000 INFO @ Fri, 10 Aug 2018 02:27:38: 7000000 INFO @ Fri, 10 Aug 2018 02:27:40: 7000000 INFO @ Fri, 10 Aug 2018 02:27:40: 7000000 INFO @ Fri, 10 Aug 2018 02:27:43: 8000000 INFO @ Fri, 10 Aug 2018 02:27:46: 8000000 INFO @ Fri, 10 Aug 2018 02:27:46: 8000000 INFO @ Fri, 10 Aug 2018 02:27:48: 9000000 INFO @ Fri, 10 Aug 2018 02:27:52: 9000000 INFO @ Fri, 10 Aug 2018 02:27:52: 9000000 INFO @ Fri, 10 Aug 2018 02:27:54: 10000000 INFO @ Fri, 10 Aug 2018 02:27:58: 10000000 INFO @ Fri, 10 Aug 2018 02:27:59: 10000000 INFO @ Fri, 10 Aug 2018 02:28:00: 11000000 INFO @ Fri, 10 Aug 2018 02:28:04: 11000000 INFO @ Fri, 10 Aug 2018 02:28:05: 11000000 INFO @ Fri, 10 Aug 2018 02:28:05: 12000000 INFO @ Fri, 10 Aug 2018 02:28:10: 12000000 INFO @ Fri, 10 Aug 2018 02:28:11: 12000000 INFO @ Fri, 10 Aug 2018 02:28:11: 13000000 INFO @ Fri, 10 Aug 2018 02:28:15: 13000000 INFO @ Fri, 10 Aug 2018 02:28:17: 14000000 INFO @ Fri, 10 Aug 2018 02:28:17: 13000000 INFO @ Fri, 10 Aug 2018 02:28:21: 14000000 INFO @ Fri, 10 Aug 2018 02:28:23: 15000000 INFO @ Fri, 10 Aug 2018 02:28:24: 14000000 INFO @ Fri, 10 Aug 2018 02:28:27: 15000000 INFO @ Fri, 10 Aug 2018 02:28:29: 16000000 INFO @ Fri, 10 Aug 2018 02:28:30: 15000000 INFO @ Fri, 10 Aug 2018 02:28:33: 16000000 INFO @ Fri, 10 Aug 2018 02:28:35: 17000000 INFO @ Fri, 10 Aug 2018 02:28:36: 16000000 INFO @ Fri, 10 Aug 2018 02:28:39: 17000000 INFO @ Fri, 10 Aug 2018 02:28:41: 18000000 INFO @ Fri, 10 Aug 2018 02:28:43: 17000000 INFO @ Fri, 10 Aug 2018 02:28:44: 18000000 INFO @ Fri, 10 Aug 2018 02:28:47: 19000000 INFO @ Fri, 10 Aug 2018 02:28:49: 18000000 INFO @ Fri, 10 Aug 2018 02:28:50: 19000000 INFO @ Fri, 10 Aug 2018 02:28:52: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:28:52: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:28:52: #1 total tags in treatment: 9702645 INFO @ Fri, 10 Aug 2018 02:28:52: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:28:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:28:53: #1 tags after filtering in treatment: 5603574 INFO @ Fri, 10 Aug 2018 02:28:53: #1 Redundant rate of treatment: 0.42 INFO @ Fri, 10 Aug 2018 02:28:53: #1 finished! INFO @ Fri, 10 Aug 2018 02:28:53: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:28:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:28:53: #2 number of paired peaks: 0 WARNING @ Fri, 10 Aug 2018 02:28:53: 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 @ Fri, 10 Aug 2018 02:28:53: Process for pairing-model is terminated! cat: SRX2198736.10_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 `SRX2198736.10_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 `SRX2198736.10_*.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 `SRX2198736.10_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 @ Fri, 10 Aug 2018 02:28:55: 19000000 INFO @ Fri, 10 Aug 2018 02:28:55: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:28:55: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:28:55: #1 total tags in treatment: 9702645 INFO @ Fri, 10 Aug 2018 02:28:55: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:28:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:28:56: #1 tags after filtering in treatment: 5603574 INFO @ Fri, 10 Aug 2018 02:28:56: #1 Redundant rate of treatment: 0.42 INFO @ Fri, 10 Aug 2018 02:28:56: #1 finished! INFO @ Fri, 10 Aug 2018 02:28:56: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:28:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:28:56: #2 number of paired peaks: 0 WARNING @ Fri, 10 Aug 2018 02:28:56: 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 @ Fri, 10 Aug 2018 02:28:56: Process for pairing-model is terminated! cat: SRX2198736.05_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 `SRX2198736.05_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 `SRX2198736.05_*.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 `SRX2198736.05_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 @ Fri, 10 Aug 2018 02:29:00: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:29:00: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:29:00: #1 total tags in treatment: 9702645 INFO @ Fri, 10 Aug 2018 02:29:00: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:29:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:29:00: #1 tags after filtering in treatment: 5603574 INFO @ Fri, 10 Aug 2018 02:29:00: #1 Redundant rate of treatment: 0.42 INFO @ Fri, 10 Aug 2018 02:29:00: #1 finished! INFO @ Fri, 10 Aug 2018 02:29:00: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:29:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:29:01: #2 number of paired peaks: 0 WARNING @ Fri, 10 Aug 2018 02:29:01: 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 @ Fri, 10 Aug 2018 02:29:01: Process for pairing-model is terminated! cat: SRX2198736.20_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 `SRX2198736.20_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 `SRX2198736.20_*.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 `SRX2198736.20_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。