Job ID = 11244903 sra ファイルのダウンロード中... Completed: 319304K bytes transferred in 9 seconds (269813K 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 9833019 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554651/SRR7696324.sra Written 9833019 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554651/SRR7696324.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: 00:06:04 9833019 reads; of these: 9833019 (100.00%) were paired; of these: 1475865 (15.01%) aligned concordantly 0 times 7106231 (72.27%) aligned concordantly exactly 1 time 1250923 (12.72%) aligned concordantly >1 times ---- 1475865 pairs aligned concordantly 0 times; of these: 213897 (14.49%) aligned discordantly 1 time ---- 1261968 pairs aligned 0 times concordantly or discordantly; of these: 2523936 mates make up the pairs; of these: 2199851 (87.16%) aligned 0 times 199848 (7.92%) aligned exactly 1 time 124237 (4.92%) aligned >1 times 88.81% overall alignment rate Time searching: 00:06:04 Overall time: 00:06:04 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] 238415 / 8529194 = 0.0280 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 @ Tue, 09 Oct 2018 22:52:59: # Command line: callpeak -t SRX4554651.bam -f BAM -g 12100000 -n SRX4554651.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554651.05 # format = BAM # ChIP-seq file = ['SRX4554651.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 @ Tue, 09 Oct 2018 22:52:59: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:52:59: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:52:59: # Command line: callpeak -t SRX4554651.bam -f BAM -g 12100000 -n SRX4554651.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554651.20 # format = BAM # ChIP-seq file = ['SRX4554651.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 @ Tue, 09 Oct 2018 22:52:59: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:52:59: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:52:59: # Command line: callpeak -t SRX4554651.bam -f BAM -g 12100000 -n SRX4554651.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554651.10 # format = BAM # ChIP-seq file = ['SRX4554651.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 @ Tue, 09 Oct 2018 22:52:59: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:52:59: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:53:05: 1000000 INFO @ Tue, 09 Oct 2018 22:53:05: 1000000 INFO @ Tue, 09 Oct 2018 22:53:05: 1000000 INFO @ Tue, 09 Oct 2018 22:53:10: 2000000 INFO @ Tue, 09 Oct 2018 22:53:11: 2000000 INFO @ Tue, 09 Oct 2018 22:53:11: 2000000 INFO @ Tue, 09 Oct 2018 22:53:15: 3000000 INFO @ Tue, 09 Oct 2018 22:53:17: 3000000 INFO @ Tue, 09 Oct 2018 22:53:17: 3000000 INFO @ Tue, 09 Oct 2018 22:53:21: 4000000 INFO @ Tue, 09 Oct 2018 22:53:22: 4000000 INFO @ Tue, 09 Oct 2018 22:53:22: 4000000 INFO @ Tue, 09 Oct 2018 22:53:26: 5000000 INFO @ Tue, 09 Oct 2018 22:53:28: 5000000 INFO @ Tue, 09 Oct 2018 22:53:28: 5000000 INFO @ Tue, 09 Oct 2018 22:53:31: 6000000 INFO @ Tue, 09 Oct 2018 22:53:34: 6000000 INFO @ Tue, 09 Oct 2018 22:53:34: 6000000 INFO @ Tue, 09 Oct 2018 22:53:36: 7000000 INFO @ Tue, 09 Oct 2018 22:53:40: 7000000 INFO @ Tue, 09 Oct 2018 22:53:40: 7000000 INFO @ Tue, 09 Oct 2018 22:53:42: 8000000 INFO @ Tue, 09 Oct 2018 22:53:45: 8000000 INFO @ Tue, 09 Oct 2018 22:53:45: 8000000 INFO @ Tue, 09 Oct 2018 22:53:47: 9000000 INFO @ Tue, 09 Oct 2018 22:53:51: 9000000 INFO @ Tue, 09 Oct 2018 22:53:51: 9000000 INFO @ Tue, 09 Oct 2018 22:53:53: 10000000 INFO @ Tue, 09 Oct 2018 22:53:57: 10000000 INFO @ Tue, 09 Oct 2018 22:53:57: 10000000 INFO @ Tue, 09 Oct 2018 22:53:58: 11000000 INFO @ Tue, 09 Oct 2018 22:54:02: 11000000 INFO @ Tue, 09 Oct 2018 22:54:02: 11000000 INFO @ Tue, 09 Oct 2018 22:54:03: 12000000 INFO @ Tue, 09 Oct 2018 22:54:08: 12000000 INFO @ Tue, 09 Oct 2018 22:54:08: 12000000 INFO @ Tue, 09 Oct 2018 22:54:09: 13000000 INFO @ Tue, 09 Oct 2018 22:54:14: 13000000 INFO @ Tue, 09 Oct 2018 22:54:14: 13000000 INFO @ Tue, 09 Oct 2018 22:54:14: 14000000 INFO @ Tue, 09 Oct 2018 22:54:19: 14000000 INFO @ Tue, 09 Oct 2018 22:54:19: 14000000 INFO @ Tue, 09 Oct 2018 22:54:20: 15000000 INFO @ Tue, 09 Oct 2018 22:54:25: 15000000 INFO @ Tue, 09 Oct 2018 22:54:25: 15000000 INFO @ Tue, 09 Oct 2018 22:54:25: 16000000 INFO @ Tue, 09 Oct 2018 22:54:30: 16000000 INFO @ Tue, 09 Oct 2018 22:54:30: 16000000 INFO @ Tue, 09 Oct 2018 22:54:30: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:54:30: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:54:30: #1 total tags in treatment: 8123312 INFO @ Tue, 09 Oct 2018 22:54:30: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:54:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:54:31: #1 tags after filtering in treatment: 5520148 INFO @ Tue, 09 Oct 2018 22:54:31: #1 Redundant rate of treatment: 0.32 INFO @ Tue, 09 Oct 2018 22:54:31: #1 finished! INFO @ Tue, 09 Oct 2018 22:54:31: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:54:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:54:31: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:54:31: 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 @ Tue, 09 Oct 2018 22:54:31: Process for pairing-model is terminated! cat: SRX4554651.10_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 `SRX4554651.10_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 `SRX4554651.10_*.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 `SRX4554651.10_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 @ Tue, 09 Oct 2018 22:54:36: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:54:36: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:54:36: #1 total tags in treatment: 8123312 INFO @ Tue, 09 Oct 2018 22:54:36: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:54:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:54:36: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:54:36: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:54:36: #1 total tags in treatment: 8123312 INFO @ Tue, 09 Oct 2018 22:54:36: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:54:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:54:36: #1 tags after filtering in treatment: 5520148 INFO @ Tue, 09 Oct 2018 22:54:36: #1 Redundant rate of treatment: 0.32 INFO @ Tue, 09 Oct 2018 22:54:36: #1 finished! INFO @ Tue, 09 Oct 2018 22:54:36: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:54:36: #1 tags after filtering in treatment: 5520148 INFO @ Tue, 09 Oct 2018 22:54:36: #1 Redundant rate of treatment: 0.32 INFO @ Tue, 09 Oct 2018 22:54:36: #1 finished! INFO @ Tue, 09 Oct 2018 22:54:36: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:54:36: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:54:36: 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 @ Tue, 09 Oct 2018 22:54:36: Process for pairing-model is terminated! INFO @ Tue, 09 Oct 2018 22:54:36: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:54:36: 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 @ Tue, 09 Oct 2018 22:54:36: Process for pairing-model is terminated! cat: SRX4554651.20_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 cat: SRX4554651.05_peaks.narrowPeakneedLargeMem: trying to allocate 0 bytes (limit: 17179869184) : 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 `SRX4554651.20_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 `SRX4554651.20_*.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 `SRX4554651.20_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4554651.05_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 `SRX4554651.05_*.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 `SRX4554651.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。