Job ID = 11245038 sra ファイルのダウンロード中... Completed: 427626K bytes transferred in 10 seconds (327024K 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 8733011 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554750/SRR7696423.sra Written 8733011 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554750/SRR7696423.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: 00:07:04 8733011 reads; of these: 8733011 (100.00%) were paired; of these: 395694 (4.53%) aligned concordantly 0 times 7954437 (91.08%) aligned concordantly exactly 1 time 382880 (4.38%) aligned concordantly >1 times ---- 395694 pairs aligned concordantly 0 times; of these: 75904 (19.18%) aligned discordantly 1 time ---- 319790 pairs aligned 0 times concordantly or discordantly; of these: 639580 mates make up the pairs; of these: 524316 (81.98%) aligned 0 times 97864 (15.30%) aligned exactly 1 time 17400 (2.72%) aligned >1 times 97.00% overall alignment rate Time searching: 00:07:04 Overall time: 00:07:04 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] 637372 / 8396840 = 0.0759 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 23:24:20: # Command line: callpeak -t SRX4554750.bam -f BAM -g 12100000 -n SRX4554750.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554750.05 # format = BAM # ChIP-seq file = ['SRX4554750.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 23:24:20: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:24:20: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:24:20: # Command line: callpeak -t SRX4554750.bam -f BAM -g 12100000 -n SRX4554750.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554750.20 # format = BAM # ChIP-seq file = ['SRX4554750.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 23:24:20: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:24:20: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:24:20: # Command line: callpeak -t SRX4554750.bam -f BAM -g 12100000 -n SRX4554750.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554750.10 # format = BAM # ChIP-seq file = ['SRX4554750.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 23:24:20: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:24:20: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:24:27: 1000000 INFO @ Tue, 09 Oct 2018 23:24:27: 1000000 INFO @ Tue, 09 Oct 2018 23:24:27: 1000000 INFO @ Tue, 09 Oct 2018 23:24:33: 2000000 INFO @ Tue, 09 Oct 2018 23:24:33: 2000000 INFO @ Tue, 09 Oct 2018 23:24:34: 2000000 INFO @ Tue, 09 Oct 2018 23:24:40: 3000000 INFO @ Tue, 09 Oct 2018 23:24:40: 3000000 INFO @ Tue, 09 Oct 2018 23:24:40: 3000000 INFO @ Tue, 09 Oct 2018 23:24:46: 4000000 INFO @ Tue, 09 Oct 2018 23:24:47: 4000000 INFO @ Tue, 09 Oct 2018 23:24:47: 4000000 INFO @ Tue, 09 Oct 2018 23:24:53: 5000000 INFO @ Tue, 09 Oct 2018 23:24:53: 5000000 INFO @ Tue, 09 Oct 2018 23:24:54: 5000000 INFO @ Tue, 09 Oct 2018 23:25:00: 6000000 INFO @ Tue, 09 Oct 2018 23:25:00: 6000000 INFO @ Tue, 09 Oct 2018 23:25:01: 6000000 INFO @ Tue, 09 Oct 2018 23:25:06: 7000000 INFO @ Tue, 09 Oct 2018 23:25:07: 7000000 INFO @ Tue, 09 Oct 2018 23:25:07: 7000000 INFO @ Tue, 09 Oct 2018 23:25:12: 8000000 INFO @ Tue, 09 Oct 2018 23:25:14: 8000000 INFO @ Tue, 09 Oct 2018 23:25:14: 8000000 INFO @ Tue, 09 Oct 2018 23:25:19: 9000000 INFO @ Tue, 09 Oct 2018 23:25:20: 9000000 INFO @ Tue, 09 Oct 2018 23:25:22: 9000000 INFO @ Tue, 09 Oct 2018 23:25:25: 10000000 INFO @ Tue, 09 Oct 2018 23:25:27: 10000000 INFO @ Tue, 09 Oct 2018 23:25:29: 10000000 INFO @ Tue, 09 Oct 2018 23:25:31: 11000000 INFO @ Tue, 09 Oct 2018 23:25:33: 11000000 INFO @ Tue, 09 Oct 2018 23:25:37: 11000000 INFO @ Tue, 09 Oct 2018 23:25:38: 12000000 INFO @ Tue, 09 Oct 2018 23:25:40: 12000000 INFO @ Tue, 09 Oct 2018 23:25:44: 13000000 INFO @ Tue, 09 Oct 2018 23:25:44: 12000000 INFO @ Tue, 09 Oct 2018 23:25:46: 13000000 INFO @ Tue, 09 Oct 2018 23:25:50: 14000000 INFO @ Tue, 09 Oct 2018 23:25:52: 13000000 INFO @ Tue, 09 Oct 2018 23:25:53: 14000000 INFO @ Tue, 09 Oct 2018 23:25:56: 15000000 INFO @ Tue, 09 Oct 2018 23:25:59: 14000000 INFO @ Tue, 09 Oct 2018 23:26:00: 15000000 INFO @ Tue, 09 Oct 2018 23:26:01: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:26:01: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:26:01: #1 total tags in treatment: 7700529 INFO @ Tue, 09 Oct 2018 23:26:01: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:26:01: #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 23:26:01: #1 tags after filtering in treatment: 4192914 INFO @ Tue, 09 Oct 2018 23:26:01: #1 Redundant rate of treatment: 0.46 INFO @ Tue, 09 Oct 2018 23:26:01: #1 finished! INFO @ Tue, 09 Oct 2018 23:26:01: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:26:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:26:01: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:26:01: 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 @ Tue, 09 Oct 2018 23:26:01: Process for pairing-model is terminated! cat: SRX4554750.20_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 `SRX4554750.20_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 `SRX4554750.20_*.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 `SRX4554750.20_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 @ Tue, 09 Oct 2018 23:26:04: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:26:04: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:26:04: #1 total tags in treatment: 7700529 INFO @ Tue, 09 Oct 2018 23:26:04: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:26:04: #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 23:26:04: #1 tags after filtering in treatment: 4192914 INFO @ Tue, 09 Oct 2018 23:26:04: #1 Redundant rate of treatment: 0.46 INFO @ Tue, 09 Oct 2018 23:26:04: #1 finished! INFO @ Tue, 09 Oct 2018 23:26:04: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:26:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:26:04: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:26:04: 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 23:26:04: Process for pairing-model is terminated! cat: SRX4554750.10_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 `SRX4554750.10_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 `SRX4554750.10_*.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 `SRX4554750.10_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 23:26:07: 15000000 INFO @ Tue, 09 Oct 2018 23:26:12: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:26:12: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:26:12: #1 total tags in treatment: 7700529 INFO @ Tue, 09 Oct 2018 23:26:12: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:26:12: #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 23:26:12: #1 tags after filtering in treatment: 4192914 INFO @ Tue, 09 Oct 2018 23:26:12: #1 Redundant rate of treatment: 0.46 INFO @ Tue, 09 Oct 2018 23:26:12: #1 finished! INFO @ Tue, 09 Oct 2018 23:26:12: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:26:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:26:12: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:26:12: 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 @ Tue, 09 Oct 2018 23:26:12: Process for pairing-model is terminated! cat: SRX4554750.05_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 `SRX4554750.05_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 `SRX4554750.05_*.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 `SRX4554750.05_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。