Job ID = 11245052 sra ファイルのダウンロード中... Completed: 179290K bytes transferred in 12 seconds (119781K 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 5649659 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554764/SRR7696436.sra Written 5649659 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554764/SRR7696436.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: 00:02:42 5649659 reads; of these: 5649659 (100.00%) were paired; of these: 2696388 (47.73%) aligned concordantly 0 times 2840784 (50.28%) aligned concordantly exactly 1 time 112487 (1.99%) aligned concordantly >1 times ---- 2696388 pairs aligned concordantly 0 times; of these: 8498 (0.32%) aligned discordantly 1 time ---- 2687890 pairs aligned 0 times concordantly or discordantly; of these: 5375780 mates make up the pairs; of these: 3724101 (69.28%) aligned 0 times 1574091 (29.28%) aligned exactly 1 time 77588 (1.44%) aligned >1 times 67.04% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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_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] 78725 / 2961419 = 0.0266 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 23:18:45: # Command line: callpeak -t SRX4554764.bam -f BAM -g 12100000 -n SRX4554764.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554764.10 # format = BAM # ChIP-seq file = ['SRX4554764.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 23:18:45: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:18:45: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:18:45: # Command line: callpeak -t SRX4554764.bam -f BAM -g 12100000 -n SRX4554764.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554764.20 # format = BAM # ChIP-seq file = ['SRX4554764.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 23:18:45: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:18:45: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:18:45: # Command line: callpeak -t SRX4554764.bam -f BAM -g 12100000 -n SRX4554764.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554764.05 # format = BAM # ChIP-seq file = ['SRX4554764.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 23:18:45: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:18:45: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:18:51: 1000000 INFO @ Tue, 09 Oct 2018 23:18:51: 1000000 INFO @ Tue, 09 Oct 2018 23:18:51: 1000000 INFO @ Tue, 09 Oct 2018 23:18:57: 2000000 INFO @ Tue, 09 Oct 2018 23:18:57: 2000000 INFO @ Tue, 09 Oct 2018 23:18:57: 2000000 INFO @ Tue, 09 Oct 2018 23:19:03: 3000000 INFO @ Tue, 09 Oct 2018 23:19:03: 3000000 INFO @ Tue, 09 Oct 2018 23:19:04: 3000000 INFO @ Tue, 09 Oct 2018 23:19:09: 4000000 INFO @ Tue, 09 Oct 2018 23:19:10: 4000000 INFO @ Tue, 09 Oct 2018 23:19:10: 4000000 INFO @ Tue, 09 Oct 2018 23:19:15: 5000000 INFO @ Tue, 09 Oct 2018 23:19:16: 5000000 INFO @ Tue, 09 Oct 2018 23:19:16: 5000000 INFO @ Tue, 09 Oct 2018 23:19:23: 6000000 INFO @ Tue, 09 Oct 2018 23:19:23: 6000000 INFO @ Tue, 09 Oct 2018 23:19:24: 6000000 INFO @ Tue, 09 Oct 2018 23:19:29: 7000000 INFO @ Tue, 09 Oct 2018 23:19:29: 7000000 INFO @ Tue, 09 Oct 2018 23:19:30: 7000000 INFO @ Tue, 09 Oct 2018 23:19:31: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:19:31: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:19:31: #1 total tags in treatment: 2874571 INFO @ Tue, 09 Oct 2018 23:19:31: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:19:31: #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 23:19:31: #1 tags after filtering in treatment: 2102071 INFO @ Tue, 09 Oct 2018 23:19:31: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 09 Oct 2018 23:19:31: #1 finished! INFO @ Tue, 09 Oct 2018 23:19:31: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:19:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:19:31: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:19:31: 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 23:19:31: Process for pairing-model is terminated! cat: SRX4554764.10_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 `SRX4554764.10_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 `SRX4554764.10_*.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 `SRX4554764.10_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 23:19:32: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:19:32: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:19:32: #1 total tags in treatment: 2874571 INFO @ Tue, 09 Oct 2018 23:19:32: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:19:32: #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 23:19:32: #1 tags after filtering in treatment: 2102071 INFO @ Tue, 09 Oct 2018 23:19:32: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 09 Oct 2018 23:19:32: #1 finished! INFO @ Tue, 09 Oct 2018 23:19:32: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:19:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:19:32: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:19:32: 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 23:19:32: Process for pairing-model is terminated! cat: SRX4554764.20_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 `SRX4554764.20_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 `SRX4554764.20_*.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 `SRX4554764.20_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 23:19:32: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:19:32: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:19:32: #1 total tags in treatment: 2874571 INFO @ Tue, 09 Oct 2018 23:19:32: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:19:32: #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 23:19:32: #1 tags after filtering in treatment: 2102071 INFO @ Tue, 09 Oct 2018 23:19:32: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 09 Oct 2018 23:19:32: #1 finished! INFO @ Tue, 09 Oct 2018 23:19:32: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:19:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:19:33: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:19:33: 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 23:19:33: Process for pairing-model is terminated! cat: SRX4554764.05_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 `SRX4554764.05_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 `SRX4554764.05_*.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 `SRX4554764.05_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。