Job ID = 10937483 sra ファイルのダウンロード中... Completed: 453044K bytes transferred in 12 seconds (301409K 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 4813901 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010302/SRR5833295.sra Written 4813901 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010302/SRR5833295.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: 00:05:57 4813901 reads; of these: 4813901 (100.00%) were paired; of these: 375142 (7.79%) aligned concordantly 0 times 3790039 (78.73%) aligned concordantly exactly 1 time 648720 (13.48%) aligned concordantly >1 times ---- 375142 pairs aligned concordantly 0 times; of these: 57884 (15.43%) aligned discordantly 1 time ---- 317258 pairs aligned 0 times concordantly or discordantly; of these: 634516 mates make up the pairs; of these: 520361 (82.01%) aligned 0 times 76484 (12.05%) aligned exactly 1 time 37671 (5.94%) aligned >1 times 94.60% overall alignment rate Time searching: 00:05:57 Overall time: 00:05:57 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] 82154 / 4460175 = 0.0184 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 02:30:14: # Command line: callpeak -t SRX3010302.bam -f BAM -g 12100000 -n SRX3010302.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3010302.05 # format = BAM # ChIP-seq file = ['SRX3010302.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 02:30:14: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:30:14: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:30:14: # Command line: callpeak -t SRX3010302.bam -f BAM -g 12100000 -n SRX3010302.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3010302.20 # format = BAM # ChIP-seq file = ['SRX3010302.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 02:30:14: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:30:14: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:30:14: # Command line: callpeak -t SRX3010302.bam -f BAM -g 12100000 -n SRX3010302.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3010302.10 # format = BAM # ChIP-seq file = ['SRX3010302.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 02:30:14: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:30:14: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:30:21: 1000000 INFO @ Fri, 10 Aug 2018 02:30:21: 1000000 INFO @ Fri, 10 Aug 2018 02:30:21: 1000000 INFO @ Fri, 10 Aug 2018 02:30:28: 2000000 INFO @ Fri, 10 Aug 2018 02:30:28: 2000000 INFO @ Fri, 10 Aug 2018 02:30:28: 2000000 INFO @ Fri, 10 Aug 2018 02:30:35: 3000000 INFO @ Fri, 10 Aug 2018 02:30:35: 3000000 INFO @ Fri, 10 Aug 2018 02:30:35: 3000000 INFO @ Fri, 10 Aug 2018 02:30:42: 4000000 INFO @ Fri, 10 Aug 2018 02:30:42: 4000000 INFO @ Fri, 10 Aug 2018 02:30:42: 4000000 INFO @ Fri, 10 Aug 2018 02:30:48: 5000000 INFO @ Fri, 10 Aug 2018 02:30:49: 5000000 INFO @ Fri, 10 Aug 2018 02:30:49: 5000000 INFO @ Fri, 10 Aug 2018 02:30:55: 6000000 INFO @ Fri, 10 Aug 2018 02:30:56: 6000000 INFO @ Fri, 10 Aug 2018 02:30:56: 6000000 INFO @ Fri, 10 Aug 2018 02:31:03: 7000000 INFO @ Fri, 10 Aug 2018 02:31:03: 7000000 INFO @ Fri, 10 Aug 2018 02:31:04: 7000000 INFO @ Fri, 10 Aug 2018 02:31:10: 8000000 INFO @ Fri, 10 Aug 2018 02:31:10: 8000000 INFO @ Fri, 10 Aug 2018 02:31:11: 8000000 INFO @ Fri, 10 Aug 2018 02:31:17: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:31:17: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:31:17: #1 total tags in treatment: 4356722 INFO @ Fri, 10 Aug 2018 02:31:17: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:31:17: #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 02:31:17: #1 tags after filtering in treatment: 3536710 INFO @ Fri, 10 Aug 2018 02:31:17: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Aug 2018 02:31:17: #1 finished! INFO @ Fri, 10 Aug 2018 02:31:17: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:31:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:31:17: #2 number of paired peaks: 83 WARNING @ Fri, 10 Aug 2018 02:31:17: Too few paired peaks (83) 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 02:31:17: Process for pairing-model is terminated! cat: SRX3010302.10_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 `SRX3010302.10_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 `SRX3010302.10_*.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 `SRX3010302.10_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 02:31:18: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:31:18: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:31:18: #1 total tags in treatment: 4356722 INFO @ Fri, 10 Aug 2018 02:31:18: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:31:18: #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 02:31:18: #1 tags after filtering in treatment: 3536710 INFO @ Fri, 10 Aug 2018 02:31:18: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Aug 2018 02:31:18: #1 finished! INFO @ Fri, 10 Aug 2018 02:31:18: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:31:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:31:18: #2 number of paired peaks: 83 WARNING @ Fri, 10 Aug 2018 02:31:18: Too few paired peaks (83) 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 02:31:18: Process for pairing-model is terminated! cat: SRX3010302.05_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 `SRX3010302.05_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 `SRX3010302.05_*.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 `SRX3010302.05_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 02:31:18: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:31:18: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:31:18: #1 total tags in treatment: 4356722 INFO @ Fri, 10 Aug 2018 02:31:18: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:31:18: #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 02:31:18: #1 tags after filtering in treatment: 3536710 INFO @ Fri, 10 Aug 2018 02:31:18: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Aug 2018 02:31:18: #1 finished! INFO @ Fri, 10 Aug 2018 02:31:18: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:31:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:31:19: #2 number of paired peaks: 83 WARNING @ Fri, 10 Aug 2018 02:31:19: Too few paired peaks (83) 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 02:31:19: Process for pairing-model is terminated! cat: SRX3010302.20_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 `SRX3010302.20_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 `SRX3010302.20_*.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 `SRX3010302.20_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。