Job ID = 11244864 sra ファイルのダウンロード中... Completed: 324279K bytes transferred in 6 seconds (413373K 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 3333201 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765656/SRR6807379.sra Written 3333201 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765656/SRR6807379.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: 00:04:22 3333201 reads; of these: 3333201 (100.00%) were paired; of these: 100412 (3.01%) aligned concordantly 0 times 2941227 (88.24%) aligned concordantly exactly 1 time 291562 (8.75%) aligned concordantly >1 times ---- 100412 pairs aligned concordantly 0 times; of these: 47310 (47.12%) aligned discordantly 1 time ---- 53102 pairs aligned 0 times concordantly or discordantly; of these: 106204 mates make up the pairs; of these: 59643 (56.16%) aligned 0 times 32947 (31.02%) aligned exactly 1 time 13614 (12.82%) aligned >1 times 99.11% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 177123 / 3257445 = 0.0544 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 22:17:51: # Command line: callpeak -t SRX3765656.bam -f BAM -g 12100000 -n SRX3765656.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3765656.20 # format = BAM # ChIP-seq file = ['SRX3765656.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 22:17:51: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:17:51: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:17:51: # Command line: callpeak -t SRX3765656.bam -f BAM -g 12100000 -n SRX3765656.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3765656.05 # format = BAM # ChIP-seq file = ['SRX3765656.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 22:17:51: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:17:51: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:17:51: # Command line: callpeak -t SRX3765656.bam -f BAM -g 12100000 -n SRX3765656.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3765656.10 # format = BAM # ChIP-seq file = ['SRX3765656.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 22:17:51: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:17:51: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:18:00: 1000000 INFO @ Tue, 09 Oct 2018 22:18:00: 1000000 INFO @ Tue, 09 Oct 2018 22:18:00: 1000000 INFO @ Tue, 09 Oct 2018 22:18:09: 2000000 INFO @ Tue, 09 Oct 2018 22:18:09: 2000000 INFO @ Tue, 09 Oct 2018 22:18:09: 2000000 INFO @ Tue, 09 Oct 2018 22:18:18: 3000000 INFO @ Tue, 09 Oct 2018 22:18:19: 3000000 INFO @ Tue, 09 Oct 2018 22:18:19: 3000000 INFO @ Tue, 09 Oct 2018 22:18:27: 4000000 INFO @ Tue, 09 Oct 2018 22:18:27: 4000000 INFO @ Tue, 09 Oct 2018 22:18:27: 4000000 INFO @ Tue, 09 Oct 2018 22:18:35: 5000000 INFO @ Tue, 09 Oct 2018 22:18:35: 5000000 INFO @ Tue, 09 Oct 2018 22:18:35: 5000000 INFO @ Tue, 09 Oct 2018 22:18:43: 6000000 INFO @ Tue, 09 Oct 2018 22:18:43: 6000000 INFO @ Tue, 09 Oct 2018 22:18:44: 6000000 INFO @ Tue, 09 Oct 2018 22:18:45: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:18:45: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:18:45: #1 total tags in treatment: 3055841 INFO @ Tue, 09 Oct 2018 22:18:45: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:18:45: #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 22:18:45: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:18:45: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:18:45: #1 total tags in treatment: 3055841 INFO @ Tue, 09 Oct 2018 22:18:45: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:18:45: #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 22:18:45: #1 tags after filtering in treatment: 2312929 INFO @ Tue, 09 Oct 2018 22:18:45: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 09 Oct 2018 22:18:45: #1 finished! INFO @ Tue, 09 Oct 2018 22:18:45: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:18:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:18:45: #1 tags after filtering in treatment: 2312929 INFO @ Tue, 09 Oct 2018 22:18:45: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 09 Oct 2018 22:18:45: #1 finished! INFO @ Tue, 09 Oct 2018 22:18:45: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:18:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:18:45: #2 number of paired peaks: 16 WARNING @ Tue, 09 Oct 2018 22:18:45: Too few paired peaks (16) 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 22:18:45: Process for pairing-model is terminated! INFO @ Tue, 09 Oct 2018 22:18:45: #2 number of paired peaks: 16 WARNING @ Tue, 09 Oct 2018 22:18:45: Too few paired peaks (16) 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 22:18:45: Process for pairing-model is terminated! cat: SRX3765656.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX3765656.05_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184)needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3765656.20_model.r'rm: cannot remove `SRX3765656.05_model.r': そのようなファイルやディレクトリはありません : 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 `SRX3765656.20_*.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 `SRX3765656.05_*.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 `SRX3765656.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `SRX3765656.05_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 CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:18:46: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:18:46: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:18:46: #1 total tags in treatment: 3055841 INFO @ Tue, 09 Oct 2018 22:18:46: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:18:46: #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 22:18:46: #1 tags after filtering in treatment: 2312929 INFO @ Tue, 09 Oct 2018 22:18:46: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 09 Oct 2018 22:18:46: #1 finished! INFO @ Tue, 09 Oct 2018 22:18:46: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:18:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:18:46: #2 number of paired peaks: 16 WARNING @ Tue, 09 Oct 2018 22:18:46: Too few paired peaks (16) 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 22:18:46: Process for pairing-model is terminated! cat: SRX3765656.10_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 `SRX3765656.10_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 `SRX3765656.10_*.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 `SRX3765656.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。