Job ID = 11244865 sra ファイルのダウンロード中... Completed: 405198K bytes transferred in 6 seconds (474807K 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 4171338 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765657/SRR6807380.sra Written 4171338 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765657/SRR6807380.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: 00:04:53 4171338 reads; of these: 4171338 (100.00%) were paired; of these: 115768 (2.78%) aligned concordantly 0 times 3734494 (89.53%) aligned concordantly exactly 1 time 321076 (7.70%) aligned concordantly >1 times ---- 115768 pairs aligned concordantly 0 times; of these: 48892 (42.23%) aligned discordantly 1 time ---- 66876 pairs aligned 0 times concordantly or discordantly; of these: 133752 mates make up the pairs; of these: 81096 (60.63%) aligned 0 times 39692 (29.68%) aligned exactly 1 time 12964 (9.69%) aligned >1 times 99.03% overall alignment rate Time searching: 00:04:53 Overall time: 00:04:53 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] 230645 / 4083780 = 0.0565 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 22:19:22: # Command line: callpeak -t SRX3765657.bam -f BAM -g 12100000 -n SRX3765657.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3765657.20 # format = BAM # ChIP-seq file = ['SRX3765657.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 22:19:22: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:19:22: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:19:22: # Command line: callpeak -t SRX3765657.bam -f BAM -g 12100000 -n SRX3765657.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3765657.05 # format = BAM # ChIP-seq file = ['SRX3765657.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 22:19:22: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:19:22: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:19:22: # Command line: callpeak -t SRX3765657.bam -f BAM -g 12100000 -n SRX3765657.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3765657.10 # format = BAM # ChIP-seq file = ['SRX3765657.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 22:19:22: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:19:22: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:19:30: 1000000 INFO @ Tue, 09 Oct 2018 22:19:30: 1000000 INFO @ Tue, 09 Oct 2018 22:19:30: 1000000 INFO @ Tue, 09 Oct 2018 22:19:38: 2000000 INFO @ Tue, 09 Oct 2018 22:19:38: 2000000 INFO @ Tue, 09 Oct 2018 22:19:38: 2000000 INFO @ Tue, 09 Oct 2018 22:19:46: 3000000 INFO @ Tue, 09 Oct 2018 22:19:46: 3000000 INFO @ Tue, 09 Oct 2018 22:19:46: 3000000 INFO @ Tue, 09 Oct 2018 22:19:54: 4000000 INFO @ Tue, 09 Oct 2018 22:19:54: 4000000 INFO @ Tue, 09 Oct 2018 22:19:54: 4000000 INFO @ Tue, 09 Oct 2018 22:20:02: 5000000 INFO @ Tue, 09 Oct 2018 22:20:02: 5000000 INFO @ Tue, 09 Oct 2018 22:20:03: 5000000 INFO @ Tue, 09 Oct 2018 22:20:10: 6000000 INFO @ Tue, 09 Oct 2018 22:20:10: 6000000 INFO @ Tue, 09 Oct 2018 22:20:11: 6000000 INFO @ Tue, 09 Oct 2018 22:20:17: 7000000 INFO @ Tue, 09 Oct 2018 22:20:19: 7000000 INFO @ Tue, 09 Oct 2018 22:20:19: 7000000 INFO @ Tue, 09 Oct 2018 22:20:24: #1 tag size is determined as 101 bps INFO @ Tue, 09 Oct 2018 22:20:24: #1 tag size = 101 INFO @ Tue, 09 Oct 2018 22:20:24: #1 total tags in treatment: 3825241 INFO @ Tue, 09 Oct 2018 22:20:24: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:20:24: #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 22:20:24: #1 tags after filtering in treatment: 2790352 INFO @ Tue, 09 Oct 2018 22:20:24: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 09 Oct 2018 22:20:24: #1 finished! INFO @ Tue, 09 Oct 2018 22:20:24: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:20:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:20:24: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:20:24: 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 22:20:24: Process for pairing-model is terminated! cat: SRX3765657.10_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 `SRX3765657.10_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 `SRX3765657.10_*.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 `SRX3765657.10_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 22:20:25: #1 tag size is determined as 101 bps INFO @ Tue, 09 Oct 2018 22:20:25: #1 tag size = 101 INFO @ Tue, 09 Oct 2018 22:20:25: #1 total tags in treatment: 3825241 INFO @ Tue, 09 Oct 2018 22:20:25: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:20:25: #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 22:20:25: #1 tags after filtering in treatment: 2790352 INFO @ Tue, 09 Oct 2018 22:20:25: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 09 Oct 2018 22:20:25: #1 finished! INFO @ Tue, 09 Oct 2018 22:20:25: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:20:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:20:26: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:20:26: 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 22:20:26: Process for pairing-model is terminated! cat: SRX3765657.05_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 `SRX3765657.05_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 `SRX3765657.05_*.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 `SRX3765657.05_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 @ Tue, 09 Oct 2018 22:20:26: #1 tag size is determined as 101 bps INFO @ Tue, 09 Oct 2018 22:20:26: #1 tag size = 101 INFO @ Tue, 09 Oct 2018 22:20:26: #1 total tags in treatment: 3825241 INFO @ Tue, 09 Oct 2018 22:20:26: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:20:26: #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 22:20:26: #1 tags after filtering in treatment: 2790352 INFO @ Tue, 09 Oct 2018 22:20:26: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 09 Oct 2018 22:20:26: #1 finished! INFO @ Tue, 09 Oct 2018 22:20:26: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:20:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:20:26: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:20:26: 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 22:20:26: Process for pairing-model is terminated! cat: SRX3765657.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3765657.20_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 `SRX3765657.20_*.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 `SRX3765657.20_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。