Job ID = 11244857 sra ファイルのダウンロード中... Completed: 891837K bytes transferred in 11 seconds (647544K 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 9206811 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765651/SRR6807374.sra Written 9206811 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765651/SRR6807374.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: 00:12:30 9206811 reads; of these: 9206811 (100.00%) were paired; of these: 240547 (2.61%) aligned concordantly 0 times 7950063 (86.35%) aligned concordantly exactly 1 time 1016201 (11.04%) aligned concordantly >1 times ---- 240547 pairs aligned concordantly 0 times; of these: 66918 (27.82%) aligned discordantly 1 time ---- 173629 pairs aligned 0 times concordantly or discordantly; of these: 347258 mates make up the pairs; of these: 239019 (68.83%) aligned 0 times 79168 (22.80%) aligned exactly 1 time 29071 (8.37%) aligned >1 times 98.70% overall alignment rate Time searching: 00:12:30 Overall time: 00:12:30 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] 939320 / 8900072 = 0.1055 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 22:31:30: # Command line: callpeak -t SRX3765651.bam -f BAM -g 12100000 -n SRX3765651.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3765651.20 # format = BAM # ChIP-seq file = ['SRX3765651.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 22:31:30: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:31:30: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:31:30: # Command line: callpeak -t SRX3765651.bam -f BAM -g 12100000 -n SRX3765651.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3765651.05 # format = BAM # ChIP-seq file = ['SRX3765651.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 22:31:30: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:31:30: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:31:30: # Command line: callpeak -t SRX3765651.bam -f BAM -g 12100000 -n SRX3765651.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3765651.10 # format = BAM # ChIP-seq file = ['SRX3765651.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 22:31:30: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:31:30: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:31:38: 1000000 INFO @ Tue, 09 Oct 2018 22:31:38: 1000000 INFO @ Tue, 09 Oct 2018 22:31:38: 1000000 INFO @ Tue, 09 Oct 2018 22:31:46: 2000000 INFO @ Tue, 09 Oct 2018 22:31:47: 2000000 INFO @ Tue, 09 Oct 2018 22:31:47: 2000000 INFO @ Tue, 09 Oct 2018 22:31:54: 3000000 INFO @ Tue, 09 Oct 2018 22:31:56: 3000000 INFO @ Tue, 09 Oct 2018 22:31:56: 3000000 INFO @ Tue, 09 Oct 2018 22:32:02: 4000000 INFO @ Tue, 09 Oct 2018 22:32:05: 4000000 INFO @ Tue, 09 Oct 2018 22:32:05: 4000000 INFO @ Tue, 09 Oct 2018 22:32:10: 5000000 INFO @ Tue, 09 Oct 2018 22:32:13: 5000000 INFO @ Tue, 09 Oct 2018 22:32:13: 5000000 INFO @ Tue, 09 Oct 2018 22:32:18: 6000000 INFO @ Tue, 09 Oct 2018 22:32:22: 6000000 INFO @ Tue, 09 Oct 2018 22:32:22: 6000000 INFO @ Tue, 09 Oct 2018 22:32:26: 7000000 INFO @ Tue, 09 Oct 2018 22:32:31: 7000000 INFO @ Tue, 09 Oct 2018 22:32:31: 7000000 INFO @ Tue, 09 Oct 2018 22:32:34: 8000000 INFO @ Tue, 09 Oct 2018 22:32:39: 8000000 INFO @ Tue, 09 Oct 2018 22:32:39: 8000000 INFO @ Tue, 09 Oct 2018 22:32:42: 9000000 INFO @ Tue, 09 Oct 2018 22:32:48: 9000000 INFO @ Tue, 09 Oct 2018 22:32:48: 9000000 INFO @ Tue, 09 Oct 2018 22:32:51: 10000000 INFO @ Tue, 09 Oct 2018 22:32:58: 10000000 INFO @ Tue, 09 Oct 2018 22:32:58: 10000000 INFO @ Tue, 09 Oct 2018 22:33:01: 11000000 INFO @ Tue, 09 Oct 2018 22:33:07: 11000000 INFO @ Tue, 09 Oct 2018 22:33:07: 11000000 INFO @ Tue, 09 Oct 2018 22:33:11: 12000000 INFO @ Tue, 09 Oct 2018 22:33:17: 12000000 INFO @ Tue, 09 Oct 2018 22:33:17: 12000000 INFO @ Tue, 09 Oct 2018 22:33:21: 13000000 INFO @ Tue, 09 Oct 2018 22:33:27: 13000000 INFO @ Tue, 09 Oct 2018 22:33:27: 13000000 INFO @ Tue, 09 Oct 2018 22:33:31: 14000000 INFO @ Tue, 09 Oct 2018 22:33:36: 14000000 INFO @ Tue, 09 Oct 2018 22:33:36: 14000000 INFO @ Tue, 09 Oct 2018 22:33:41: 15000000 INFO @ Tue, 09 Oct 2018 22:33:46: 15000000 INFO @ Tue, 09 Oct 2018 22:33:46: 15000000 INFO @ Tue, 09 Oct 2018 22:33:51: 16000000 INFO @ Tue, 09 Oct 2018 22:33:53: #1 tag size is determined as 101 bps INFO @ Tue, 09 Oct 2018 22:33:53: #1 tag size = 101 INFO @ Tue, 09 Oct 2018 22:33:53: #1 total tags in treatment: 8028197 INFO @ Tue, 09 Oct 2018 22:33:53: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:33:53: #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 22:33:54: #1 tags after filtering in treatment: 4771388 INFO @ Tue, 09 Oct 2018 22:33:54: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 09 Oct 2018 22:33:54: #1 finished! INFO @ Tue, 09 Oct 2018 22:33:54: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:33:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:33:54: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:33:54: 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 22:33:54: Process for pairing-model is terminated! cat: SRX3765651.10_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 `SRX3765651.10_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 `SRX3765651.10_*.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 `SRX3765651.10_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 22:33:55: 16000000 INFO @ Tue, 09 Oct 2018 22:33:55: 16000000 INFO @ Tue, 09 Oct 2018 22:33:57: #1 tag size is determined as 101 bps INFO @ Tue, 09 Oct 2018 22:33:57: #1 tag size = 101 INFO @ Tue, 09 Oct 2018 22:33:57: #1 total tags in treatment: 8028197 INFO @ Tue, 09 Oct 2018 22:33:57: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:33:57: #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 22:33:57: #1 tag size is determined as 101 bps INFO @ Tue, 09 Oct 2018 22:33:57: #1 tag size = 101 INFO @ Tue, 09 Oct 2018 22:33:57: #1 total tags in treatment: 8028197 INFO @ Tue, 09 Oct 2018 22:33:57: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:33:57: #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 22:33:58: #1 tags after filtering in treatment: 4771388 INFO @ Tue, 09 Oct 2018 22:33:58: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 09 Oct 2018 22:33:58: #1 finished! INFO @ Tue, 09 Oct 2018 22:33:58: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:33:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:33:58: #1 tags after filtering in treatment: 4771388 INFO @ Tue, 09 Oct 2018 22:33:58: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 09 Oct 2018 22:33:58: #1 finished! INFO @ Tue, 09 Oct 2018 22:33:58: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:33:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:33:58: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:33:58: 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 22:33:58: Process for pairing-model is terminated! INFO @ Tue, 09 Oct 2018 22:33:58: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:33:58: 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 22:33:58: Process for pairing-model is terminated! cat: SRX3765651.20_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: SRX3765651.05_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3765651.20_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 `SRX3765651.20_*.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 `SRX3765651.20_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3765651.05_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 `SRX3765651.05_*.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 `SRX3765651.05_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。