Job ID = 11244869 sra ファイルのダウンロード中... Completed: 851930K bytes transferred in 10 seconds (691277K 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 8714779 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765661/SRR6807384.sra Written 8714779 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765661/SRR6807384.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: 00:12:50 8714779 reads; of these: 8714779 (100.00%) were paired; of these: 421752 (4.84%) aligned concordantly 0 times 6804750 (78.08%) aligned concordantly exactly 1 time 1488277 (17.08%) aligned concordantly >1 times ---- 421752 pairs aligned concordantly 0 times; of these: 77192 (18.30%) aligned discordantly 1 time ---- 344560 pairs aligned 0 times concordantly or discordantly; of these: 689120 mates make up the pairs; of these: 542008 (78.65%) aligned 0 times 90743 (13.17%) aligned exactly 1 time 56369 (8.18%) aligned >1 times 96.89% overall alignment rate Time searching: 00:12:50 Overall time: 00:12:50 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] 870423 / 8343377 = 0.1043 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 22:36:02: # Command line: callpeak -t SRX3765661.bam -f BAM -g 12100000 -n SRX3765661.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3765661.20 # format = BAM # ChIP-seq file = ['SRX3765661.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 22:36:02: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:36:02: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:36:02: # Command line: callpeak -t SRX3765661.bam -f BAM -g 12100000 -n SRX3765661.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3765661.05 # format = BAM # ChIP-seq file = ['SRX3765661.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 22:36:02: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:36:02: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:36:02: # Command line: callpeak -t SRX3765661.bam -f BAM -g 12100000 -n SRX3765661.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3765661.10 # format = BAM # ChIP-seq file = ['SRX3765661.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 22:36:02: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:36:02: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:36:09: 1000000 INFO @ Tue, 09 Oct 2018 22:36:09: 1000000 INFO @ Tue, 09 Oct 2018 22:36:09: 1000000 INFO @ Tue, 09 Oct 2018 22:36:15: 2000000 INFO @ Tue, 09 Oct 2018 22:36:15: 2000000 INFO @ Tue, 09 Oct 2018 22:36:16: 2000000 INFO @ Tue, 09 Oct 2018 22:36:22: 3000000 INFO @ Tue, 09 Oct 2018 22:36:23: 3000000 INFO @ Tue, 09 Oct 2018 22:36:23: 3000000 INFO @ Tue, 09 Oct 2018 22:36:29: 4000000 INFO @ Tue, 09 Oct 2018 22:36:30: 4000000 INFO @ Tue, 09 Oct 2018 22:36:30: 4000000 INFO @ Tue, 09 Oct 2018 22:36:36: 5000000 INFO @ Tue, 09 Oct 2018 22:36:36: 5000000 INFO @ Tue, 09 Oct 2018 22:36:36: 5000000 INFO @ Tue, 09 Oct 2018 22:36:43: 6000000 INFO @ Tue, 09 Oct 2018 22:36:43: 6000000 INFO @ Tue, 09 Oct 2018 22:36:43: 6000000 INFO @ Tue, 09 Oct 2018 22:36:50: 7000000 INFO @ Tue, 09 Oct 2018 22:36:50: 7000000 INFO @ Tue, 09 Oct 2018 22:36:51: 7000000 INFO @ Tue, 09 Oct 2018 22:36:57: 8000000 INFO @ Tue, 09 Oct 2018 22:36:57: 8000000 INFO @ Tue, 09 Oct 2018 22:36:58: 8000000 INFO @ Tue, 09 Oct 2018 22:37:04: 9000000 INFO @ Tue, 09 Oct 2018 22:37:05: 9000000 INFO @ Tue, 09 Oct 2018 22:37:05: 9000000 INFO @ Tue, 09 Oct 2018 22:37:10: 10000000 INFO @ Tue, 09 Oct 2018 22:37:12: 10000000 INFO @ Tue, 09 Oct 2018 22:37:13: 10000000 INFO @ Tue, 09 Oct 2018 22:37:17: 11000000 INFO @ Tue, 09 Oct 2018 22:37:19: 11000000 INFO @ Tue, 09 Oct 2018 22:37:20: 11000000 INFO @ Tue, 09 Oct 2018 22:37:24: 12000000 INFO @ Tue, 09 Oct 2018 22:37:26: 12000000 INFO @ Tue, 09 Oct 2018 22:37:27: 12000000 INFO @ Tue, 09 Oct 2018 22:37:31: 13000000 INFO @ Tue, 09 Oct 2018 22:37:34: 13000000 INFO @ Tue, 09 Oct 2018 22:37:35: 13000000 INFO @ Tue, 09 Oct 2018 22:37:37: 14000000 INFO @ Tue, 09 Oct 2018 22:37:41: 14000000 INFO @ Tue, 09 Oct 2018 22:37:42: 14000000 INFO @ Tue, 09 Oct 2018 22:37:44: 15000000 INFO @ Tue, 09 Oct 2018 22:37:45: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:37:45: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:37:45: #1 total tags in treatment: 7425898 INFO @ Tue, 09 Oct 2018 22:37:45: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:37:45: #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 22:37:45: #1 tags after filtering in treatment: 5475504 INFO @ Tue, 09 Oct 2018 22:37:45: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 09 Oct 2018 22:37:45: #1 finished! INFO @ Tue, 09 Oct 2018 22:37:45: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:37:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:37:46: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:37:46: 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 22:37:46: Process for pairing-model is terminated! cat: SRX3765661.10_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 `SRX3765661.10_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 `SRX3765661.10_*.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 `SRX3765661.10_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 22:37:48: 15000000 INFO @ Tue, 09 Oct 2018 22:37:49: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:37:49: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:37:49: #1 total tags in treatment: 7425898 INFO @ Tue, 09 Oct 2018 22:37:49: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:37:49: #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 22:37:49: #1 tags after filtering in treatment: 5475504 INFO @ Tue, 09 Oct 2018 22:37:49: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 09 Oct 2018 22:37:49: #1 finished! INFO @ Tue, 09 Oct 2018 22:37:49: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:37:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:37:50: 15000000 INFO @ Tue, 09 Oct 2018 22:37:50: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:37:50: 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 22:37:50: Process for pairing-model is terminated! cat: SRX3765661.05_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 `SRX3765661.05_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 `SRX3765661.05_*.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 `SRX3765661.05_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 22:37:51: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:37:51: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:37:51: #1 total tags in treatment: 7425898 INFO @ Tue, 09 Oct 2018 22:37:51: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:37:51: #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 22:37:51: #1 tags after filtering in treatment: 5475504 INFO @ Tue, 09 Oct 2018 22:37:51: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 09 Oct 2018 22:37:51: #1 finished! INFO @ Tue, 09 Oct 2018 22:37:51: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:37:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:37:51: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:37:51: 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 22:37:51: Process for pairing-model is terminated! cat: SRX3765661.20_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 `SRX3765661.20_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 `SRX3765661.20_*.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 `SRX3765661.20_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。