Job ID = 10536344 sra ファイルのダウンロード中... Completed: 1004480K bytes transferred in 81 seconds (101549K 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... Written 28391853 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433211/SRR6333852.sra Written 28391853 spots total 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: 00:13:08 28391853 reads; of these: 28391853 (100.00%) were paired; of these: 13301728 (46.85%) aligned concordantly 0 times 13707217 (48.28%) aligned concordantly exactly 1 time 1382908 (4.87%) aligned concordantly >1 times ---- 13301728 pairs aligned concordantly 0 times; of these: 141464 (1.06%) aligned discordantly 1 time ---- 13160264 pairs aligned 0 times concordantly or discordantly; of these: 26320528 mates make up the pairs; of these: 26007622 (98.81%) aligned 0 times 254397 (0.97%) aligned exactly 1 time 58509 (0.22%) aligned >1 times 54.20% overall alignment rate Time searching: 00:13:08 Overall time: 00:13:08 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 16 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] 10027409 / 15105720 = 0.6638 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 @ Thu, 05 Apr 2018 09:07:34: # Command line: callpeak -t SRX3433211.bam -f BAM -g 12100000 -n SRX3433211.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433211.10 # format = BAM # ChIP-seq file = ['SRX3433211.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 @ Thu, 05 Apr 2018 09:07:34: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:07:34: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:07:34: # Command line: callpeak -t SRX3433211.bam -f BAM -g 12100000 -n SRX3433211.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433211.20 # format = BAM # ChIP-seq file = ['SRX3433211.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 @ Thu, 05 Apr 2018 09:07:34: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:07:34: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:07:34: # Command line: callpeak -t SRX3433211.bam -f BAM -g 12100000 -n SRX3433211.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433211.05 # format = BAM # ChIP-seq file = ['SRX3433211.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 @ Thu, 05 Apr 2018 09:07:34: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:07:34: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:07:39: 1000000 INFO @ Thu, 05 Apr 2018 09:07:39: 1000000 INFO @ Thu, 05 Apr 2018 09:07:39: 1000000 INFO @ Thu, 05 Apr 2018 09:07:45: 2000000 INFO @ Thu, 05 Apr 2018 09:07:45: 2000000 INFO @ Thu, 05 Apr 2018 09:07:45: 2000000 INFO @ Thu, 05 Apr 2018 09:07:50: 3000000 INFO @ Thu, 05 Apr 2018 09:07:50: 3000000 INFO @ Thu, 05 Apr 2018 09:07:50: 3000000 INFO @ Thu, 05 Apr 2018 09:07:55: 4000000 INFO @ Thu, 05 Apr 2018 09:07:55: 4000000 INFO @ Thu, 05 Apr 2018 09:07:55: 4000000 INFO @ Thu, 05 Apr 2018 09:08:00: 5000000 INFO @ Thu, 05 Apr 2018 09:08:00: 5000000 INFO @ Thu, 05 Apr 2018 09:08:00: 5000000 INFO @ Thu, 05 Apr 2018 09:08:05: 6000000 INFO @ Thu, 05 Apr 2018 09:08:06: 6000000 INFO @ Thu, 05 Apr 2018 09:08:06: 6000000 INFO @ Thu, 05 Apr 2018 09:08:10: 7000000 INFO @ Thu, 05 Apr 2018 09:08:11: 7000000 INFO @ Thu, 05 Apr 2018 09:08:11: 7000000 INFO @ Thu, 05 Apr 2018 09:08:15: 8000000 INFO @ Thu, 05 Apr 2018 09:08:16: 8000000 INFO @ Thu, 05 Apr 2018 09:08:16: 8000000 INFO @ Thu, 05 Apr 2018 09:08:21: 9000000 INFO @ Thu, 05 Apr 2018 09:08:21: 9000000 INFO @ Thu, 05 Apr 2018 09:08:21: 9000000 INFO @ Thu, 05 Apr 2018 09:08:26: 10000000 INFO @ Thu, 05 Apr 2018 09:08:27: 10000000 INFO @ Thu, 05 Apr 2018 09:08:27: 10000000 INFO @ Thu, 05 Apr 2018 09:08:29: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:08:29: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:08:29: #1 total tags in treatment: 5072797 INFO @ Thu, 05 Apr 2018 09:08:29: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:08:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:08:30: #1 tags after filtering in treatment: 3977499 INFO @ Thu, 05 Apr 2018 09:08:30: #1 Redundant rate of treatment: 0.22 INFO @ Thu, 05 Apr 2018 09:08:30: #1 finished! INFO @ Thu, 05 Apr 2018 09:08:30: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:08:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:08:30: #2 number of paired peaks: 77 WARNING @ Thu, 05 Apr 2018 09:08:30: Too few paired peaks (77) 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 @ Thu, 05 Apr 2018 09:08:30: Process for pairing-model is terminated! cat: SRX3433211.05_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 `SRX3433211.05_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 `SRX3433211.05_*.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 `SRX3433211.05_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 @ Thu, 05 Apr 2018 09:08:30: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:08:30: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:08:30: #1 total tags in treatment: 5072797 INFO @ Thu, 05 Apr 2018 09:08:30: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:08:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:08:30: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:08:30: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:08:30: #1 total tags in treatment: 5072797 INFO @ Thu, 05 Apr 2018 09:08:30: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:08:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:08:30: #1 tags after filtering in treatment: 3977499 INFO @ Thu, 05 Apr 2018 09:08:30: #1 Redundant rate of treatment: 0.22 INFO @ Thu, 05 Apr 2018 09:08:30: #1 finished! INFO @ Thu, 05 Apr 2018 09:08:30: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:08:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:08:31: #1 tags after filtering in treatment: 3977499 INFO @ Thu, 05 Apr 2018 09:08:31: #1 Redundant rate of treatment: 0.22 INFO @ Thu, 05 Apr 2018 09:08:31: #1 finished! INFO @ Thu, 05 Apr 2018 09:08:31: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:08:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:08:31: #2 number of paired peaks: 77 WARNING @ Thu, 05 Apr 2018 09:08:31: Too few paired peaks (77) 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 @ Thu, 05 Apr 2018 09:08:31: Process for pairing-model is terminated! cat: SRX3433211.10_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 `SRX3433211.10_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 `SRX3433211.10_*.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 `SRX3433211.10_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 @ Thu, 05 Apr 2018 09:08:31: #2 number of paired peaks: 77 WARNING @ Thu, 05 Apr 2018 09:08:31: Too few paired peaks (77) 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 @ Thu, 05 Apr 2018 09:08:31: Process for pairing-model is terminated! cat: SRX3433211.20_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 `SRX3433211.20_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 `SRX3433211.20_*.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 `SRX3433211.20_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。