Job ID = 11244806 sra ファイルのダウンロード中... Completed: 685144K bytes transferred in 17 seconds (320193K 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 7060693 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3659041/SRR6682735.sra Written 7060693 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3659041/SRR6682735.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: 00:11:00 7060693 reads; of these: 7060693 (100.00%) were paired; of these: 347365 (4.92%) aligned concordantly 0 times 5677711 (80.41%) aligned concordantly exactly 1 time 1035617 (14.67%) aligned concordantly >1 times ---- 347365 pairs aligned concordantly 0 times; of these: 52839 (15.21%) aligned discordantly 1 time ---- 294526 pairs aligned 0 times concordantly or discordantly; of these: 589052 mates make up the pairs; of these: 495309 (84.09%) aligned 0 times 63769 (10.83%) aligned exactly 1 time 29974 (5.09%) aligned >1 times 96.49% overall alignment rate Time searching: 00:11:00 Overall time: 00:11:00 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] 2046809 / 6698175 = 0.3056 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 22:06:43: # Command line: callpeak -t SRX3659041.bam -f BAM -g 12100000 -n SRX3659041.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3659041.10 # format = BAM # ChIP-seq file = ['SRX3659041.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 22:06:43: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:06:43: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:06:43: # Command line: callpeak -t SRX3659041.bam -f BAM -g 12100000 -n SRX3659041.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3659041.05 # format = BAM # ChIP-seq file = ['SRX3659041.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 22:06:43: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:06:43: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:06:43: # Command line: callpeak -t SRX3659041.bam -f BAM -g 12100000 -n SRX3659041.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3659041.20 # format = BAM # ChIP-seq file = ['SRX3659041.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 22:06:43: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:06:43: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:06:52: 1000000 INFO @ Tue, 09 Oct 2018 22:06:52: 1000000 INFO @ Tue, 09 Oct 2018 22:06:52: 1000000 INFO @ Tue, 09 Oct 2018 22:07:00: 2000000 INFO @ Tue, 09 Oct 2018 22:07:01: 2000000 INFO @ Tue, 09 Oct 2018 22:07:01: 2000000 INFO @ Tue, 09 Oct 2018 22:07:09: 3000000 INFO @ Tue, 09 Oct 2018 22:07:09: 3000000 INFO @ Tue, 09 Oct 2018 22:07:10: 3000000 INFO @ Tue, 09 Oct 2018 22:07:17: 4000000 INFO @ Tue, 09 Oct 2018 22:07:18: 4000000 INFO @ Tue, 09 Oct 2018 22:07:18: 4000000 INFO @ Tue, 09 Oct 2018 22:07:26: 5000000 INFO @ Tue, 09 Oct 2018 22:07:26: 5000000 INFO @ Tue, 09 Oct 2018 22:07:27: 5000000 INFO @ Tue, 09 Oct 2018 22:07:34: 6000000 INFO @ Tue, 09 Oct 2018 22:07:35: 6000000 INFO @ Tue, 09 Oct 2018 22:07:36: 6000000 INFO @ Tue, 09 Oct 2018 22:07:42: 7000000 INFO @ Tue, 09 Oct 2018 22:07:44: 7000000 INFO @ Tue, 09 Oct 2018 22:07:45: 7000000 INFO @ Tue, 09 Oct 2018 22:07:51: 8000000 INFO @ Tue, 09 Oct 2018 22:07:52: 8000000 INFO @ Tue, 09 Oct 2018 22:07:54: 8000000 INFO @ Tue, 09 Oct 2018 22:08:00: 9000000 INFO @ Tue, 09 Oct 2018 22:08:00: 9000000 INFO @ Tue, 09 Oct 2018 22:08:03: 9000000 INFO @ Tue, 09 Oct 2018 22:08:04: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:08:04: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:08:04: #1 total tags in treatment: 4672927 INFO @ Tue, 09 Oct 2018 22:08:04: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:08:04: #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 22:08:04: #1 tags after filtering in treatment: 3717613 INFO @ Tue, 09 Oct 2018 22:08:04: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 09 Oct 2018 22:08:04: #1 finished! INFO @ Tue, 09 Oct 2018 22:08:04: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:08:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:08:04: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:08:04: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:08:04: #1 total tags in treatment: 4672927 INFO @ Tue, 09 Oct 2018 22:08:04: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:08:04: #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 22:08:05: #1 tags after filtering in treatment: 3717613 INFO @ Tue, 09 Oct 2018 22:08:05: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 09 Oct 2018 22:08:05: #1 finished! INFO @ Tue, 09 Oct 2018 22:08:05: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:08:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:08:05: #2 number of paired peaks: 97 WARNING @ Tue, 09 Oct 2018 22:08:05: Too few paired peaks (97) 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 22:08:05: Process for pairing-model is terminated! cat: SRX3659041.05_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 `SRX3659041.05_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 `SRX3659041.05_*.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 `SRX3659041.05_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 22:08:05: #2 number of paired peaks: 97 WARNING @ Tue, 09 Oct 2018 22:08:05: Too few paired peaks (97) 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 22:08:05: Process for pairing-model is terminated! cat: SRX3659041.20_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 `SRX3659041.20_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 `SRX3659041.20_*.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 `SRX3659041.20_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 INFO @ Tue, 09 Oct 2018 22:08:07: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:08:07: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:08:07: #1 total tags in treatment: 4672927 INFO @ Tue, 09 Oct 2018 22:08:07: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:08:07: #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 22:08:07: #1 tags after filtering in treatment: 3717613 INFO @ Tue, 09 Oct 2018 22:08:07: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 09 Oct 2018 22:08:07: #1 finished! INFO @ Tue, 09 Oct 2018 22:08:07: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:08:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:08:07: #2 number of paired peaks: 97 WARNING @ Tue, 09 Oct 2018 22:08:07: Too few paired peaks (97) 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 22:08:07: Process for pairing-model is terminated! cat: SRX3659041.10_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 `SRX3659041.10_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 `SRX3659041.10_*.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 `SRX3659041.10_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。