Job ID = 11245063 sra ファイルのダウンロード中... Completed: 153753K bytes transferred in 8 seconds (143271K 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 4465715 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554776/SRR7696448.sra Written 4465715 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554776/SRR7696448.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: 00:02:09 4465715 reads; of these: 4465715 (100.00%) were paired; of these: 2281365 (51.09%) aligned concordantly 0 times 2106602 (47.17%) aligned concordantly exactly 1 time 77748 (1.74%) aligned concordantly >1 times ---- 2281365 pairs aligned concordantly 0 times; of these: 2709 (0.12%) aligned discordantly 1 time ---- 2278656 pairs aligned 0 times concordantly or discordantly; of these: 4557312 mates make up the pairs; of these: 2791585 (61.26%) aligned 0 times 1688163 (37.04%) aligned exactly 1 time 77564 (1.70%) aligned >1 times 68.74% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 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] 65265 / 2186796 = 0.0298 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 23:21:26: # Command line: callpeak -t SRX4554776.bam -f BAM -g 12100000 -n SRX4554776.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554776.10 # format = BAM # ChIP-seq file = ['SRX4554776.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 23:21:26: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:21:26: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:21:26: # Command line: callpeak -t SRX4554776.bam -f BAM -g 12100000 -n SRX4554776.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554776.05 # format = BAM # ChIP-seq file = ['SRX4554776.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 23:21:26: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:21:26: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:21:26: # Command line: callpeak -t SRX4554776.bam -f BAM -g 12100000 -n SRX4554776.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554776.20 # format = BAM # ChIP-seq file = ['SRX4554776.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 23:21:26: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:21:26: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:21:32: 1000000 INFO @ Tue, 09 Oct 2018 23:21:32: 1000000 INFO @ Tue, 09 Oct 2018 23:21:33: 1000000 INFO @ Tue, 09 Oct 2018 23:21:39: 2000000 INFO @ Tue, 09 Oct 2018 23:21:39: 2000000 INFO @ Tue, 09 Oct 2018 23:21:40: 2000000 INFO @ Tue, 09 Oct 2018 23:21:45: 3000000 INFO @ Tue, 09 Oct 2018 23:21:45: 3000000 INFO @ Tue, 09 Oct 2018 23:21:48: 3000000 INFO @ Tue, 09 Oct 2018 23:21:51: 4000000 INFO @ Tue, 09 Oct 2018 23:21:51: 4000000 INFO @ Tue, 09 Oct 2018 23:21:55: 4000000 INFO @ Tue, 09 Oct 2018 23:21:58: 5000000 INFO @ Tue, 09 Oct 2018 23:21:58: 5000000 INFO @ Tue, 09 Oct 2018 23:22:02: 5000000 INFO @ Tue, 09 Oct 2018 23:22:04: 6000000 INFO @ Tue, 09 Oct 2018 23:22:04: 6000000 INFO @ Tue, 09 Oct 2018 23:22:04: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:22:04: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:22:04: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:22:04: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:22:04: #1 total tags in treatment: 2119091 INFO @ Tue, 09 Oct 2018 23:22:04: #1 total tags in treatment: 2119091 INFO @ Tue, 09 Oct 2018 23:22:04: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:22:04: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:22:04: #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 23:22:04: #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 23:22:04: #1 tags after filtering in treatment: 1520048 INFO @ Tue, 09 Oct 2018 23:22:04: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 09 Oct 2018 23:22:04: #1 finished! INFO @ Tue, 09 Oct 2018 23:22:04: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:22:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:22:04: #1 tags after filtering in treatment: 1520048 INFO @ Tue, 09 Oct 2018 23:22:04: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 09 Oct 2018 23:22:04: #1 finished! INFO @ Tue, 09 Oct 2018 23:22:04: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:22:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:22:04: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:22:04: 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 23:22:04: Process for pairing-model is terminated! INFO @ Tue, 09 Oct 2018 23:22:04: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:22:04: 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 23:22:04: Process for pairing-model is terminated! cat: SRX4554776.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX4554776.10_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)pass1 - making usageList (0 chroms): 1 millis : 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4554776.05_model.r'rm: cannot remove `SRX4554776.10_model.r': そのようなファイルやディレクトリはありません : 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 `SRX4554776.05_*.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 `SRX4554776.10_*.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 `SRX4554776.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4554776.10_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 CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:22:08: 6000000 INFO @ Tue, 09 Oct 2018 23:22:08: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:22:08: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:22:08: #1 total tags in treatment: 2119091 INFO @ Tue, 09 Oct 2018 23:22:08: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:22:08: #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 23:22:08: #1 tags after filtering in treatment: 1520048 INFO @ Tue, 09 Oct 2018 23:22:08: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 09 Oct 2018 23:22:08: #1 finished! INFO @ Tue, 09 Oct 2018 23:22:08: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:22:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:22:08: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:22:08: 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 23:22:08: Process for pairing-model is terminated! cat: SRX4554776.20_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 `SRX4554776.20_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 `SRX4554776.20_*.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 `SRX4554776.20_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。