Job ID = 11245168 sra ファイルのダウンロード中... Completed: 331853K bytes transferred in 6 seconds (423064K 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 6827179 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669614/SRR7818197.sra Written 6827179 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669614/SRR7818197.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: 00:04:48 6827179 reads; of these: 6827179 (100.00%) were paired; of these: 726952 (10.65%) aligned concordantly 0 times 5305517 (77.71%) aligned concordantly exactly 1 time 794710 (11.64%) aligned concordantly >1 times ---- 726952 pairs aligned concordantly 0 times; of these: 29956 (4.12%) aligned discordantly 1 time ---- 696996 pairs aligned 0 times concordantly or discordantly; of these: 1393992 mates make up the pairs; of these: 1114619 (79.96%) aligned 0 times 196804 (14.12%) aligned exactly 1 time 82569 (5.92%) aligned >1 times 91.84% overall alignment rate Time searching: 00:04:48 Overall time: 00:04:48 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] 88074 / 6117798 = 0.0144 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 23:48:57: # Command line: callpeak -t SRX4669614.bam -f BAM -g 12100000 -n SRX4669614.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669614.05 # format = BAM # ChIP-seq file = ['SRX4669614.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 23:48:57: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:48:57: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:48:57: # Command line: callpeak -t SRX4669614.bam -f BAM -g 12100000 -n SRX4669614.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669614.20 # format = BAM # ChIP-seq file = ['SRX4669614.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 23:48:57: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:48:57: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:48:57: # Command line: callpeak -t SRX4669614.bam -f BAM -g 12100000 -n SRX4669614.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669614.10 # format = BAM # ChIP-seq file = ['SRX4669614.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 23:48:57: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:48:57: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:49:03: 1000000 INFO @ Tue, 09 Oct 2018 23:49:03: 1000000 INFO @ Tue, 09 Oct 2018 23:49:03: 1000000 INFO @ Tue, 09 Oct 2018 23:49:09: 2000000 INFO @ Tue, 09 Oct 2018 23:49:10: 2000000 INFO @ Tue, 09 Oct 2018 23:49:10: 2000000 INFO @ Tue, 09 Oct 2018 23:49:15: 3000000 INFO @ Tue, 09 Oct 2018 23:49:16: 3000000 INFO @ Tue, 09 Oct 2018 23:49:16: 3000000 INFO @ Tue, 09 Oct 2018 23:49:21: 4000000 INFO @ Tue, 09 Oct 2018 23:49:22: 4000000 INFO @ Tue, 09 Oct 2018 23:49:22: 4000000 INFO @ Tue, 09 Oct 2018 23:49:27: 5000000 INFO @ Tue, 09 Oct 2018 23:49:29: 5000000 INFO @ Tue, 09 Oct 2018 23:49:29: 5000000 INFO @ Tue, 09 Oct 2018 23:49:33: 6000000 INFO @ Tue, 09 Oct 2018 23:49:35: 6000000 INFO @ Tue, 09 Oct 2018 23:49:35: 6000000 INFO @ Tue, 09 Oct 2018 23:49:40: 7000000 INFO @ Tue, 09 Oct 2018 23:49:41: 7000000 INFO @ Tue, 09 Oct 2018 23:49:42: 7000000 INFO @ Tue, 09 Oct 2018 23:49:46: 8000000 INFO @ Tue, 09 Oct 2018 23:49:48: 8000000 INFO @ Tue, 09 Oct 2018 23:49:48: 8000000 INFO @ Tue, 09 Oct 2018 23:49:52: 9000000 INFO @ Tue, 09 Oct 2018 23:49:54: 9000000 INFO @ Tue, 09 Oct 2018 23:49:55: 9000000 INFO @ Tue, 09 Oct 2018 23:49:58: 10000000 INFO @ Tue, 09 Oct 2018 23:50:01: 10000000 INFO @ Tue, 09 Oct 2018 23:50:01: 10000000 INFO @ Tue, 09 Oct 2018 23:50:04: 11000000 INFO @ Tue, 09 Oct 2018 23:50:08: 11000000 INFO @ Tue, 09 Oct 2018 23:50:08: 11000000 INFO @ Tue, 09 Oct 2018 23:50:10: 12000000 INFO @ Tue, 09 Oct 2018 23:50:12: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:50:12: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:50:12: #1 total tags in treatment: 6012564 INFO @ Tue, 09 Oct 2018 23:50:12: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:50:12: #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 23:50:12: #1 tags after filtering in treatment: 4847288 INFO @ Tue, 09 Oct 2018 23:50:12: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 09 Oct 2018 23:50:12: #1 finished! INFO @ Tue, 09 Oct 2018 23:50:12: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:50:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:50:13: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:50:13: 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 23:50:13: Process for pairing-model is terminated! cat: SRX4669614.05_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 `SRX4669614.05_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 `SRX4669614.05_*.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 `SRX4669614.05_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 23:50:14: 12000000 INFO @ Tue, 09 Oct 2018 23:50:14: 12000000 INFO @ Tue, 09 Oct 2018 23:50:16: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:50:16: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:50:16: #1 total tags in treatment: 6012564 INFO @ Tue, 09 Oct 2018 23:50:16: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:50:16: #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 23:50:16: #1 tags after filtering in treatment: 4847288 INFO @ Tue, 09 Oct 2018 23:50:16: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 09 Oct 2018 23:50:16: #1 finished! INFO @ Tue, 09 Oct 2018 23:50:16: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:50:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:50:17: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:50:17: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:50:17: #1 total tags in treatment: 6012564 INFO @ Tue, 09 Oct 2018 23:50:17: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:50:17: #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 23:50:17: #1 tags after filtering in treatment: 4847288 INFO @ Tue, 09 Oct 2018 23:50:17: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 09 Oct 2018 23:50:17: #1 finished! INFO @ Tue, 09 Oct 2018 23:50:17: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:50:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:50:17: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:50:17: 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 23:50:17: Process for pairing-model is terminated! cat: SRX4669614.10_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 `SRX4669614.10_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 `SRX4669614.10_*.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 `SRX4669614.10_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 23:50:17: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:50:17: 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 23:50:17: Process for pairing-model is terminated! cat: SRX4669614.20_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 `SRX4669614.20_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 `SRX4669614.20_*.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 `SRX4669614.20_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。