Job ID = 11244949 sra ファイルのダウンロード中... Completed: 199787K bytes transferred in 6 seconds (261664K 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 6165208 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554679/SRR7696352.sra Written 6165208 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554679/SRR7696352.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: 00:02:26 6165208 reads; of these: 6165208 (100.00%) were paired; of these: 4181903 (67.83%) aligned concordantly 0 times 1345810 (21.83%) aligned concordantly exactly 1 time 637495 (10.34%) aligned concordantly >1 times ---- 4181903 pairs aligned concordantly 0 times; of these: 39824 (0.95%) aligned discordantly 1 time ---- 4142079 pairs aligned 0 times concordantly or discordantly; of these: 8284158 mates make up the pairs; of these: 8174743 (98.68%) aligned 0 times 46229 (0.56%) aligned exactly 1 time 63186 (0.76%) aligned >1 times 33.70% overall alignment rate Time searching: 00:02:26 Overall time: 00:02:26 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] 76888 / 2014396 = 0.0382 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 22:58:32: # Command line: callpeak -t SRX4554679.bam -f BAM -g 12100000 -n SRX4554679.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554679.05 # format = BAM # ChIP-seq file = ['SRX4554679.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 22:58:32: # Command line: callpeak -t SRX4554679.bam -f BAM -g 12100000 -n SRX4554679.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554679.20 # format = BAM # ChIP-seq file = ['SRX4554679.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 22:58:32: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:58:32: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:58:32: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:58:32: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:58:32: # Command line: callpeak -t SRX4554679.bam -f BAM -g 12100000 -n SRX4554679.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554679.10 # format = BAM # ChIP-seq file = ['SRX4554679.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 22:58:32: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:58:32: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:58:38: 1000000 INFO @ Tue, 09 Oct 2018 22:58:38: 1000000 INFO @ Tue, 09 Oct 2018 22:58:39: 1000000 INFO @ Tue, 09 Oct 2018 22:58:45: 2000000 INFO @ Tue, 09 Oct 2018 22:58:45: 2000000 INFO @ Tue, 09 Oct 2018 22:58:45: 2000000 INFO @ Tue, 09 Oct 2018 22:58:51: 3000000 INFO @ Tue, 09 Oct 2018 22:58:51: 3000000 INFO @ Tue, 09 Oct 2018 22:58:52: 3000000 INFO @ Tue, 09 Oct 2018 22:58:58: 4000000 INFO @ Tue, 09 Oct 2018 22:58:58: 4000000 INFO @ Tue, 09 Oct 2018 22:58:58: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:58:58: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:58:58: #1 total tags in treatment: 1907203 INFO @ Tue, 09 Oct 2018 22:58:58: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:58:58: #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 22:58:58: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:58:58: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:58:58: #1 total tags in treatment: 1907203 INFO @ Tue, 09 Oct 2018 22:58:58: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:58:58: #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 22:58:58: #1 tags after filtering in treatment: 1271368 INFO @ Tue, 09 Oct 2018 22:58:58: #1 Redundant rate of treatment: 0.33 INFO @ Tue, 09 Oct 2018 22:58:58: #1 finished! INFO @ Tue, 09 Oct 2018 22:58:58: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:58:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:58:58: #1 tags after filtering in treatment: 1271368 INFO @ Tue, 09 Oct 2018 22:58:58: #1 Redundant rate of treatment: 0.33 INFO @ Tue, 09 Oct 2018 22:58:58: #1 finished! INFO @ Tue, 09 Oct 2018 22:58:58: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:58:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:58:58: #2 number of paired peaks: 190 WARNING @ Tue, 09 Oct 2018 22:58:58: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Tue, 09 Oct 2018 22:58:58: start model_add_line... INFO @ Tue, 09 Oct 2018 22:58:58: #2 number of paired peaks: 190 WARNING @ Tue, 09 Oct 2018 22:58:58: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Tue, 09 Oct 2018 22:58:58: start model_add_line... INFO @ Tue, 09 Oct 2018 22:58:58: start X-correlation... INFO @ Tue, 09 Oct 2018 22:58:58: end of X-cor INFO @ Tue, 09 Oct 2018 22:58:58: #2 finished! INFO @ Tue, 09 Oct 2018 22:58:58: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:58:58: #2 alternative fragment length(s) may be 0,33,70,93,111,129,203,432,462,486,519,539,548,566,583,586 bps INFO @ Tue, 09 Oct 2018 22:58:58: #2.2 Generate R script for model : SRX4554679.10_model.r INFO @ Tue, 09 Oct 2018 22:58:58: start X-correlation... INFO @ Tue, 09 Oct 2018 22:58:58: end of X-cor INFO @ Tue, 09 Oct 2018 22:58:58: #2 finished! INFO @ Tue, 09 Oct 2018 22:58:58: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:58:58: #2 alternative fragment length(s) may be 0,33,70,93,111,129,203,432,462,486,519,539,548,566,583,586 bps INFO @ Tue, 09 Oct 2018 22:58:58: #2.2 Generate R script for model : SRX4554679.05_model.r WARNING @ Tue, 09 Oct 2018 22:58:58: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:58:58: #2 You may need to consider one of the other alternative d(s): 0,33,70,93,111,129,203,432,462,486,519,539,548,566,583,586 WARNING @ Tue, 09 Oct 2018 22:58:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 09 Oct 2018 22:58:58: #3 Call peaks... WARNING @ Tue, 09 Oct 2018 22:58:58: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:58:58: #2 You may need to consider one of the other alternative d(s): 0,33,70,93,111,129,203,432,462,486,519,539,548,566,583,586 WARNING @ Tue, 09 Oct 2018 22:58:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 09 Oct 2018 22:58:58: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:58:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:58:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:58:59: 4000000 INFO @ Tue, 09 Oct 2018 22:58:59: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:58:59: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:58:59: #1 total tags in treatment: 1907203 INFO @ Tue, 09 Oct 2018 22:58:59: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:58:59: #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 22:58:59: #1 tags after filtering in treatment: 1271368 INFO @ Tue, 09 Oct 2018 22:58:59: #1 Redundant rate of treatment: 0.33 INFO @ Tue, 09 Oct 2018 22:58:59: #1 finished! INFO @ Tue, 09 Oct 2018 22:58:59: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:58:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:58:59: #2 number of paired peaks: 190 WARNING @ Tue, 09 Oct 2018 22:58:59: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Tue, 09 Oct 2018 22:58:59: start model_add_line... INFO @ Tue, 09 Oct 2018 22:58:59: start X-correlation... INFO @ Tue, 09 Oct 2018 22:58:59: end of X-cor INFO @ Tue, 09 Oct 2018 22:58:59: #2 finished! INFO @ Tue, 09 Oct 2018 22:58:59: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:58:59: #2 alternative fragment length(s) may be 0,33,70,93,111,129,203,432,462,486,519,539,548,566,583,586 bps INFO @ Tue, 09 Oct 2018 22:58:59: #2.2 Generate R script for model : SRX4554679.20_model.r WARNING @ Tue, 09 Oct 2018 22:58:59: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:58:59: #2 You may need to consider one of the other alternative d(s): 0,33,70,93,111,129,203,432,462,486,519,539,548,566,583,586 WARNING @ Tue, 09 Oct 2018 22:58:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 09 Oct 2018 22:58:59: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:58:59: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 ls: cannot access SRX4554679.05.bed: そのようなファイルやディレクトリはありません mv: cannot stat `SRX4554679.05.bed': そのようなファイルやディレクトリはありません /var/spool/uge/nt021i/job_scripts/11244949: line 254: 46776 終了しました MACS $i /var/spool/uge/nt021i/job_scripts/11244949: line 254: 46777 終了しました MACS $i /var/spool/uge/nt021i/job_scripts/11244949: line 254: 46778 終了しました MACS $i mv: cannot stat `SRX4554679.05.bb': そのようなファイルやディレクトリはありません ls: cannot access SRX4554679.10.bed: そのようなファイルやディレクトリはありません mv: cannot stat `SRX4554679.10.bed': そのようなファイルやディレクトリはありません mv: cannot stat `SRX4554679.10.bb': そのようなファイルやディレクトリはありません ls: cannot access SRX4554679.20.bed: そのようなファイルやディレクトリはありません mv: cannot stat `SRX4554679.20.bed': そのようなファイルやディレクトリはありません mv: cannot stat `SRX4554679.20.bb': そのようなファイルやディレクトリはありません