Job ID = 11244875 sra ファイルのダウンロード中... Completed: 541276K bytes transferred in 7 seconds (580688K 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 5586230 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765837/SRR6807570.sra Written 5586230 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765837/SRR6807570.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: 00:06:48 5586230 reads; of these: 5586230 (100.00%) were paired; of these: 153326 (2.74%) aligned concordantly 0 times 4903191 (87.77%) aligned concordantly exactly 1 time 529713 (9.48%) aligned concordantly >1 times ---- 153326 pairs aligned concordantly 0 times; of these: 68066 (44.39%) aligned discordantly 1 time ---- 85260 pairs aligned 0 times concordantly or discordantly; of these: 170520 mates make up the pairs; of these: 86489 (50.72%) aligned 0 times 59851 (35.10%) aligned exactly 1 time 24180 (14.18%) aligned >1 times 99.23% overall alignment rate Time searching: 00:06:48 Overall time: 00:06:48 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] 255406 / 5455701 = 0.0468 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 22:35:51: # Command line: callpeak -t SRX3765837.bam -f BAM -g 12100000 -n SRX3765837.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3765837.20 # format = BAM # ChIP-seq file = ['SRX3765837.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 22:35:51: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:35:51: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:35:51: # Command line: callpeak -t SRX3765837.bam -f BAM -g 12100000 -n SRX3765837.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3765837.05 # format = BAM # ChIP-seq file = ['SRX3765837.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 22:35:51: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:35:51: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:35:51: # Command line: callpeak -t SRX3765837.bam -f BAM -g 12100000 -n SRX3765837.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3765837.10 # format = BAM # ChIP-seq file = ['SRX3765837.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 22:35:51: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:35:51: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:35:58: 1000000 INFO @ Tue, 09 Oct 2018 22:35:58: 1000000 INFO @ Tue, 09 Oct 2018 22:35:58: 1000000 INFO @ Tue, 09 Oct 2018 22:36:05: 2000000 INFO @ Tue, 09 Oct 2018 22:36:05: 2000000 INFO @ Tue, 09 Oct 2018 22:36:05: 2000000 INFO @ Tue, 09 Oct 2018 22:36:11: 3000000 INFO @ Tue, 09 Oct 2018 22:36:12: 3000000 INFO @ Tue, 09 Oct 2018 22:36:12: 3000000 INFO @ Tue, 09 Oct 2018 22:36:18: 4000000 INFO @ Tue, 09 Oct 2018 22:36:18: 4000000 INFO @ Tue, 09 Oct 2018 22:36:19: 4000000 INFO @ Tue, 09 Oct 2018 22:36:25: 5000000 INFO @ Tue, 09 Oct 2018 22:36:25: 5000000 INFO @ Tue, 09 Oct 2018 22:36:26: 5000000 INFO @ Tue, 09 Oct 2018 22:36:32: 6000000 INFO @ Tue, 09 Oct 2018 22:36:32: 6000000 INFO @ Tue, 09 Oct 2018 22:36:33: 6000000 INFO @ Tue, 09 Oct 2018 22:36:38: 7000000 INFO @ Tue, 09 Oct 2018 22:36:39: 7000000 INFO @ Tue, 09 Oct 2018 22:36:39: 7000000 INFO @ Tue, 09 Oct 2018 22:36:45: 8000000 INFO @ Tue, 09 Oct 2018 22:36:46: 8000000 INFO @ Tue, 09 Oct 2018 22:36:46: 8000000 INFO @ Tue, 09 Oct 2018 22:36:52: 9000000 INFO @ Tue, 09 Oct 2018 22:36:52: 9000000 INFO @ Tue, 09 Oct 2018 22:36:53: 9000000 INFO @ Tue, 09 Oct 2018 22:36:59: 10000000 INFO @ Tue, 09 Oct 2018 22:36:59: 10000000 INFO @ Tue, 09 Oct 2018 22:37:00: 10000000 INFO @ Tue, 09 Oct 2018 22:37:03: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:37:03: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:37:03: #1 total tags in treatment: 5178408 INFO @ Tue, 09 Oct 2018 22:37:03: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:37:03: #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 22:37:03: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:37:03: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:37:03: #1 total tags in treatment: 5178408 INFO @ Tue, 09 Oct 2018 22:37:03: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:37:03: #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 22:37:03: #1 tags after filtering in treatment: 3798930 INFO @ Tue, 09 Oct 2018 22:37:03: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 09 Oct 2018 22:37:03: #1 finished! INFO @ Tue, 09 Oct 2018 22:37:03: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:37:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:37:03: #1 tags after filtering in treatment: 3798930 INFO @ Tue, 09 Oct 2018 22:37:03: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 09 Oct 2018 22:37:03: #1 finished! INFO @ Tue, 09 Oct 2018 22:37:03: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:37:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:37:03: #2 number of paired peaks: 168 WARNING @ Tue, 09 Oct 2018 22:37:03: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Tue, 09 Oct 2018 22:37:03: start model_add_line... INFO @ Tue, 09 Oct 2018 22:37:03: start X-correlation... INFO @ Tue, 09 Oct 2018 22:37:03: #2 number of paired peaks: 168 WARNING @ Tue, 09 Oct 2018 22:37:03: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Tue, 09 Oct 2018 22:37:03: start model_add_line... INFO @ Tue, 09 Oct 2018 22:37:03: end of X-cor INFO @ Tue, 09 Oct 2018 22:37:03: #2 finished! INFO @ Tue, 09 Oct 2018 22:37:03: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:37:03: #2 alternative fragment length(s) may be 0,39,63,88,94,112,119,142,161,182,197,214,250,280,350,363,397,412,429,453,522,542,565,589 bps INFO @ Tue, 09 Oct 2018 22:37:03: #2.2 Generate R script for model : SRX3765837.20_model.r WARNING @ Tue, 09 Oct 2018 22:37:03: #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 22:37:03: #2 You may need to consider one of the other alternative d(s): 0,39,63,88,94,112,119,142,161,182,197,214,250,280,350,363,397,412,429,453,522,542,565,589 WARNING @ Tue, 09 Oct 2018 22:37:03: #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 22:37:03: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:37:03: start X-correlation... INFO @ Tue, 09 Oct 2018 22:37:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:37:03: end of X-cor INFO @ Tue, 09 Oct 2018 22:37:03: #2 finished! INFO @ Tue, 09 Oct 2018 22:37:03: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:37:03: #2 alternative fragment length(s) may be 0,39,63,88,94,112,119,142,161,182,197,214,250,280,350,363,397,412,429,453,522,542,565,589 bps INFO @ Tue, 09 Oct 2018 22:37:03: #2.2 Generate R script for model : SRX3765837.05_model.r WARNING @ Tue, 09 Oct 2018 22:37:03: #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 22:37:03: #2 You may need to consider one of the other alternative d(s): 0,39,63,88,94,112,119,142,161,182,197,214,250,280,350,363,397,412,429,453,522,542,565,589 WARNING @ Tue, 09 Oct 2018 22:37:03: #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 22:37:03: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:37:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:37:04: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:37:04: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:37:04: #1 total tags in treatment: 5178408 INFO @ Tue, 09 Oct 2018 22:37:04: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:37:04: #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 22:37:04: #1 tags after filtering in treatment: 3798930 INFO @ Tue, 09 Oct 2018 22:37:04: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 09 Oct 2018 22:37:04: #1 finished! INFO @ Tue, 09 Oct 2018 22:37:04: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:37:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:37:04: #2 number of paired peaks: 168 WARNING @ Tue, 09 Oct 2018 22:37:04: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Tue, 09 Oct 2018 22:37:04: start model_add_line... INFO @ Tue, 09 Oct 2018 22:37:04: start X-correlation... INFO @ Tue, 09 Oct 2018 22:37:04: end of X-cor INFO @ Tue, 09 Oct 2018 22:37:04: #2 finished! INFO @ Tue, 09 Oct 2018 22:37:04: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:37:04: #2 alternative fragment length(s) may be 0,39,63,88,94,112,119,142,161,182,197,214,250,280,350,363,397,412,429,453,522,542,565,589 bps INFO @ Tue, 09 Oct 2018 22:37:04: #2.2 Generate R script for model : SRX3765837.10_model.r WARNING @ Tue, 09 Oct 2018 22:37:04: #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 22:37:04: #2 You may need to consider one of the other alternative d(s): 0,39,63,88,94,112,119,142,161,182,197,214,250,280,350,363,397,412,429,453,522,542,565,589 WARNING @ Tue, 09 Oct 2018 22:37:04: #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 22:37:04: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:37:04: #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 SRX3765837.05.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 `SRX3765837.05.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/nt124i/job_scripts/11244875: line 254: 6766 終了しました MACS $i /var/spool/uge/nt124i/job_scripts/11244875: line 254: 6767 終了しました MACS $i /var/spool/uge/nt124i/job_scripts/11244875: line 254: 6768 終了しました MACS $i mv: cannot stat `SRX3765837.05.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 SRX3765837.10.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 `SRX3765837.10.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 `SRX3765837.10.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 SRX3765837.20.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 `SRX3765837.20.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 `SRX3765837.20.bb': そのようなファイルやディレクトリはありません