Job ID = 11244810 sra ファイルのダウンロード中... Completed: 541276K bytes transferred in 14 seconds (295737K 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/SRX3659044/SRR6682738.sra Written 5586230 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3659044/SRR6682738.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: 00:06:46 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 59852 (35.10%) aligned exactly 1 time 24179 (14.18%) aligned >1 times 99.23% overall alignment rate Time searching: 00:06:46 Overall time: 00:06:46 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 22:03:39: # Command line: callpeak -t SRX3659044.bam -f BAM -g 12100000 -n SRX3659044.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3659044.05 # format = BAM # ChIP-seq file = ['SRX3659044.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 22:03:39: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:03:39: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:03:39: # Command line: callpeak -t SRX3659044.bam -f BAM -g 12100000 -n SRX3659044.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3659044.10 # format = BAM # ChIP-seq file = ['SRX3659044.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 22:03:39: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:03:39: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:03:39: # Command line: callpeak -t SRX3659044.bam -f BAM -g 12100000 -n SRX3659044.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3659044.20 # format = BAM # ChIP-seq file = ['SRX3659044.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 22:03:39: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:03:39: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:03:46: 1000000 INFO @ Tue, 09 Oct 2018 22:03:46: 1000000 INFO @ Tue, 09 Oct 2018 22:03:46: 1000000 INFO @ Tue, 09 Oct 2018 22:03:53: 2000000 INFO @ Tue, 09 Oct 2018 22:03:53: 2000000 INFO @ Tue, 09 Oct 2018 22:03:53: 2000000 INFO @ Tue, 09 Oct 2018 22:03:59: 3000000 INFO @ Tue, 09 Oct 2018 22:04:00: 3000000 INFO @ Tue, 09 Oct 2018 22:04:00: 3000000 INFO @ Tue, 09 Oct 2018 22:04:06: 4000000 INFO @ Tue, 09 Oct 2018 22:04:07: 4000000 INFO @ Tue, 09 Oct 2018 22:04:07: 4000000 INFO @ Tue, 09 Oct 2018 22:04:12: 5000000 INFO @ Tue, 09 Oct 2018 22:04:14: 5000000 INFO @ Tue, 09 Oct 2018 22:04:14: 5000000 INFO @ Tue, 09 Oct 2018 22:04:19: 6000000 INFO @ Tue, 09 Oct 2018 22:04:21: 6000000 INFO @ Tue, 09 Oct 2018 22:04:21: 6000000 INFO @ Tue, 09 Oct 2018 22:04:26: 7000000 INFO @ Tue, 09 Oct 2018 22:04:28: 7000000 INFO @ Tue, 09 Oct 2018 22:04:29: 7000000 INFO @ Tue, 09 Oct 2018 22:04:33: 8000000 INFO @ Tue, 09 Oct 2018 22:04:35: 8000000 INFO @ Tue, 09 Oct 2018 22:04:36: 8000000 INFO @ Tue, 09 Oct 2018 22:04:39: 9000000 INFO @ Tue, 09 Oct 2018 22:04:42: 9000000 INFO @ Tue, 09 Oct 2018 22:04:43: 9000000 INFO @ Tue, 09 Oct 2018 22:04:46: 10000000 INFO @ Tue, 09 Oct 2018 22:04:49: 10000000 INFO @ Tue, 09 Oct 2018 22:04:51: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:04:51: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:04:51: #1 total tags in treatment: 5178408 INFO @ Tue, 09 Oct 2018 22:04:51: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:04:51: #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 22:04:51: 10000000 INFO @ Tue, 09 Oct 2018 22:04:51: #1 tags after filtering in treatment: 3798930 INFO @ Tue, 09 Oct 2018 22:04:51: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 09 Oct 2018 22:04:51: #1 finished! INFO @ Tue, 09 Oct 2018 22:04:51: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:04:51: #2 number of paired peaks: 168 WARNING @ Tue, 09 Oct 2018 22:04:51: 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 22:04:51: start model_add_line... INFO @ Tue, 09 Oct 2018 22:04:51: start X-correlation... INFO @ Tue, 09 Oct 2018 22:04:51: end of X-cor INFO @ Tue, 09 Oct 2018 22:04:51: #2 finished! INFO @ Tue, 09 Oct 2018 22:04:51: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:04:51: #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 22:04:51: #2.2 Generate R script for model : SRX3659044.20_model.r WARNING @ Tue, 09 Oct 2018 22:04:51: #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 22:04:51: #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 22:04:51: #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 22:04:51: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:04:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:04:53: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:04:53: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:04:53: #1 total tags in treatment: 5178408 INFO @ Tue, 09 Oct 2018 22:04:53: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:04:53: #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 22:04:53: #1 tags after filtering in treatment: 3798930 INFO @ Tue, 09 Oct 2018 22:04:53: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 09 Oct 2018 22:04:53: #1 finished! INFO @ Tue, 09 Oct 2018 22:04:53: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:04:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:04:53: #2 number of paired peaks: 168 WARNING @ Tue, 09 Oct 2018 22:04:53: 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 22:04:53: start model_add_line... INFO @ Tue, 09 Oct 2018 22:04:53: start X-correlation... INFO @ Tue, 09 Oct 2018 22:04:53: end of X-cor INFO @ Tue, 09 Oct 2018 22:04:53: #2 finished! INFO @ Tue, 09 Oct 2018 22:04:53: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:04:53: #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 22:04:53: #2.2 Generate R script for model : SRX3659044.05_model.r WARNING @ Tue, 09 Oct 2018 22:04:53: #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 22:04:53: #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 22:04:53: #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 22:04:53: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:04:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:04:55: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:04:55: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:04:55: #1 total tags in treatment: 5178408 INFO @ Tue, 09 Oct 2018 22:04:55: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:04:55: #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 22:04:55: #1 tags after filtering in treatment: 3798930 INFO @ Tue, 09 Oct 2018 22:04:55: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 09 Oct 2018 22:04:55: #1 finished! INFO @ Tue, 09 Oct 2018 22:04:55: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:04:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:04:55: #2 number of paired peaks: 168 WARNING @ Tue, 09 Oct 2018 22:04:55: 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 22:04:55: start model_add_line... INFO @ Tue, 09 Oct 2018 22:04:55: start X-correlation... INFO @ Tue, 09 Oct 2018 22:04:55: end of X-cor INFO @ Tue, 09 Oct 2018 22:04:55: #2 finished! INFO @ Tue, 09 Oct 2018 22:04:55: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:04:55: #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 22:04:55: #2.2 Generate R script for model : SRX3659044.10_model.r WARNING @ Tue, 09 Oct 2018 22:04:55: #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 22:04:55: #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 22:04:55: #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 22:04:55: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:04:55: #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 SRX3659044.05.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 `SRX3659044.05.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/nt163i/job_scripts/11244810: line 254: 51029 終了しました MACS $i /var/spool/uge/nt163i/job_scripts/11244810: line 254: 51030 終了しました MACS $i /var/spool/uge/nt163i/job_scripts/11244810: line 254: 51032 終了しました MACS $i mv: cannot stat `SRX3659044.05.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 SRX3659044.10.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 `SRX3659044.10.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 `SRX3659044.10.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 SRX3659044.20.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 `SRX3659044.20.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 `SRX3659044.20.bb': そのようなファイルやディレクトリはありません