Job ID = 10937473 sra ファイルのダウンロード中... Completed: 486075K bytes transferred in 7 seconds (533896K 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 8903900 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198740/SRR4304470.sra Written 8903900 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198740/SRR4304470.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: 00:15:43 8903900 reads; of these: 8903900 (100.00%) were paired; of these: 1526473 (17.14%) aligned concordantly 0 times 4112768 (46.19%) aligned concordantly exactly 1 time 3264659 (36.67%) aligned concordantly >1 times ---- 1526473 pairs aligned concordantly 0 times; of these: 279281 (18.30%) aligned discordantly 1 time ---- 1247192 pairs aligned 0 times concordantly or discordantly; of these: 2494384 mates make up the pairs; of these: 1883497 (75.51%) aligned 0 times 81238 (3.26%) aligned exactly 1 time 529649 (21.23%) aligned >1 times 89.42% overall alignment rate Time searching: 00:15:43 Overall time: 00:15:43 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] 470564 / 7601941 = 0.0619 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 @ Fri, 10 Aug 2018 02:39:18: # Command line: callpeak -t SRX2198740.bam -f BAM -g 12100000 -n SRX2198740.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2198740.10 # format = BAM # ChIP-seq file = ['SRX2198740.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 @ Fri, 10 Aug 2018 02:39:18: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:39:18: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:39:18: # Command line: callpeak -t SRX2198740.bam -f BAM -g 12100000 -n SRX2198740.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2198740.20 # format = BAM # ChIP-seq file = ['SRX2198740.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 @ Fri, 10 Aug 2018 02:39:18: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:39:18: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:39:18: # Command line: callpeak -t SRX2198740.bam -f BAM -g 12100000 -n SRX2198740.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2198740.05 # format = BAM # ChIP-seq file = ['SRX2198740.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 @ Fri, 10 Aug 2018 02:39:18: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:39:18: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:39:25: 1000000 INFO @ Fri, 10 Aug 2018 02:39:25: 1000000 INFO @ Fri, 10 Aug 2018 02:39:25: 1000000 INFO @ Fri, 10 Aug 2018 02:39:31: 2000000 INFO @ Fri, 10 Aug 2018 02:39:31: 2000000 INFO @ Fri, 10 Aug 2018 02:39:32: 2000000 INFO @ Fri, 10 Aug 2018 02:39:38: 3000000 INFO @ Fri, 10 Aug 2018 02:39:38: 3000000 INFO @ Fri, 10 Aug 2018 02:39:39: 3000000 INFO @ Fri, 10 Aug 2018 02:39:44: 4000000 INFO @ Fri, 10 Aug 2018 02:39:44: 4000000 INFO @ Fri, 10 Aug 2018 02:39:46: 4000000 INFO @ Fri, 10 Aug 2018 02:39:50: 5000000 INFO @ Fri, 10 Aug 2018 02:39:50: 5000000 INFO @ Fri, 10 Aug 2018 02:39:53: 5000000 INFO @ Fri, 10 Aug 2018 02:39:57: 6000000 INFO @ Fri, 10 Aug 2018 02:39:57: 6000000 INFO @ Fri, 10 Aug 2018 02:40:00: 6000000 INFO @ Fri, 10 Aug 2018 02:40:03: 7000000 INFO @ Fri, 10 Aug 2018 02:40:03: 7000000 INFO @ Fri, 10 Aug 2018 02:40:07: 7000000 INFO @ Fri, 10 Aug 2018 02:40:10: 8000000 INFO @ Fri, 10 Aug 2018 02:40:10: 8000000 INFO @ Fri, 10 Aug 2018 02:40:14: 8000000 INFO @ Fri, 10 Aug 2018 02:40:16: 9000000 INFO @ Fri, 10 Aug 2018 02:40:16: 9000000 INFO @ Fri, 10 Aug 2018 02:40:20: 9000000 INFO @ Fri, 10 Aug 2018 02:40:22: 10000000 INFO @ Fri, 10 Aug 2018 02:40:22: 10000000 INFO @ Fri, 10 Aug 2018 02:40:27: 10000000 INFO @ Fri, 10 Aug 2018 02:40:28: 11000000 INFO @ Fri, 10 Aug 2018 02:40:28: 11000000 INFO @ Fri, 10 Aug 2018 02:40:34: 11000000 INFO @ Fri, 10 Aug 2018 02:40:35: 12000000 INFO @ Fri, 10 Aug 2018 02:40:35: 12000000 INFO @ Fri, 10 Aug 2018 02:40:41: 13000000 INFO @ Fri, 10 Aug 2018 02:40:41: 13000000 INFO @ Fri, 10 Aug 2018 02:40:41: 12000000 INFO @ Fri, 10 Aug 2018 02:40:48: 14000000 INFO @ Fri, 10 Aug 2018 02:40:48: 14000000 INFO @ Fri, 10 Aug 2018 02:40:48: 13000000 INFO @ Fri, 10 Aug 2018 02:40:54: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:40:54: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:40:54: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:40:54: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:40:54: #1 total tags in treatment: 6912526 INFO @ Fri, 10 Aug 2018 02:40:54: #1 total tags in treatment: 6912526 INFO @ Fri, 10 Aug 2018 02:40:54: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:40:54: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:40:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:40:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:40:54: #1 tags after filtering in treatment: 3809359 INFO @ Fri, 10 Aug 2018 02:40:54: #1 tags after filtering in treatment: 3809359 INFO @ Fri, 10 Aug 2018 02:40:54: #1 Redundant rate of treatment: 0.45 INFO @ Fri, 10 Aug 2018 02:40:54: #1 Redundant rate of treatment: 0.45 INFO @ Fri, 10 Aug 2018 02:40:54: #1 finished! INFO @ Fri, 10 Aug 2018 02:40:54: #1 finished! INFO @ Fri, 10 Aug 2018 02:40:54: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:40:54: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:40:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:40:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:40:54: #2 number of paired peaks: 245 WARNING @ Fri, 10 Aug 2018 02:40:54: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Fri, 10 Aug 2018 02:40:54: start model_add_line... INFO @ Fri, 10 Aug 2018 02:40:54: start X-correlation... INFO @ Fri, 10 Aug 2018 02:40:54: end of X-cor INFO @ Fri, 10 Aug 2018 02:40:54: #2 finished! INFO @ Fri, 10 Aug 2018 02:40:54: #2 predicted fragment length is 0 bps INFO @ Fri, 10 Aug 2018 02:40:54: #2 alternative fragment length(s) may be 0,17,39,70,131,155,214,277,323,341,378,473,496,566,573 bps INFO @ Fri, 10 Aug 2018 02:40:54: #2.2 Generate R script for model : SRX2198740.20_model.r INFO @ Fri, 10 Aug 2018 02:40:55: #2 number of paired peaks: 245 WARNING @ Fri, 10 Aug 2018 02:40:55: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Fri, 10 Aug 2018 02:40:55: start model_add_line... WARNING @ Fri, 10 Aug 2018 02:40:55: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 02:40:55: #2 You may need to consider one of the other alternative d(s): 0,17,39,70,131,155,214,277,323,341,378,473,496,566,573 WARNING @ Fri, 10 Aug 2018 02:40:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 02:40:55: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:40:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:40:55: start X-correlation... INFO @ Fri, 10 Aug 2018 02:40:55: end of X-cor INFO @ Fri, 10 Aug 2018 02:40:55: #2 finished! INFO @ Fri, 10 Aug 2018 02:40:55: #2 predicted fragment length is 0 bps INFO @ Fri, 10 Aug 2018 02:40:55: #2 alternative fragment length(s) may be 0,17,39,70,131,155,214,277,323,341,378,473,496,566,573 bps INFO @ Fri, 10 Aug 2018 02:40:55: #2.2 Generate R script for model : SRX2198740.05_model.r WARNING @ Fri, 10 Aug 2018 02:40:55: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 02:40:55: #2 You may need to consider one of the other alternative d(s): 0,17,39,70,131,155,214,277,323,341,378,473,496,566,573 WARNING @ Fri, 10 Aug 2018 02:40:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 02:40:55: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:40:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:40:55: 14000000 INFO @ Fri, 10 Aug 2018 02:41:01: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:41:01: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:41:01: #1 total tags in treatment: 6912526 INFO @ Fri, 10 Aug 2018 02:41:01: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:41:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:41:02: #1 tags after filtering in treatment: 3809359 INFO @ Fri, 10 Aug 2018 02:41:02: #1 Redundant rate of treatment: 0.45 INFO @ Fri, 10 Aug 2018 02:41:02: #1 finished! INFO @ Fri, 10 Aug 2018 02:41:02: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:41:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:41:02: #2 number of paired peaks: 245 WARNING @ Fri, 10 Aug 2018 02:41:02: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Fri, 10 Aug 2018 02:41:02: start model_add_line... INFO @ Fri, 10 Aug 2018 02:41:02: start X-correlation... INFO @ Fri, 10 Aug 2018 02:41:02: end of X-cor INFO @ Fri, 10 Aug 2018 02:41:02: #2 finished! INFO @ Fri, 10 Aug 2018 02:41:02: #2 predicted fragment length is 0 bps INFO @ Fri, 10 Aug 2018 02:41:02: #2 alternative fragment length(s) may be 0,17,39,70,131,155,214,277,323,341,378,473,496,566,573 bps INFO @ Fri, 10 Aug 2018 02:41:02: #2.2 Generate R script for model : SRX2198740.10_model.r WARNING @ Fri, 10 Aug 2018 02:41:02: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 02:41:02: #2 You may need to consider one of the other alternative d(s): 0,17,39,70,131,155,214,277,323,341,378,473,496,566,573 WARNING @ Fri, 10 Aug 2018 02:41:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 02:41:02: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:41:02: #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 SRX2198740.05.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 `SRX2198740.05.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/nt134i/job_scripts/10937473: line 254: 52345 終了しました MACS $i /var/spool/uge/nt134i/job_scripts/10937473: line 254: 52346 終了しました MACS $i /var/spool/uge/nt134i/job_scripts/10937473: line 254: 52348 終了しました MACS $i mv: cannot stat `SRX2198740.05.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 SRX2198740.10.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 `SRX2198740.10.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 `SRX2198740.10.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 SRX2198740.20.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 `SRX2198740.20.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 `SRX2198740.20.bb': そのようなファイルやディレクトリはありません