Job ID = 10937470 sra ファイルのダウンロード中... Completed: 589468K bytes transferred in 6 seconds (783872K 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 10792028 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198739/SRR4304469.sra Written 10792028 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198739/SRR4304469.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: 00:21:01 10792028 reads; of these: 10792028 (100.00%) were paired; of these: 2077840 (19.25%) aligned concordantly 0 times 4615947 (42.77%) aligned concordantly exactly 1 time 4098241 (37.97%) aligned concordantly >1 times ---- 2077840 pairs aligned concordantly 0 times; of these: 349540 (16.82%) aligned discordantly 1 time ---- 1728300 pairs aligned 0 times concordantly or discordantly; of these: 3456600 mates make up the pairs; of these: 2525761 (73.07%) aligned 0 times 97780 (2.83%) aligned exactly 1 time 833059 (24.10%) aligned >1 times 88.30% overall alignment rate Time searching: 00:21:01 Overall time: 00:21:01 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] 665962 / 8988003 = 0.0741 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 02:45:18: # Command line: callpeak -t SRX2198739.bam -f BAM -g 12100000 -n SRX2198739.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2198739.05 # format = BAM # ChIP-seq file = ['SRX2198739.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 02:45:18: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:45:18: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:45:18: # Command line: callpeak -t SRX2198739.bam -f BAM -g 12100000 -n SRX2198739.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2198739.20 # format = BAM # ChIP-seq file = ['SRX2198739.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 02:45:18: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:45:18: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:45:18: # Command line: callpeak -t SRX2198739.bam -f BAM -g 12100000 -n SRX2198739.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2198739.10 # format = BAM # ChIP-seq file = ['SRX2198739.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 02:45:18: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:45:18: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:45:23: 1000000 INFO @ Fri, 10 Aug 2018 02:45:24: 1000000 INFO @ Fri, 10 Aug 2018 02:45:24: 1000000 INFO @ Fri, 10 Aug 2018 02:45:29: 2000000 INFO @ Fri, 10 Aug 2018 02:45:30: 2000000 INFO @ Fri, 10 Aug 2018 02:45:30: 2000000 INFO @ Fri, 10 Aug 2018 02:45:34: 3000000 INFO @ Fri, 10 Aug 2018 02:45:36: 3000000 INFO @ Fri, 10 Aug 2018 02:45:37: 3000000 INFO @ Fri, 10 Aug 2018 02:45:40: 4000000 INFO @ Fri, 10 Aug 2018 02:45:43: 4000000 INFO @ Fri, 10 Aug 2018 02:45:44: 4000000 INFO @ Fri, 10 Aug 2018 02:45:46: 5000000 INFO @ Fri, 10 Aug 2018 02:45:49: 5000000 INFO @ Fri, 10 Aug 2018 02:45:51: 5000000 INFO @ Fri, 10 Aug 2018 02:45:52: 6000000 INFO @ Fri, 10 Aug 2018 02:45:56: 6000000 INFO @ Fri, 10 Aug 2018 02:45:57: 6000000 INFO @ Fri, 10 Aug 2018 02:45:58: 7000000 INFO @ Fri, 10 Aug 2018 02:46:02: 7000000 INFO @ Fri, 10 Aug 2018 02:46:03: 8000000 INFO @ Fri, 10 Aug 2018 02:46:04: 7000000 INFO @ Fri, 10 Aug 2018 02:46:09: 9000000 INFO @ Fri, 10 Aug 2018 02:46:09: 8000000 INFO @ Fri, 10 Aug 2018 02:46:11: 8000000 INFO @ Fri, 10 Aug 2018 02:46:14: 10000000 INFO @ Fri, 10 Aug 2018 02:46:15: 9000000 INFO @ Fri, 10 Aug 2018 02:46:17: 9000000 INFO @ Fri, 10 Aug 2018 02:46:20: 11000000 INFO @ Fri, 10 Aug 2018 02:46:21: 10000000 INFO @ Fri, 10 Aug 2018 02:46:23: 10000000 INFO @ Fri, 10 Aug 2018 02:46:26: 12000000 INFO @ Fri, 10 Aug 2018 02:46:26: 11000000 INFO @ Fri, 10 Aug 2018 02:46:29: 11000000 INFO @ Fri, 10 Aug 2018 02:46:32: 12000000 INFO @ Fri, 10 Aug 2018 02:46:32: 13000000 INFO @ Fri, 10 Aug 2018 02:46:35: 12000000 INFO @ Fri, 10 Aug 2018 02:46:38: 13000000 INFO @ Fri, 10 Aug 2018 02:46:38: 14000000 INFO @ Fri, 10 Aug 2018 02:46:41: 13000000 INFO @ Fri, 10 Aug 2018 02:46:44: 14000000 INFO @ Fri, 10 Aug 2018 02:46:44: 15000000 INFO @ Fri, 10 Aug 2018 02:46:47: 14000000 INFO @ Fri, 10 Aug 2018 02:46:49: 15000000 INFO @ Fri, 10 Aug 2018 02:46:50: 16000000 INFO @ Fri, 10 Aug 2018 02:46:53: 15000000 INFO @ Fri, 10 Aug 2018 02:46:55: 16000000 INFO @ Fri, 10 Aug 2018 02:46:56: 17000000 INFO @ Fri, 10 Aug 2018 02:46:59: 16000000 INFO @ Fri, 10 Aug 2018 02:47:00: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:47:00: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:47:00: #1 total tags in treatment: 8055635 INFO @ Fri, 10 Aug 2018 02:47:00: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:47:00: #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 02:47:00: #1 tags after filtering in treatment: 4020805 INFO @ Fri, 10 Aug 2018 02:47:00: #1 Redundant rate of treatment: 0.50 INFO @ Fri, 10 Aug 2018 02:47:00: #1 finished! INFO @ Fri, 10 Aug 2018 02:47:00: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:47:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:47:01: #2 number of paired peaks: 245 WARNING @ Fri, 10 Aug 2018 02:47:01: 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 02:47:01: start model_add_line... INFO @ Fri, 10 Aug 2018 02:47:01: start X-correlation... INFO @ Fri, 10 Aug 2018 02:47:01: end of X-cor INFO @ Fri, 10 Aug 2018 02:47:01: #2 finished! INFO @ Fri, 10 Aug 2018 02:47:01: #2 predicted fragment length is 0 bps INFO @ Fri, 10 Aug 2018 02:47:01: #2 alternative fragment length(s) may be 0,30,83,123,145,181,462,518,538,573 bps INFO @ Fri, 10 Aug 2018 02:47:01: #2.2 Generate R script for model : SRX2198739.10_model.r WARNING @ Fri, 10 Aug 2018 02:47:01: #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 02:47:01: #2 You may need to consider one of the other alternative d(s): 0,30,83,123,145,181,462,518,538,573 WARNING @ Fri, 10 Aug 2018 02:47:01: #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 02:47:01: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:47:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:47:01: 17000000 INFO @ Fri, 10 Aug 2018 02:47:05: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:47:05: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:47:05: #1 total tags in treatment: 8055635 INFO @ Fri, 10 Aug 2018 02:47:05: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:47:05: #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 02:47:05: #1 tags after filtering in treatment: 4020805 INFO @ Fri, 10 Aug 2018 02:47:05: #1 Redundant rate of treatment: 0.50 INFO @ Fri, 10 Aug 2018 02:47:05: #1 finished! INFO @ Fri, 10 Aug 2018 02:47:05: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:47:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:47:05: 17000000 INFO @ Fri, 10 Aug 2018 02:47:06: #2 number of paired peaks: 245 WARNING @ Fri, 10 Aug 2018 02:47:06: 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 02:47:06: start model_add_line... INFO @ Fri, 10 Aug 2018 02:47:06: start X-correlation... INFO @ Fri, 10 Aug 2018 02:47:06: end of X-cor INFO @ Fri, 10 Aug 2018 02:47:06: #2 finished! INFO @ Fri, 10 Aug 2018 02:47:06: #2 predicted fragment length is 0 bps INFO @ Fri, 10 Aug 2018 02:47:06: #2 alternative fragment length(s) may be 0,30,83,123,145,181,462,518,538,573 bps INFO @ Fri, 10 Aug 2018 02:47:06: #2.2 Generate R script for model : SRX2198739.20_model.r WARNING @ Fri, 10 Aug 2018 02:47:06: #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 02:47:06: #2 You may need to consider one of the other alternative d(s): 0,30,83,123,145,181,462,518,538,573 WARNING @ Fri, 10 Aug 2018 02:47:06: #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 02:47:06: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:47:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:47:10: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:47:10: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:47:10: #1 total tags in treatment: 8055635 INFO @ Fri, 10 Aug 2018 02:47:10: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:47:10: #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 02:47:10: #1 tags after filtering in treatment: 4020805 INFO @ Fri, 10 Aug 2018 02:47:10: #1 Redundant rate of treatment: 0.50 INFO @ Fri, 10 Aug 2018 02:47:10: #1 finished! INFO @ Fri, 10 Aug 2018 02:47:10: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:47:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:47:10: #2 number of paired peaks: 245 WARNING @ Fri, 10 Aug 2018 02:47:10: 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 02:47:10: start model_add_line... INFO @ Fri, 10 Aug 2018 02:47:10: start X-correlation... INFO @ Fri, 10 Aug 2018 02:47:10: end of X-cor INFO @ Fri, 10 Aug 2018 02:47:10: #2 finished! INFO @ Fri, 10 Aug 2018 02:47:10: #2 predicted fragment length is 0 bps INFO @ Fri, 10 Aug 2018 02:47:10: #2 alternative fragment length(s) may be 0,30,83,123,145,181,462,518,538,573 bps INFO @ Fri, 10 Aug 2018 02:47:10: #2.2 Generate R script for model : SRX2198739.05_model.r WARNING @ Fri, 10 Aug 2018 02:47:10: #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 02:47:10: #2 You may need to consider one of the other alternative d(s): 0,30,83,123,145,181,462,518,538,573 WARNING @ Fri, 10 Aug 2018 02:47:10: #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 02:47:10: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:47:10: #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 SRX2198739.05.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 `SRX2198739.05.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/nt123i/job_scripts/10937470: line 254: 13349 終了しました MACS $i /var/spool/uge/nt123i/job_scripts/10937470: line 254: 13350 終了しました MACS $i /var/spool/uge/nt123i/job_scripts/10937470: line 254: 13352 終了しました MACS $i mv: cannot stat `SRX2198739.05.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 SRX2198739.10.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 `SRX2198739.10.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 `SRX2198739.10.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 SRX2198739.20.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 `SRX2198739.20.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 `SRX2198739.20.bb': そのようなファイルやディレクトリはありません