Job ID = 10937695 sra ファイルのダウンロード中... Completed: 273668K bytes transferred in 8 seconds (249481K 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 8988875 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3467909/SRR6372872.sra Written 8988875 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3467909/SRR6372872.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: 00:05:35 8988875 reads; of these: 8988875 (100.00%) were paired; of these: 1532285 (17.05%) aligned concordantly 0 times 6618454 (73.63%) aligned concordantly exactly 1 time 838136 (9.32%) aligned concordantly >1 times ---- 1532285 pairs aligned concordantly 0 times; of these: 153036 (9.99%) aligned discordantly 1 time ---- 1379249 pairs aligned 0 times concordantly or discordantly; of these: 2758498 mates make up the pairs; of these: 2233679 (80.97%) aligned 0 times 400330 (14.51%) aligned exactly 1 time 124489 (4.51%) aligned >1 times 87.58% overall alignment rate Time searching: 00:05:35 Overall time: 00:05:35 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] 388831 / 7545428 = 0.0515 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 03:01:13: # Command line: callpeak -t SRX3467909.bam -f BAM -g 12100000 -n SRX3467909.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3467909.05 # format = BAM # ChIP-seq file = ['SRX3467909.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 03:01:13: #1 read tag files... INFO @ Fri, 10 Aug 2018 03:01:13: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 03:01:13: # Command line: callpeak -t SRX3467909.bam -f BAM -g 12100000 -n SRX3467909.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3467909.20 # format = BAM # ChIP-seq file = ['SRX3467909.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 03:01:13: #1 read tag files... INFO @ Fri, 10 Aug 2018 03:01:13: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 03:01:13: # Command line: callpeak -t SRX3467909.bam -f BAM -g 12100000 -n SRX3467909.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3467909.10 # format = BAM # ChIP-seq file = ['SRX3467909.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 03:01:13: #1 read tag files... INFO @ Fri, 10 Aug 2018 03:01:13: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 03:01:18: 1000000 INFO @ Fri, 10 Aug 2018 03:01:18: 1000000 INFO @ Fri, 10 Aug 2018 03:01:18: 1000000 INFO @ Fri, 10 Aug 2018 03:01:23: 2000000 INFO @ Fri, 10 Aug 2018 03:01:23: 2000000 INFO @ Fri, 10 Aug 2018 03:01:24: 2000000 INFO @ Fri, 10 Aug 2018 03:01:28: 3000000 INFO @ Fri, 10 Aug 2018 03:01:29: 3000000 INFO @ Fri, 10 Aug 2018 03:01:30: 3000000 INFO @ Fri, 10 Aug 2018 03:01:33: 4000000 INFO @ Fri, 10 Aug 2018 03:01:35: 4000000 INFO @ Fri, 10 Aug 2018 03:01:35: 4000000 INFO @ Fri, 10 Aug 2018 03:01:38: 5000000 INFO @ Fri, 10 Aug 2018 03:01:40: 5000000 INFO @ Fri, 10 Aug 2018 03:01:41: 5000000 INFO @ Fri, 10 Aug 2018 03:01:43: 6000000 INFO @ Fri, 10 Aug 2018 03:01:46: 6000000 INFO @ Fri, 10 Aug 2018 03:01:46: 6000000 INFO @ Fri, 10 Aug 2018 03:01:49: 7000000 INFO @ Fri, 10 Aug 2018 03:01:51: 7000000 INFO @ Fri, 10 Aug 2018 03:01:52: 7000000 INFO @ Fri, 10 Aug 2018 03:01:54: 8000000 INFO @ Fri, 10 Aug 2018 03:01:57: 8000000 INFO @ Fri, 10 Aug 2018 03:01:58: 8000000 INFO @ Fri, 10 Aug 2018 03:01:59: 9000000 INFO @ Fri, 10 Aug 2018 03:02:02: 9000000 INFO @ Fri, 10 Aug 2018 03:02:04: 9000000 INFO @ Fri, 10 Aug 2018 03:02:04: 10000000 INFO @ Fri, 10 Aug 2018 03:02:08: 10000000 INFO @ Fri, 10 Aug 2018 03:02:09: 10000000 INFO @ Fri, 10 Aug 2018 03:02:10: 11000000 INFO @ Fri, 10 Aug 2018 03:02:13: 11000000 INFO @ Fri, 10 Aug 2018 03:02:15: 12000000 INFO @ Fri, 10 Aug 2018 03:02:15: 11000000 INFO @ Fri, 10 Aug 2018 03:02:19: 12000000 INFO @ Fri, 10 Aug 2018 03:02:20: 13000000 INFO @ Fri, 10 Aug 2018 03:02:20: 12000000 INFO @ Fri, 10 Aug 2018 03:02:24: 13000000 INFO @ Fri, 10 Aug 2018 03:02:25: 14000000 INFO @ Fri, 10 Aug 2018 03:02:26: 13000000 INFO @ Fri, 10 Aug 2018 03:02:30: 14000000 INFO @ Fri, 10 Aug 2018 03:02:30: #1 tag size is determined as 36 bps INFO @ Fri, 10 Aug 2018 03:02:30: #1 tag size = 36 INFO @ Fri, 10 Aug 2018 03:02:30: #1 total tags in treatment: 7069638 INFO @ Fri, 10 Aug 2018 03:02:30: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 03:02:30: #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 03:02:31: #1 tags after filtering in treatment: 4468083 INFO @ Fri, 10 Aug 2018 03:02:31: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 10 Aug 2018 03:02:31: #1 finished! INFO @ Fri, 10 Aug 2018 03:02:31: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 03:02:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 03:02:31: #2 number of paired peaks: 146 WARNING @ Fri, 10 Aug 2018 03:02:31: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Fri, 10 Aug 2018 03:02:31: start model_add_line... INFO @ Fri, 10 Aug 2018 03:02:31: start X-correlation... INFO @ Fri, 10 Aug 2018 03:02:31: end of X-cor INFO @ Fri, 10 Aug 2018 03:02:31: #2 finished! INFO @ Fri, 10 Aug 2018 03:02:31: #2 predicted fragment length is 0 bps INFO @ Fri, 10 Aug 2018 03:02:31: #2 alternative fragment length(s) may be 0,32,50,90,109,141,184,213,230,270,304,331,345,375,396,418,454,481,497,511,526,551,580 bps INFO @ Fri, 10 Aug 2018 03:02:31: #2.2 Generate R script for model : SRX3467909.20_model.r WARNING @ Fri, 10 Aug 2018 03:02:31: #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 03:02:31: #2 You may need to consider one of the other alternative d(s): 0,32,50,90,109,141,184,213,230,270,304,331,345,375,396,418,454,481,497,511,526,551,580 WARNING @ Fri, 10 Aug 2018 03:02:31: #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 03:02:31: #3 Call peaks... INFO @ Fri, 10 Aug 2018 03:02:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 03:02:32: 14000000 INFO @ Fri, 10 Aug 2018 03:02:36: #1 tag size is determined as 36 bps INFO @ Fri, 10 Aug 2018 03:02:36: #1 tag size = 36 INFO @ Fri, 10 Aug 2018 03:02:36: #1 total tags in treatment: 7069638 INFO @ Fri, 10 Aug 2018 03:02:36: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 03:02:36: #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 03:02:36: #1 tags after filtering in treatment: 4468083 INFO @ Fri, 10 Aug 2018 03:02:36: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 10 Aug 2018 03:02:36: #1 finished! INFO @ Fri, 10 Aug 2018 03:02:36: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 03:02:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 03:02:36: #2 number of paired peaks: 146 WARNING @ Fri, 10 Aug 2018 03:02:36: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Fri, 10 Aug 2018 03:02:36: start model_add_line... INFO @ Fri, 10 Aug 2018 03:02:36: start X-correlation... INFO @ Fri, 10 Aug 2018 03:02:36: end of X-cor INFO @ Fri, 10 Aug 2018 03:02:36: #2 finished! INFO @ Fri, 10 Aug 2018 03:02:36: #2 predicted fragment length is 0 bps INFO @ Fri, 10 Aug 2018 03:02:36: #2 alternative fragment length(s) may be 0,32,50,90,109,141,184,213,230,270,304,331,345,375,396,418,454,481,497,511,526,551,580 bps INFO @ Fri, 10 Aug 2018 03:02:36: #2.2 Generate R script for model : SRX3467909.05_model.r WARNING @ Fri, 10 Aug 2018 03:02:36: #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 03:02:36: #2 You may need to consider one of the other alternative d(s): 0,32,50,90,109,141,184,213,230,270,304,331,345,375,396,418,454,481,497,511,526,551,580 WARNING @ Fri, 10 Aug 2018 03:02:36: #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 03:02:36: #3 Call peaks... INFO @ Fri, 10 Aug 2018 03:02:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 03:02:38: #1 tag size is determined as 36 bps INFO @ Fri, 10 Aug 2018 03:02:38: #1 tag size = 36 INFO @ Fri, 10 Aug 2018 03:02:38: #1 total tags in treatment: 7069638 INFO @ Fri, 10 Aug 2018 03:02:38: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 03:02:38: #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 03:02:38: #1 tags after filtering in treatment: 4468083 INFO @ Fri, 10 Aug 2018 03:02:38: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 10 Aug 2018 03:02:38: #1 finished! INFO @ Fri, 10 Aug 2018 03:02:38: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 03:02:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 03:02:38: #2 number of paired peaks: 146 WARNING @ Fri, 10 Aug 2018 03:02:38: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Fri, 10 Aug 2018 03:02:38: start model_add_line... INFO @ Fri, 10 Aug 2018 03:02:38: start X-correlation... INFO @ Fri, 10 Aug 2018 03:02:38: end of X-cor INFO @ Fri, 10 Aug 2018 03:02:38: #2 finished! INFO @ Fri, 10 Aug 2018 03:02:38: #2 predicted fragment length is 0 bps INFO @ Fri, 10 Aug 2018 03:02:38: #2 alternative fragment length(s) may be 0,32,50,90,109,141,184,213,230,270,304,331,345,375,396,418,454,481,497,511,526,551,580 bps INFO @ Fri, 10 Aug 2018 03:02:38: #2.2 Generate R script for model : SRX3467909.10_model.r WARNING @ Fri, 10 Aug 2018 03:02:38: #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 03:02:38: #2 You may need to consider one of the other alternative d(s): 0,32,50,90,109,141,184,213,230,270,304,331,345,375,396,418,454,481,497,511,526,551,580 WARNING @ Fri, 10 Aug 2018 03:02:38: #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 03:02:38: #3 Call peaks... INFO @ Fri, 10 Aug 2018 03:02:38: #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 SRX3467909.05.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 `SRX3467909.05.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/nt141i/job_scripts/10937695: line 254: 63215 終了しました MACS $i /var/spool/uge/nt141i/job_scripts/10937695: line 254: 63216 終了しました MACS $i /var/spool/uge/nt141i/job_scripts/10937695: line 254: 63218 終了しました MACS $i mv: cannot stat `SRX3467909.05.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 SRX3467909.10.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 `SRX3467909.10.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 `SRX3467909.10.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 SRX3467909.20.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 `SRX3467909.20.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 `SRX3467909.20.bb': そのようなファイルやディレクトリはありません