Job ID = 11244933 sra ファイルのダウンロード中... Completed: 363626K bytes transferred in 9 seconds (319651K 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 11049185 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554670/SRR7696343.sra Written 11049185 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554670/SRR7696343.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: 00:03:29 11049185 reads; of these: 11049185 (100.00%) were paired; of these: 7537997 (68.22%) aligned concordantly 0 times 2528060 (22.88%) aligned concordantly exactly 1 time 983128 (8.90%) aligned concordantly >1 times ---- 7537997 pairs aligned concordantly 0 times; of these: 111735 (1.48%) aligned discordantly 1 time ---- 7426262 pairs aligned 0 times concordantly or discordantly; of these: 14852524 mates make up the pairs; of these: 14649199 (98.63%) aligned 0 times 87346 (0.59%) aligned exactly 1 time 115979 (0.78%) aligned >1 times 33.71% overall alignment rate Time searching: 00:03:29 Overall time: 00:03:29 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] 161312 / 3599335 = 0.0448 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 22:58:19: # Command line: callpeak -t SRX4554670.bam -f BAM -g 12100000 -n SRX4554670.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554670.20 # format = BAM # ChIP-seq file = ['SRX4554670.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 22:58:19: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:58:19: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:58:19: # Command line: callpeak -t SRX4554670.bam -f BAM -g 12100000 -n SRX4554670.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554670.10 # format = BAM # ChIP-seq file = ['SRX4554670.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 22:58:19: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:58:19: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:58:19: # Command line: callpeak -t SRX4554670.bam -f BAM -g 12100000 -n SRX4554670.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554670.05 # format = BAM # ChIP-seq file = ['SRX4554670.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 22:58:19: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:58:19: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:58:26: 1000000 INFO @ Tue, 09 Oct 2018 22:58:26: 1000000 INFO @ Tue, 09 Oct 2018 22:58:26: 1000000 INFO @ Tue, 09 Oct 2018 22:58:33: 2000000 INFO @ Tue, 09 Oct 2018 22:58:33: 2000000 INFO @ Tue, 09 Oct 2018 22:58:33: 2000000 INFO @ Tue, 09 Oct 2018 22:58:40: 3000000 INFO @ Tue, 09 Oct 2018 22:58:41: 3000000 INFO @ Tue, 09 Oct 2018 22:58:41: 3000000 INFO @ Tue, 09 Oct 2018 22:58:47: 4000000 INFO @ Tue, 09 Oct 2018 22:58:48: 4000000 INFO @ Tue, 09 Oct 2018 22:58:48: 4000000 INFO @ Tue, 09 Oct 2018 22:58:54: 5000000 INFO @ Tue, 09 Oct 2018 22:58:55: 5000000 INFO @ Tue, 09 Oct 2018 22:58:55: 5000000 INFO @ Tue, 09 Oct 2018 22:59:01: 6000000 INFO @ Tue, 09 Oct 2018 22:59:02: 6000000 INFO @ Tue, 09 Oct 2018 22:59:02: 6000000 INFO @ Tue, 09 Oct 2018 22:59:08: 7000000 INFO @ Tue, 09 Oct 2018 22:59:08: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:59:08: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:59:08: #1 total tags in treatment: 3352857 INFO @ Tue, 09 Oct 2018 22:59:08: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:59:08: #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 22:59:09: #1 tags after filtering in treatment: 2318900 INFO @ Tue, 09 Oct 2018 22:59:09: #1 Redundant rate of treatment: 0.31 INFO @ Tue, 09 Oct 2018 22:59:09: #1 finished! INFO @ Tue, 09 Oct 2018 22:59:09: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:59:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:59:09: #2 number of paired peaks: 256 WARNING @ Tue, 09 Oct 2018 22:59:09: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Tue, 09 Oct 2018 22:59:09: start model_add_line... INFO @ Tue, 09 Oct 2018 22:59:09: start X-correlation... INFO @ Tue, 09 Oct 2018 22:59:09: end of X-cor INFO @ Tue, 09 Oct 2018 22:59:09: #2 finished! INFO @ Tue, 09 Oct 2018 22:59:09: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:59:09: #2 alternative fragment length(s) may be 0,19,38,59,75,98,119,153,157,203,240,593,598 bps INFO @ Tue, 09 Oct 2018 22:59:09: #2.2 Generate R script for model : SRX4554670.10_model.r WARNING @ Tue, 09 Oct 2018 22:59:09: #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 22:59:09: #2 You may need to consider one of the other alternative d(s): 0,19,38,59,75,98,119,153,157,203,240,593,598 WARNING @ Tue, 09 Oct 2018 22:59:09: #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 22:59:09: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:59:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:59:09: 7000000 INFO @ Tue, 09 Oct 2018 22:59:09: 7000000 INFO @ Tue, 09 Oct 2018 22:59:10: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:59:10: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:59:10: #1 total tags in treatment: 3352857 INFO @ Tue, 09 Oct 2018 22:59:10: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:59:10: #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 22:59:10: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:59:10: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:59:10: #1 total tags in treatment: 3352857 INFO @ Tue, 09 Oct 2018 22:59:10: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:59:10: #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 22:59:10: #1 tags after filtering in treatment: 2318900 INFO @ Tue, 09 Oct 2018 22:59:10: #1 Redundant rate of treatment: 0.31 INFO @ Tue, 09 Oct 2018 22:59:10: #1 finished! INFO @ Tue, 09 Oct 2018 22:59:10: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:59:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:59:10: #1 tags after filtering in treatment: 2318900 INFO @ Tue, 09 Oct 2018 22:59:10: #1 Redundant rate of treatment: 0.31 INFO @ Tue, 09 Oct 2018 22:59:10: #1 finished! INFO @ Tue, 09 Oct 2018 22:59:10: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:59:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:59:10: #2 number of paired peaks: 256 WARNING @ Tue, 09 Oct 2018 22:59:10: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Tue, 09 Oct 2018 22:59:10: start model_add_line... INFO @ Tue, 09 Oct 2018 22:59:10: #2 number of paired peaks: 256 WARNING @ Tue, 09 Oct 2018 22:59:10: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Tue, 09 Oct 2018 22:59:10: start model_add_line... INFO @ Tue, 09 Oct 2018 22:59:10: start X-correlation... INFO @ Tue, 09 Oct 2018 22:59:10: end of X-cor INFO @ Tue, 09 Oct 2018 22:59:10: #2 finished! INFO @ Tue, 09 Oct 2018 22:59:10: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:59:10: #2 alternative fragment length(s) may be 0,19,38,59,75,98,119,153,157,203,240,593,598 bps INFO @ Tue, 09 Oct 2018 22:59:10: #2.2 Generate R script for model : SRX4554670.05_model.r INFO @ Tue, 09 Oct 2018 22:59:10: start X-correlation... WARNING @ Tue, 09 Oct 2018 22:59:10: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:59:10: #2 You may need to consider one of the other alternative d(s): 0,19,38,59,75,98,119,153,157,203,240,593,598 WARNING @ Tue, 09 Oct 2018 22:59:10: #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 22:59:10: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:59:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:59:10: end of X-cor INFO @ Tue, 09 Oct 2018 22:59:10: #2 finished! INFO @ Tue, 09 Oct 2018 22:59:10: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:59:10: #2 alternative fragment length(s) may be 0,19,38,59,75,98,119,153,157,203,240,593,598 bps INFO @ Tue, 09 Oct 2018 22:59:10: #2.2 Generate R script for model : SRX4554670.20_model.r WARNING @ Tue, 09 Oct 2018 22:59:10: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:59:10: #2 You may need to consider one of the other alternative d(s): 0,19,38,59,75,98,119,153,157,203,240,593,598 WARNING @ Tue, 09 Oct 2018 22:59:10: #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 22:59:10: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:59:10: #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 SRX4554670.05.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 `SRX4554670.05.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/nt003i/job_scripts/11244933: line 254: 19857 終了しました MACS $i /var/spool/uge/nt003i/job_scripts/11244933: line 254: 19858 終了しました MACS $i /var/spool/uge/nt003i/job_scripts/11244933: line 254: 19860 終了しました MACS $i mv: cannot stat `SRX4554670.05.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 SRX4554670.10.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 `SRX4554670.10.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 `SRX4554670.10.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 SRX4554670.20.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 `SRX4554670.20.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 `SRX4554670.20.bb': そのようなファイルやディレクトリはありません