Job ID = 10320315 sra ファイルのダウンロード中... Completed: 372217K bytes transferred in 56 seconds (53951K 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: SINGLE fastq に変換中... Written 13123452 spots for /home/okishinya/chipatlas/results/ce10/SRX3043406/SRR5875890.sra Written 13123452 spots total 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: 00:04:37 13123452 reads; of these: 13123452 (100.00%) were unpaired; of these: 255849 (1.95%) aligned 0 times 10840293 (82.60%) aligned exactly 1 time 2027310 (15.45%) aligned >1 times 98.05% overall alignment rate Time searching: 00:04:37 Overall time: 00:04:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1535926 / 12867603 = 0.1194 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 @ Thu, 11 Jan 2018 02:13:53: # Command line: callpeak -t SRX3043406.bam -f BAM -g ce -n SRX3043406.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3043406.20 # format = BAM # ChIP-seq file = ['SRX3043406.bam'] # control file = None # effective genome size = 9.00e+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 @ Thu, 11 Jan 2018 02:13:53: # Command line: callpeak -t SRX3043406.bam -f BAM -g ce -n SRX3043406.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3043406.10 # format = BAM # ChIP-seq file = ['SRX3043406.bam'] # control file = None # effective genome size = 9.00e+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 @ Thu, 11 Jan 2018 02:13:53: # Command line: callpeak -t SRX3043406.bam -f BAM -g ce -n SRX3043406.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3043406.05 # format = BAM # ChIP-seq file = ['SRX3043406.bam'] # control file = None # effective genome size = 9.00e+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 @ Thu, 11 Jan 2018 02:13:53: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:13:53: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:13:53: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:13:53: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:13:53: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:13:53: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:14:00: 1000000 INFO @ Thu, 11 Jan 2018 02:14:00: 1000000 INFO @ Thu, 11 Jan 2018 02:14:00: 1000000 INFO @ Thu, 11 Jan 2018 02:14:07: 2000000 INFO @ Thu, 11 Jan 2018 02:14:07: 2000000 INFO @ Thu, 11 Jan 2018 02:14:07: 2000000 INFO @ Thu, 11 Jan 2018 02:14:14: 3000000 INFO @ Thu, 11 Jan 2018 02:14:15: 3000000 INFO @ Thu, 11 Jan 2018 02:14:15: 3000000 INFO @ Thu, 11 Jan 2018 02:14:21: 4000000 INFO @ Thu, 11 Jan 2018 02:14:22: 4000000 INFO @ Thu, 11 Jan 2018 02:14:22: 4000000 INFO @ Thu, 11 Jan 2018 02:14:28: 5000000 INFO @ Thu, 11 Jan 2018 02:14:29: 5000000 INFO @ Thu, 11 Jan 2018 02:14:29: 5000000 INFO @ Thu, 11 Jan 2018 02:14:35: 6000000 INFO @ Thu, 11 Jan 2018 02:14:37: 6000000 INFO @ Thu, 11 Jan 2018 02:14:37: 6000000 INFO @ Thu, 11 Jan 2018 02:14:42: 7000000 INFO @ Thu, 11 Jan 2018 02:14:44: 7000000 INFO @ Thu, 11 Jan 2018 02:14:44: 7000000 INFO @ Thu, 11 Jan 2018 02:14:49: 8000000 INFO @ Thu, 11 Jan 2018 02:14:51: 8000000 INFO @ Thu, 11 Jan 2018 02:14:51: 8000000 INFO @ Thu, 11 Jan 2018 02:14:56: 9000000 INFO @ Thu, 11 Jan 2018 02:14:58: 9000000 INFO @ Thu, 11 Jan 2018 02:14:58: 9000000 INFO @ Thu, 11 Jan 2018 02:15:03: 10000000 INFO @ Thu, 11 Jan 2018 02:15:06: 10000000 INFO @ Thu, 11 Jan 2018 02:15:06: 10000000 INFO @ Thu, 11 Jan 2018 02:15:10: 11000000 INFO @ Thu, 11 Jan 2018 02:15:12: #1 tag size is determined as 50 bps INFO @ Thu, 11 Jan 2018 02:15:12: #1 tag size = 50 INFO @ Thu, 11 Jan 2018 02:15:12: #1 total tags in treatment: 11331677 INFO @ Thu, 11 Jan 2018 02:15:12: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:15:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:15:13: #1 tags after filtering in treatment: 11331677 INFO @ Thu, 11 Jan 2018 02:15:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:15:13: #1 finished! INFO @ Thu, 11 Jan 2018 02:15:13: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:15:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:15:13: 11000000 INFO @ Thu, 11 Jan 2018 02:15:13: 11000000 INFO @ Thu, 11 Jan 2018 02:15:13: #2 number of paired peaks: 160 WARNING @ Thu, 11 Jan 2018 02:15:13: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Thu, 11 Jan 2018 02:15:13: start model_add_line... INFO @ Thu, 11 Jan 2018 02:15:14: start X-correlation... INFO @ Thu, 11 Jan 2018 02:15:14: end of X-cor INFO @ Thu, 11 Jan 2018 02:15:14: #2 finished! INFO @ Thu, 11 Jan 2018 02:15:14: #2 predicted fragment length is 0 bps INFO @ Thu, 11 Jan 2018 02:15:14: #2 alternative fragment length(s) may be 0,15,51,442,507,572 bps INFO @ Thu, 11 Jan 2018 02:15:14: #2.2 Generate R script for model : SRX3043406.05_model.r WARNING @ Thu, 11 Jan 2018 02:15:14: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:15:14: #2 You may need to consider one of the other alternative d(s): 0,15,51,442,507,572 WARNING @ Thu, 11 Jan 2018 02:15:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:15:14: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:15:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:15:15: #1 tag size is determined as 50 bps INFO @ Thu, 11 Jan 2018 02:15:15: #1 tag size = 50 INFO @ Thu, 11 Jan 2018 02:15:15: #1 total tags in treatment: 11331677 INFO @ Thu, 11 Jan 2018 02:15:15: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:15:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:15:15: #1 tag size is determined as 50 bps INFO @ Thu, 11 Jan 2018 02:15:15: #1 tag size = 50 INFO @ Thu, 11 Jan 2018 02:15:15: #1 total tags in treatment: 11331677 INFO @ Thu, 11 Jan 2018 02:15:15: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:15:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:15:15: #1 tags after filtering in treatment: 11331677 INFO @ Thu, 11 Jan 2018 02:15:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:15:15: #1 finished! INFO @ Thu, 11 Jan 2018 02:15:15: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:15:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:15:15: #1 tags after filtering in treatment: 11331677 INFO @ Thu, 11 Jan 2018 02:15:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:15:15: #1 finished! INFO @ Thu, 11 Jan 2018 02:15:15: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:15:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:15:16: #2 number of paired peaks: 160 WARNING @ Thu, 11 Jan 2018 02:15:16: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Thu, 11 Jan 2018 02:15:16: start model_add_line... INFO @ Thu, 11 Jan 2018 02:15:16: #2 number of paired peaks: 160 WARNING @ Thu, 11 Jan 2018 02:15:16: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Thu, 11 Jan 2018 02:15:16: start model_add_line... INFO @ Thu, 11 Jan 2018 02:15:16: start X-correlation... INFO @ Thu, 11 Jan 2018 02:15:16: end of X-cor INFO @ Thu, 11 Jan 2018 02:15:16: #2 finished! INFO @ Thu, 11 Jan 2018 02:15:16: #2 predicted fragment length is 0 bps INFO @ Thu, 11 Jan 2018 02:15:16: #2 alternative fragment length(s) may be 0,15,51,442,507,572 bps INFO @ Thu, 11 Jan 2018 02:15:16: #2.2 Generate R script for model : SRX3043406.20_model.r WARNING @ Thu, 11 Jan 2018 02:15:16: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:15:16: #2 You may need to consider one of the other alternative d(s): 0,15,51,442,507,572 WARNING @ Thu, 11 Jan 2018 02:15:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:15:16: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:15:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:15:16: start X-correlation... INFO @ Thu, 11 Jan 2018 02:15:16: end of X-cor INFO @ Thu, 11 Jan 2018 02:15:16: #2 finished! INFO @ Thu, 11 Jan 2018 02:15:16: #2 predicted fragment length is 0 bps INFO @ Thu, 11 Jan 2018 02:15:16: #2 alternative fragment length(s) may be 0,15,51,442,507,572 bps INFO @ Thu, 11 Jan 2018 02:15:16: #2.2 Generate R script for model : SRX3043406.10_model.r WARNING @ Thu, 11 Jan 2018 02:15:16: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:15:16: #2 You may need to consider one of the other alternative d(s): 0,15,51,442,507,572 WARNING @ Thu, 11 Jan 2018 02:15:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:15:16: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:15:16: #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 SRX3043406.05.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 `SRX3043406.05.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/nt064i/job_scripts/10320315: line 254: 43337 終了しました MACS $i /var/spool/uge/nt064i/job_scripts/10320315: line 254: 43338 終了しました MACS $i /var/spool/uge/nt064i/job_scripts/10320315: line 254: 43340 終了しました MACS $i mv: cannot stat `SRX3043406.05.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 SRX3043406.10.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 `SRX3043406.10.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 `SRX3043406.10.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 SRX3043406.20.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 `SRX3043406.20.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 `SRX3043406.20.bb': そのようなファイルやディレクトリはありません