Job ID = 11244907 sra ファイルのダウンロード中... Completed: 353039K bytes transferred in 14 seconds (202385K 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 10864807 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554654/SRR7696328.sra Written 10864807 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554654/SRR7696328.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: 00:05:40 10864807 reads; of these: 10864807 (100.00%) were paired; of these: 4578499 (42.14%) aligned concordantly 0 times 5452158 (50.18%) aligned concordantly exactly 1 time 834150 (7.68%) aligned concordantly >1 times ---- 4578499 pairs aligned concordantly 0 times; of these: 207945 (4.54%) aligned discordantly 1 time ---- 4370554 pairs aligned 0 times concordantly or discordantly; of these: 8741108 mates make up the pairs; of these: 8483345 (97.05%) aligned 0 times 160343 (1.83%) aligned exactly 1 time 97420 (1.11%) aligned >1 times 60.96% overall alignment rate Time searching: 00:05:40 Overall time: 00:05:40 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] 206904 / 6454677 = 0.0321 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 22:54:25: # Command line: callpeak -t SRX4554654.bam -f BAM -g 12100000 -n SRX4554654.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554654.20 # format = BAM # ChIP-seq file = ['SRX4554654.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 22:54:25: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:54:25: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:54:25: # Command line: callpeak -t SRX4554654.bam -f BAM -g 12100000 -n SRX4554654.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554654.05 # format = BAM # ChIP-seq file = ['SRX4554654.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 22:54:25: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:54:25: # Command line: callpeak -t SRX4554654.bam -f BAM -g 12100000 -n SRX4554654.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554654.10 # format = BAM # ChIP-seq file = ['SRX4554654.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 22:54:25: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:54:25: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:54:25: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:54:31: 1000000 INFO @ Tue, 09 Oct 2018 22:54:31: 1000000 INFO @ Tue, 09 Oct 2018 22:54:32: 1000000 INFO @ Tue, 09 Oct 2018 22:54:38: 2000000 INFO @ Tue, 09 Oct 2018 22:54:38: 2000000 INFO @ Tue, 09 Oct 2018 22:54:39: 2000000 INFO @ Tue, 09 Oct 2018 22:54:44: 3000000 INFO @ Tue, 09 Oct 2018 22:54:44: 3000000 INFO @ Tue, 09 Oct 2018 22:54:47: 3000000 INFO @ Tue, 09 Oct 2018 22:54:50: 4000000 INFO @ Tue, 09 Oct 2018 22:54:50: 4000000 INFO @ Tue, 09 Oct 2018 22:54:54: 4000000 INFO @ Tue, 09 Oct 2018 22:54:57: 5000000 INFO @ Tue, 09 Oct 2018 22:54:57: 5000000 INFO @ Tue, 09 Oct 2018 22:55:01: 5000000 INFO @ Tue, 09 Oct 2018 22:55:03: 6000000 INFO @ Tue, 09 Oct 2018 22:55:03: 6000000 INFO @ Tue, 09 Oct 2018 22:55:08: 6000000 INFO @ Tue, 09 Oct 2018 22:55:09: 7000000 INFO @ Tue, 09 Oct 2018 22:55:09: 7000000 INFO @ Tue, 09 Oct 2018 22:55:16: 8000000 INFO @ Tue, 09 Oct 2018 22:55:16: 8000000 INFO @ Tue, 09 Oct 2018 22:55:16: 7000000 INFO @ Tue, 09 Oct 2018 22:55:22: 9000000 INFO @ Tue, 09 Oct 2018 22:55:22: 9000000 INFO @ Tue, 09 Oct 2018 22:55:23: 8000000 INFO @ Tue, 09 Oct 2018 22:55:28: 10000000 INFO @ Tue, 09 Oct 2018 22:55:29: 10000000 INFO @ Tue, 09 Oct 2018 22:55:30: 9000000 INFO @ Tue, 09 Oct 2018 22:55:35: 11000000 INFO @ Tue, 09 Oct 2018 22:55:35: 11000000 INFO @ Tue, 09 Oct 2018 22:55:38: 10000000 INFO @ Tue, 09 Oct 2018 22:55:41: 12000000 INFO @ Tue, 09 Oct 2018 22:55:41: 12000000 INFO @ Tue, 09 Oct 2018 22:55:45: 11000000 INFO @ Tue, 09 Oct 2018 22:55:46: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:55:46: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:55:46: #1 total tags in treatment: 6088671 INFO @ Tue, 09 Oct 2018 22:55:46: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:55:46: #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 22:55:47: #1 tags after filtering in treatment: 2709223 INFO @ Tue, 09 Oct 2018 22:55:47: #1 Redundant rate of treatment: 0.56 INFO @ Tue, 09 Oct 2018 22:55:47: #1 finished! INFO @ Tue, 09 Oct 2018 22:55:47: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:55:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:55:47: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:55:47: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:55:47: #1 total tags in treatment: 6088671 INFO @ Tue, 09 Oct 2018 22:55:47: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:55:47: #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 22:55:47: #1 tags after filtering in treatment: 2709223 INFO @ Tue, 09 Oct 2018 22:55:47: #1 Redundant rate of treatment: 0.56 INFO @ Tue, 09 Oct 2018 22:55:47: #1 finished! INFO @ Tue, 09 Oct 2018 22:55:47: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:55:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:55:47: #2 number of paired peaks: 1110 INFO @ Tue, 09 Oct 2018 22:55:47: start model_add_line... INFO @ Tue, 09 Oct 2018 22:55:47: start X-correlation... INFO @ Tue, 09 Oct 2018 22:55:47: end of X-cor INFO @ Tue, 09 Oct 2018 22:55:47: #2 finished! INFO @ Tue, 09 Oct 2018 22:55:47: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:55:47: #2 alternative fragment length(s) may be 0,77,82,173,187,206,225,249,597 bps INFO @ Tue, 09 Oct 2018 22:55:47: #2.2 Generate R script for model : SRX4554654.05_model.r WARNING @ Tue, 09 Oct 2018 22:55:47: #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 22:55:47: #2 You may need to consider one of the other alternative d(s): 0,77,82,173,187,206,225,249,597 WARNING @ Tue, 09 Oct 2018 22:55:47: #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 22:55:47: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:55:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:55:47: #2 number of paired peaks: 1110 INFO @ Tue, 09 Oct 2018 22:55:47: start model_add_line... INFO @ Tue, 09 Oct 2018 22:55:47: start X-correlation... INFO @ Tue, 09 Oct 2018 22:55:47: end of X-cor INFO @ Tue, 09 Oct 2018 22:55:47: #2 finished! INFO @ Tue, 09 Oct 2018 22:55:47: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:55:47: #2 alternative fragment length(s) may be 0,77,82,173,187,206,225,249,597 bps INFO @ Tue, 09 Oct 2018 22:55:47: #2.2 Generate R script for model : SRX4554654.10_model.r WARNING @ Tue, 09 Oct 2018 22:55:47: #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 22:55:47: #2 You may need to consider one of the other alternative d(s): 0,77,82,173,187,206,225,249,597 WARNING @ Tue, 09 Oct 2018 22:55:47: #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 22:55:47: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:55:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:55:52: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 09 Oct 2018 22:55:58: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:55:58: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:55:58: #1 total tags in treatment: 6088671 INFO @ Tue, 09 Oct 2018 22:55:58: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:55:58: #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 22:55:58: #1 tags after filtering in treatment: 2709223 INFO @ Tue, 09 Oct 2018 22:55:58: #1 Redundant rate of treatment: 0.56 INFO @ Tue, 09 Oct 2018 22:55:58: #1 finished! INFO @ Tue, 09 Oct 2018 22:55:58: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:55:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:55:59: #2 number of paired peaks: 1110 INFO @ Tue, 09 Oct 2018 22:55:59: start model_add_line... INFO @ Tue, 09 Oct 2018 22:55:59: start X-correlation... INFO @ Tue, 09 Oct 2018 22:55:59: end of X-cor INFO @ Tue, 09 Oct 2018 22:55:59: #2 finished! INFO @ Tue, 09 Oct 2018 22:55:59: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:55:59: #2 alternative fragment length(s) may be 0,77,82,173,187,206,225,249,597 bps INFO @ Tue, 09 Oct 2018 22:55:59: #2.2 Generate R script for model : SRX4554654.20_model.r WARNING @ Tue, 09 Oct 2018 22:55:59: #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 22:55:59: #2 You may need to consider one of the other alternative d(s): 0,77,82,173,187,206,225,249,597 WARNING @ Tue, 09 Oct 2018 22:55:59: #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 22:55:59: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:55:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 ls: cannot access SRX4554654.05.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 `SRX4554654.05.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/nt026i/job_scripts/11244907: line 254: 33310 終了しました MACS $i /var/spool/uge/nt026i/job_scripts/11244907: line 254: 33311 終了しました MACS $i /var/spool/uge/nt026i/job_scripts/11244907: line 254: 33312 終了しました MACS $i mv: cannot stat `SRX4554654.05.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 SRX4554654.10.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 `SRX4554654.10.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 `SRX4554654.10.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 SRX4554654.20.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 `SRX4554654.20.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 `SRX4554654.20.bb': そのようなファイルやディレクトリはありません