Job ID = 11244929 sra ファイルのダウンロード中... Completed: 436764K bytes transferred in 8 seconds (409643K 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 13461364 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554667/SRR7696340.sra Written 13461364 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554667/SRR7696340.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: 00:06:24 13461364 reads; of these: 13461364 (100.00%) were paired; of these: 6347966 (47.16%) aligned concordantly 0 times 6116866 (45.44%) aligned concordantly exactly 1 time 996532 (7.40%) aligned concordantly >1 times ---- 6347966 pairs aligned concordantly 0 times; of these: 233497 (3.68%) aligned discordantly 1 time ---- 6114469 pairs aligned 0 times concordantly or discordantly; of these: 12228938 mates make up the pairs; of these: 11936218 (97.61%) aligned 0 times 177474 (1.45%) aligned exactly 1 time 115246 (0.94%) aligned >1 times 55.66% overall alignment rate Time searching: 00:06:25 Overall time: 00:06:25 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] 299530 / 7302376 = 0.0410 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 23:03:18: # Command line: callpeak -t SRX4554667.bam -f BAM -g 12100000 -n SRX4554667.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554667.20 # format = BAM # ChIP-seq file = ['SRX4554667.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 23:03:18: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:03:18: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:03:18: # Command line: callpeak -t SRX4554667.bam -f BAM -g 12100000 -n SRX4554667.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554667.05 # format = BAM # ChIP-seq file = ['SRX4554667.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 23:03:18: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:03:18: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:03:18: # Command line: callpeak -t SRX4554667.bam -f BAM -g 12100000 -n SRX4554667.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554667.10 # format = BAM # ChIP-seq file = ['SRX4554667.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 23:03:18: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:03:18: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:03:24: 1000000 INFO @ Tue, 09 Oct 2018 23:03:25: 1000000 INFO @ Tue, 09 Oct 2018 23:03:25: 1000000 INFO @ Tue, 09 Oct 2018 23:03:29: 2000000 INFO @ Tue, 09 Oct 2018 23:03:31: 2000000 INFO @ Tue, 09 Oct 2018 23:03:31: 2000000 INFO @ Tue, 09 Oct 2018 23:03:34: 3000000 INFO @ Tue, 09 Oct 2018 23:03:38: 3000000 INFO @ Tue, 09 Oct 2018 23:03:38: 3000000 INFO @ Tue, 09 Oct 2018 23:03:39: 4000000 INFO @ Tue, 09 Oct 2018 23:03:44: 5000000 INFO @ Tue, 09 Oct 2018 23:03:44: 4000000 INFO @ Tue, 09 Oct 2018 23:03:44: 4000000 INFO @ Tue, 09 Oct 2018 23:03:49: 6000000 INFO @ Tue, 09 Oct 2018 23:03:51: 5000000 INFO @ Tue, 09 Oct 2018 23:03:51: 5000000 INFO @ Tue, 09 Oct 2018 23:03:54: 7000000 INFO @ Tue, 09 Oct 2018 23:03:57: 6000000 INFO @ Tue, 09 Oct 2018 23:03:57: 6000000 INFO @ Tue, 09 Oct 2018 23:03:59: 8000000 INFO @ Tue, 09 Oct 2018 23:04:04: 7000000 INFO @ Tue, 09 Oct 2018 23:04:04: 7000000 INFO @ Tue, 09 Oct 2018 23:04:04: 9000000 INFO @ Tue, 09 Oct 2018 23:04:09: 10000000 INFO @ Tue, 09 Oct 2018 23:04:10: 8000000 INFO @ Tue, 09 Oct 2018 23:04:10: 8000000 INFO @ Tue, 09 Oct 2018 23:04:14: 11000000 INFO @ Tue, 09 Oct 2018 23:04:16: 9000000 INFO @ Tue, 09 Oct 2018 23:04:16: 9000000 INFO @ Tue, 09 Oct 2018 23:04:20: 12000000 INFO @ Tue, 09 Oct 2018 23:04:22: 10000000 INFO @ Tue, 09 Oct 2018 23:04:22: 10000000 INFO @ Tue, 09 Oct 2018 23:04:26: 13000000 INFO @ Tue, 09 Oct 2018 23:04:29: 11000000 INFO @ Tue, 09 Oct 2018 23:04:29: 11000000 INFO @ Tue, 09 Oct 2018 23:04:32: 14000000 INFO @ Tue, 09 Oct 2018 23:04:34: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:04:34: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:04:34: #1 total tags in treatment: 6825509 INFO @ Tue, 09 Oct 2018 23:04:34: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:04:34: #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 23:04:35: #1 tags after filtering in treatment: 2864278 INFO @ Tue, 09 Oct 2018 23:04:35: #1 Redundant rate of treatment: 0.58 INFO @ Tue, 09 Oct 2018 23:04:35: #1 finished! INFO @ Tue, 09 Oct 2018 23:04:35: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:04:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:04:35: #2 number of paired peaks: 1133 INFO @ Tue, 09 Oct 2018 23:04:35: start model_add_line... INFO @ Tue, 09 Oct 2018 23:04:35: 12000000 INFO @ Tue, 09 Oct 2018 23:04:35: start X-correlation... INFO @ Tue, 09 Oct 2018 23:04:35: end of X-cor INFO @ Tue, 09 Oct 2018 23:04:35: #2 finished! INFO @ Tue, 09 Oct 2018 23:04:35: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 23:04:35: #2 alternative fragment length(s) may be 0,32,106,143,171,192,210,245,320,511 bps INFO @ Tue, 09 Oct 2018 23:04:35: #2.2 Generate R script for model : SRX4554667.20_model.r WARNING @ Tue, 09 Oct 2018 23:04:35: #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 23:04:35: #2 You may need to consider one of the other alternative d(s): 0,32,106,143,171,192,210,245,320,511 WARNING @ Tue, 09 Oct 2018 23:04:35: #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 23:04:35: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:04:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:04:36: 12000000 INFO @ Tue, 09 Oct 2018 23:04:41: 13000000 INFO @ Tue, 09 Oct 2018 23:04:41: 13000000 INFO @ Tue, 09 Oct 2018 23:04:47: 14000000 INFO @ Tue, 09 Oct 2018 23:04:48: 14000000 INFO @ Tue, 09 Oct 2018 23:04:50: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:04:50: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:04:50: #1 total tags in treatment: 6825509 INFO @ Tue, 09 Oct 2018 23:04:50: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:04:50: #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 23:04:50: #1 tags after filtering in treatment: 2864278 INFO @ Tue, 09 Oct 2018 23:04:50: #1 Redundant rate of treatment: 0.58 INFO @ Tue, 09 Oct 2018 23:04:50: #1 finished! INFO @ Tue, 09 Oct 2018 23:04:50: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:04:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:04:50: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:04:50: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:04:50: #1 total tags in treatment: 6825509 INFO @ Tue, 09 Oct 2018 23:04:50: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:04:50: #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 23:04:50: #1 tags after filtering in treatment: 2864278 INFO @ Tue, 09 Oct 2018 23:04:50: #1 Redundant rate of treatment: 0.58 INFO @ Tue, 09 Oct 2018 23:04:50: #1 finished! INFO @ Tue, 09 Oct 2018 23:04:50: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:04:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:04:50: #2 number of paired peaks: 1133 INFO @ Tue, 09 Oct 2018 23:04:50: start model_add_line... INFO @ Tue, 09 Oct 2018 23:04:50: start X-correlation... INFO @ Tue, 09 Oct 2018 23:04:50: end of X-cor INFO @ Tue, 09 Oct 2018 23:04:50: #2 finished! INFO @ Tue, 09 Oct 2018 23:04:50: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 23:04:50: #2 alternative fragment length(s) may be 0,32,106,143,171,192,210,245,320,511 bps INFO @ Tue, 09 Oct 2018 23:04:50: #2.2 Generate R script for model : SRX4554667.10_model.r WARNING @ Tue, 09 Oct 2018 23:04:50: #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 23:04:50: #2 You may need to consider one of the other alternative d(s): 0,32,106,143,171,192,210,245,320,511 WARNING @ Tue, 09 Oct 2018 23:04:50: #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 23:04:50: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:04:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:04:50: #2 number of paired peaks: 1133 INFO @ Tue, 09 Oct 2018 23:04:50: start model_add_line... INFO @ Tue, 09 Oct 2018 23:04:51: start X-correlation... INFO @ Tue, 09 Oct 2018 23:04:51: end of X-cor INFO @ Tue, 09 Oct 2018 23:04:51: #2 finished! INFO @ Tue, 09 Oct 2018 23:04:51: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 23:04:51: #2 alternative fragment length(s) may be 0,32,106,143,171,192,210,245,320,511 bps INFO @ Tue, 09 Oct 2018 23:04:51: #2.2 Generate R script for model : SRX4554667.05_model.r WARNING @ Tue, 09 Oct 2018 23:04:51: #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 23:04:51: #2 You may need to consider one of the other alternative d(s): 0,32,106,143,171,192,210,245,320,511 WARNING @ Tue, 09 Oct 2018 23:04:51: #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 23:04:51: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:04:51: #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 SRX4554667.05.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 `SRX4554667.05.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/11244929: line 254: 41993 終了しました MACS $i /var/spool/uge/nt026i/job_scripts/11244929: line 254: 41994 終了しました MACS $i /var/spool/uge/nt026i/job_scripts/11244929: line 254: 41995 終了しました MACS $i mv: cannot stat `SRX4554667.05.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 SRX4554667.10.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 `SRX4554667.10.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 `SRX4554667.10.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 SRX4554667.20.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 `SRX4554667.20.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 `SRX4554667.20.bb': そのようなファイルやディレクトリはありません