Job ID = 10924595 sra ファイルのダウンロード中... Completed: 665957K bytes transferred in 29 seconds (186815K 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... Read 30788149 spots for /home/okishinya/chipatlas/results/ce10/SRX4200542/SRR7298008.sra Written 30788149 spots for /home/okishinya/chipatlas/results/ce10/SRX4200542/SRR7298008.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: 00:06:06 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 171810 (0.56%) aligned 0 times 25273595 (82.09%) aligned exactly 1 time 5342744 (17.35%) aligned >1 times 99.44% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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] 4711459 / 30616339 = 0.1539 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 @ Mon, 06 Aug 2018 10:39:56: # Command line: callpeak -t SRX4200542.bam -f BAM -g ce -n SRX4200542.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4200542.20 # format = BAM # ChIP-seq file = ['SRX4200542.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 @ Mon, 06 Aug 2018 10:39:56: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:39:56: # Command line: callpeak -t SRX4200542.bam -f BAM -g ce -n SRX4200542.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4200542.10 # format = BAM # ChIP-seq file = ['SRX4200542.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 @ Mon, 06 Aug 2018 10:39:56: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:39:56: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:39:56: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:39:56: # Command line: callpeak -t SRX4200542.bam -f BAM -g ce -n SRX4200542.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4200542.05 # format = BAM # ChIP-seq file = ['SRX4200542.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 @ Mon, 06 Aug 2018 10:39:56: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:39:56: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:40:03: 1000000 INFO @ Mon, 06 Aug 2018 10:40:03: 1000000 INFO @ Mon, 06 Aug 2018 10:40:03: 1000000 INFO @ Mon, 06 Aug 2018 10:40:09: 2000000 INFO @ Mon, 06 Aug 2018 10:40:09: 2000000 INFO @ Mon, 06 Aug 2018 10:40:09: 2000000 INFO @ Mon, 06 Aug 2018 10:40:15: 3000000 INFO @ Mon, 06 Aug 2018 10:40:15: 3000000 INFO @ Mon, 06 Aug 2018 10:40:15: 3000000 INFO @ Mon, 06 Aug 2018 10:40:21: 4000000 INFO @ Mon, 06 Aug 2018 10:40:21: 4000000 INFO @ Mon, 06 Aug 2018 10:40:22: 4000000 INFO @ Mon, 06 Aug 2018 10:40:28: 5000000 INFO @ Mon, 06 Aug 2018 10:40:28: 5000000 INFO @ Mon, 06 Aug 2018 10:40:28: 5000000 INFO @ Mon, 06 Aug 2018 10:40:34: 6000000 INFO @ Mon, 06 Aug 2018 10:40:34: 6000000 INFO @ Mon, 06 Aug 2018 10:40:34: 6000000 INFO @ Mon, 06 Aug 2018 10:40:40: 7000000 INFO @ Mon, 06 Aug 2018 10:40:40: 7000000 INFO @ Mon, 06 Aug 2018 10:40:41: 7000000 INFO @ Mon, 06 Aug 2018 10:40:47: 8000000 INFO @ Mon, 06 Aug 2018 10:40:47: 8000000 INFO @ Mon, 06 Aug 2018 10:40:47: 8000000 INFO @ Mon, 06 Aug 2018 10:40:53: 9000000 INFO @ Mon, 06 Aug 2018 10:40:53: 9000000 INFO @ Mon, 06 Aug 2018 10:40:53: 9000000 INFO @ Mon, 06 Aug 2018 10:40:59: 10000000 INFO @ Mon, 06 Aug 2018 10:40:59: 10000000 INFO @ Mon, 06 Aug 2018 10:41:00: 10000000 INFO @ Mon, 06 Aug 2018 10:41:05: 11000000 INFO @ Mon, 06 Aug 2018 10:41:05: 11000000 INFO @ Mon, 06 Aug 2018 10:41:06: 11000000 INFO @ Mon, 06 Aug 2018 10:41:11: 12000000 INFO @ Mon, 06 Aug 2018 10:41:12: 12000000 INFO @ Mon, 06 Aug 2018 10:41:12: 12000000 INFO @ Mon, 06 Aug 2018 10:41:18: 13000000 INFO @ Mon, 06 Aug 2018 10:41:18: 13000000 INFO @ Mon, 06 Aug 2018 10:41:18: 13000000 INFO @ Mon, 06 Aug 2018 10:41:24: 14000000 INFO @ Mon, 06 Aug 2018 10:41:24: 14000000 INFO @ Mon, 06 Aug 2018 10:41:25: 14000000 INFO @ Mon, 06 Aug 2018 10:41:30: 15000000 INFO @ Mon, 06 Aug 2018 10:41:30: 15000000 INFO @ Mon, 06 Aug 2018 10:41:31: 15000000 INFO @ Mon, 06 Aug 2018 10:41:36: 16000000 INFO @ Mon, 06 Aug 2018 10:41:37: 16000000 INFO @ Mon, 06 Aug 2018 10:41:37: 16000000 INFO @ Mon, 06 Aug 2018 10:41:42: 17000000 INFO @ Mon, 06 Aug 2018 10:41:43: 17000000 INFO @ Mon, 06 Aug 2018 10:41:44: 17000000 INFO @ Mon, 06 Aug 2018 10:41:48: 18000000 INFO @ Mon, 06 Aug 2018 10:41:49: 18000000 INFO @ Mon, 06 Aug 2018 10:41:50: 18000000 INFO @ Mon, 06 Aug 2018 10:41:54: 19000000 INFO @ Mon, 06 Aug 2018 10:41:55: 19000000 INFO @ Mon, 06 Aug 2018 10:41:57: 19000000 INFO @ Mon, 06 Aug 2018 10:42:00: 20000000 INFO @ Mon, 06 Aug 2018 10:42:02: 20000000 INFO @ Mon, 06 Aug 2018 10:42:03: 20000000 INFO @ Mon, 06 Aug 2018 10:42:07: 21000000 INFO @ Mon, 06 Aug 2018 10:42:08: 21000000 INFO @ Mon, 06 Aug 2018 10:42:09: 21000000 INFO @ Mon, 06 Aug 2018 10:42:13: 22000000 INFO @ Mon, 06 Aug 2018 10:42:14: 22000000 INFO @ Mon, 06 Aug 2018 10:42:16: 22000000 INFO @ Mon, 06 Aug 2018 10:42:19: 23000000 INFO @ Mon, 06 Aug 2018 10:42:21: 23000000 INFO @ Mon, 06 Aug 2018 10:42:22: 23000000 INFO @ Mon, 06 Aug 2018 10:42:25: 24000000 INFO @ Mon, 06 Aug 2018 10:42:27: 24000000 INFO @ Mon, 06 Aug 2018 10:42:29: 24000000 INFO @ Mon, 06 Aug 2018 10:42:31: 25000000 INFO @ Mon, 06 Aug 2018 10:42:33: 25000000 INFO @ Mon, 06 Aug 2018 10:42:35: 25000000 INFO @ Mon, 06 Aug 2018 10:42:37: #1 tag size is determined as 36 bps INFO @ Mon, 06 Aug 2018 10:42:37: #1 tag size = 36 INFO @ Mon, 06 Aug 2018 10:42:37: #1 total tags in treatment: 25904880 INFO @ Mon, 06 Aug 2018 10:42:37: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:42:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:42:37: #1 tags after filtering in treatment: 25904880 INFO @ Mon, 06 Aug 2018 10:42:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:42:37: #1 finished! INFO @ Mon, 06 Aug 2018 10:42:37: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:42:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:42:39: #1 tag size is determined as 36 bps INFO @ Mon, 06 Aug 2018 10:42:39: #1 tag size = 36 INFO @ Mon, 06 Aug 2018 10:42:39: #1 total tags in treatment: 25904880 INFO @ Mon, 06 Aug 2018 10:42:39: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:42:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:42:39: #2 number of paired peaks: 139 WARNING @ Mon, 06 Aug 2018 10:42:39: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Mon, 06 Aug 2018 10:42:39: start model_add_line... INFO @ Mon, 06 Aug 2018 10:42:39: start X-correlation... INFO @ Mon, 06 Aug 2018 10:42:39: end of X-cor INFO @ Mon, 06 Aug 2018 10:42:39: #2 finished! INFO @ Mon, 06 Aug 2018 10:42:39: #2 predicted fragment length is 0 bps INFO @ Mon, 06 Aug 2018 10:42:39: #2 alternative fragment length(s) may be 0,30,305,418,525,554,576,598 bps INFO @ Mon, 06 Aug 2018 10:42:39: #2.2 Generate R script for model : SRX4200542.10_model.r WARNING @ Mon, 06 Aug 2018 10:42:39: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Aug 2018 10:42:39: #2 You may need to consider one of the other alternative d(s): 0,30,305,418,525,554,576,598 WARNING @ Mon, 06 Aug 2018 10:42:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Aug 2018 10:42:39: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:42:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:42:39: #1 tags after filtering in treatment: 25904880 INFO @ Mon, 06 Aug 2018 10:42:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:42:39: #1 finished! INFO @ Mon, 06 Aug 2018 10:42:39: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:42:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:42:41: #1 tag size is determined as 36 bps INFO @ Mon, 06 Aug 2018 10:42:41: #1 tag size = 36 INFO @ Mon, 06 Aug 2018 10:42:41: #1 total tags in treatment: 25904880 INFO @ Mon, 06 Aug 2018 10:42:41: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:42:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:42:41: #2 number of paired peaks: 139 WARNING @ Mon, 06 Aug 2018 10:42:41: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Mon, 06 Aug 2018 10:42:41: start model_add_line... INFO @ Mon, 06 Aug 2018 10:42:41: start X-correlation... INFO @ Mon, 06 Aug 2018 10:42:41: end of X-cor INFO @ Mon, 06 Aug 2018 10:42:41: #2 finished! INFO @ Mon, 06 Aug 2018 10:42:41: #2 predicted fragment length is 0 bps INFO @ Mon, 06 Aug 2018 10:42:41: #2 alternative fragment length(s) may be 0,30,305,418,525,554,576,598 bps INFO @ Mon, 06 Aug 2018 10:42:41: #2.2 Generate R script for model : SRX4200542.20_model.r WARNING @ Mon, 06 Aug 2018 10:42:41: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Aug 2018 10:42:41: #2 You may need to consider one of the other alternative d(s): 0,30,305,418,525,554,576,598 WARNING @ Mon, 06 Aug 2018 10:42:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Aug 2018 10:42:41: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:42:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:42:41: #1 tags after filtering in treatment: 25904880 INFO @ Mon, 06 Aug 2018 10:42:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:42:41: #1 finished! INFO @ Mon, 06 Aug 2018 10:42:41: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:42:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:42:43: #2 number of paired peaks: 139 WARNING @ Mon, 06 Aug 2018 10:42:43: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Mon, 06 Aug 2018 10:42:43: start model_add_line... INFO @ Mon, 06 Aug 2018 10:42:44: start X-correlation... INFO @ Mon, 06 Aug 2018 10:42:44: end of X-cor INFO @ Mon, 06 Aug 2018 10:42:44: #2 finished! INFO @ Mon, 06 Aug 2018 10:42:44: #2 predicted fragment length is 0 bps INFO @ Mon, 06 Aug 2018 10:42:44: #2 alternative fragment length(s) may be 0,30,305,418,525,554,576,598 bps INFO @ Mon, 06 Aug 2018 10:42:44: #2.2 Generate R script for model : SRX4200542.05_model.r WARNING @ Mon, 06 Aug 2018 10:42:44: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Aug 2018 10:42:44: #2 You may need to consider one of the other alternative d(s): 0,30,305,418,525,554,576,598 WARNING @ Mon, 06 Aug 2018 10:42:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Aug 2018 10:42:44: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:42:44: #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 SRX4200542.05.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 `SRX4200542.05.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/nt023i/job_scripts/10924595: line 254: 15610 終了しました MACS $i /var/spool/uge/nt023i/job_scripts/10924595: line 254: 15611 終了しました MACS $i /var/spool/uge/nt023i/job_scripts/10924595: line 254: 15612 終了しました MACS $i mv: cannot stat `SRX4200542.05.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 SRX4200542.10.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 `SRX4200542.10.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 `SRX4200542.10.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 SRX4200542.20.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 `SRX4200542.20.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 `SRX4200542.20.bb': そのようなファイルやディレクトリはありません