Job ID = 6527517 SRX = SRX042249 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:49:27 prefetch.2.10.7: 1) Downloading 'SRR100230'... 2020-06-29T12:49:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:55:35 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:55:35 prefetch.2.10.7: 1) 'SRR100230' was downloaded successfully Read 31509090 spots for SRR100230/SRR100230.sra Written 31509090 spots for SRR100230/SRR100230.sra 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: 00:09:00 31509090 reads; of these: 31509090 (100.00%) were unpaired; of these: 3772540 (11.97%) aligned 0 times 26112704 (82.87%) aligned exactly 1 time 1623846 (5.15%) aligned >1 times 88.03% overall alignment rate Time searching: 00:09:00 Overall time: 00:09:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 12821992 / 27736550 = 0.4623 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Mon, 29 Jun 2020 22:25:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX042249/SRX042249.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX042249/SRX042249.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX042249/SRX042249.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX042249/SRX042249.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 29 Jun 2020 22:25:05: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:25:05: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:25:11: 1000000 INFO @ Mon, 29 Jun 2020 22:25:18: 2000000 INFO @ Mon, 29 Jun 2020 22:25:24: 3000000 INFO @ Mon, 29 Jun 2020 22:25:30: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Mon, 29 Jun 2020 22:25:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX042249/SRX042249.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX042249/SRX042249.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX042249/SRX042249.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX042249/SRX042249.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 29 Jun 2020 22:25:35: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:25:35: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:25:36: 5000000 INFO @ Mon, 29 Jun 2020 22:25:41: 1000000 INFO @ Mon, 29 Jun 2020 22:25:42: 6000000 INFO @ Mon, 29 Jun 2020 22:25:46: 2000000 INFO @ Mon, 29 Jun 2020 22:25:49: 7000000 INFO @ Mon, 29 Jun 2020 22:25:52: 3000000 INFO @ Mon, 29 Jun 2020 22:25:55: 8000000 INFO @ Mon, 29 Jun 2020 22:25:57: 4000000 INFO @ Mon, 29 Jun 2020 22:26:01: 9000000 INFO @ Mon, 29 Jun 2020 22:26:03: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Mon, 29 Jun 2020 22:26:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX042249/SRX042249.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX042249/SRX042249.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX042249/SRX042249.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX042249/SRX042249.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 29 Jun 2020 22:26:05: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:26:05: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:26:07: 10000000 INFO @ Mon, 29 Jun 2020 22:26:09: 6000000 INFO @ Mon, 29 Jun 2020 22:26:11: 1000000 INFO @ Mon, 29 Jun 2020 22:26:14: 11000000 INFO @ Mon, 29 Jun 2020 22:26:15: 7000000 INFO @ Mon, 29 Jun 2020 22:26:17: 2000000 INFO @ Mon, 29 Jun 2020 22:26:20: 12000000 INFO @ Mon, 29 Jun 2020 22:26:20: 8000000 INFO @ Mon, 29 Jun 2020 22:26:23: 3000000 INFO @ Mon, 29 Jun 2020 22:26:26: 9000000 INFO @ Mon, 29 Jun 2020 22:26:26: 13000000 INFO @ Mon, 29 Jun 2020 22:26:28: 4000000 INFO @ Mon, 29 Jun 2020 22:26:32: 10000000 INFO @ Mon, 29 Jun 2020 22:26:33: 14000000 INFO @ Mon, 29 Jun 2020 22:26:34: 5000000 INFO @ Mon, 29 Jun 2020 22:26:37: 11000000 INFO @ Mon, 29 Jun 2020 22:26:38: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 22:26:38: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 22:26:38: #1 total tags in treatment: 14914558 INFO @ Mon, 29 Jun 2020 22:26:38: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:26:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:26:39: #1 tags after filtering in treatment: 14914558 INFO @ Mon, 29 Jun 2020 22:26:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:26:39: #1 finished! INFO @ Mon, 29 Jun 2020 22:26:39: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:26:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:26:40: 6000000 INFO @ Mon, 29 Jun 2020 22:26:40: #2 number of paired peaks: 3817 INFO @ Mon, 29 Jun 2020 22:26:40: start model_add_line... INFO @ Mon, 29 Jun 2020 22:26:40: start X-correlation... INFO @ Mon, 29 Jun 2020 22:26:40: end of X-cor INFO @ Mon, 29 Jun 2020 22:26:40: #2 finished! INFO @ Mon, 29 Jun 2020 22:26:40: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 22:26:40: #2 alternative fragment length(s) may be 0 bps INFO @ Mon, 29 Jun 2020 22:26:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX042249/SRX042249.05_model.r WARNING @ Mon, 29 Jun 2020 22:26:40: #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, 29 Jun 2020 22:26:40: #2 You may need to consider one of the other alternative d(s): 0 WARNING @ Mon, 29 Jun 2020 22:26:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:26:40: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:26:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:26:43: 12000000 INFO @ Mon, 29 Jun 2020 22:26:46: 7000000 INFO @ Mon, 29 Jun 2020 22:26:48: 13000000 INFO @ Mon, 29 Jun 2020 22:26:51: 8000000 INFO @ Mon, 29 Jun 2020 22:26:54: 14000000 INFO @ Mon, 29 Jun 2020 22:26:57: 9000000 INFO @ Mon, 29 Jun 2020 22:26:59: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 22:26:59: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 22:26:59: #1 total tags in treatment: 14914558 INFO @ Mon, 29 Jun 2020 22:26:59: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:26:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:26:59: #1 tags after filtering in treatment: 14914558 INFO @ Mon, 29 Jun 2020 22:26:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:26:59: #1 finished! INFO @ Mon, 29 Jun 2020 22:26:59: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:26:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:27:01: #2 number of paired peaks: 3817 INFO @ Mon, 29 Jun 2020 22:27:01: start model_add_line... INFO @ Mon, 29 Jun 2020 22:27:01: start X-correlation... INFO @ Mon, 29 Jun 2020 22:27:01: end of X-cor INFO @ Mon, 29 Jun 2020 22:27:01: #2 finished! INFO @ Mon, 29 Jun 2020 22:27:01: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 22:27:01: #2 alternative fragment length(s) may be 0 bps INFO @ Mon, 29 Jun 2020 22:27:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX042249/SRX042249.10_model.r WARNING @ Mon, 29 Jun 2020 22:27:01: #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, 29 Jun 2020 22:27:01: #2 You may need to consider one of the other alternative d(s): 0 WARNING @ Mon, 29 Jun 2020 22:27:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:27:01: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:27:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:27:02: 10000000 INFO @ Mon, 29 Jun 2020 22:27:07: 11000000 INFO @ Mon, 29 Jun 2020 22:27:13: 12000000 INFO @ Mon, 29 Jun 2020 22:27:18: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:27:23: 14000000 INFO @ Mon, 29 Jun 2020 22:27:29: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 22:27:29: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 22:27:29: #1 total tags in treatment: 14914558 INFO @ Mon, 29 Jun 2020 22:27:29: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:27:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:27:29: #1 tags after filtering in treatment: 14914558 INFO @ Mon, 29 Jun 2020 22:27:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:27:29: #1 finished! INFO @ Mon, 29 Jun 2020 22:27:29: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:27:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:27:30: #2 number of paired peaks: 3817 INFO @ Mon, 29 Jun 2020 22:27:30: start model_add_line... INFO @ Mon, 29 Jun 2020 22:27:30: start X-correlation... INFO @ Mon, 29 Jun 2020 22:27:30: end of X-cor INFO @ Mon, 29 Jun 2020 22:27:30: #2 finished! INFO @ Mon, 29 Jun 2020 22:27:30: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 22:27:30: #2 alternative fragment length(s) may be 0 bps INFO @ Mon, 29 Jun 2020 22:27:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX042249/SRX042249.20_model.r WARNING @ Mon, 29 Jun 2020 22:27:30: #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, 29 Jun 2020 22:27:30: #2 You may need to consider one of the other alternative d(s): 0 WARNING @ Mon, 29 Jun 2020 22:27:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:27:30: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:27:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at163/job_scripts/6527517: line 293: 78357 Terminated MACS $i /var/spool/uge/at163/job_scripts/6527517: line 293: 80548 Terminated MACS $i /var/spool/uge/at163/job_scripts/6527517: line 293: 83142 Terminated MACS $i ls: cannot access SRX042249.05.bed: No such file or directory mv: cannot stat ‘SRX042249.05.bed’: No such file or directory mv: cannot stat ‘SRX042249.05.bb’: No such file or directory ls: cannot access SRX042249.10.bed: No such file or directory mv: cannot stat ‘SRX042249.10.bed’: No such file or directory mv: cannot stat ‘SRX042249.10.bb’: No such file or directory ls: cannot access SRX042249.20.bed: No such file or directory mv: cannot stat ‘SRX042249.20.bed’: No such file or directory mv: cannot stat ‘SRX042249.20.bb’: No such file or directory