Job ID = 6527420 SRX = SRX5709766 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:35:22 prefetch.2.10.7: 1) Downloading 'SRR8928716'... 2020-06-29T12:35:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:37:32 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:37:32 prefetch.2.10.7: 1) 'SRR8928716' was downloaded successfully 2020-06-29T12:37:32 prefetch.2.10.7: 'SRR8928716' has 0 unresolved dependencies Read 33385313 spots for SRR8928716/SRR8928716.sra Written 33385313 spots for SRR8928716/SRR8928716.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: 00:07:22 33385313 reads; of these: 33385313 (100.00%) were unpaired; of these: 1177973 (3.53%) aligned 0 times 26911327 (80.61%) aligned exactly 1 time 5296013 (15.86%) aligned >1 times 96.47% overall alignment rate Time searching: 00:07:22 Overall time: 00:07:22 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 16 files... [bam_rmdupse_core] 7457098 / 32207340 = 0.2315 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 22:00:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709766/SRX5709766.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709766/SRX5709766.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709766/SRX5709766.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709766/SRX5709766.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, 29 Jun 2020 22:00:26: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:00:26: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:00:31: 1000000 INFO @ Mon, 29 Jun 2020 22:00:36: 2000000 INFO @ Mon, 29 Jun 2020 22:00:41: 3000000 INFO @ Mon, 29 Jun 2020 22:00:46: 4000000 INFO @ Mon, 29 Jun 2020 22:00:51: 5000000 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 22:00:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709766/SRX5709766.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709766/SRX5709766.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709766/SRX5709766.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709766/SRX5709766.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, 29 Jun 2020 22:00:56: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:00:56: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:00:56: 6000000 INFO @ Mon, 29 Jun 2020 22:01:01: 1000000 INFO @ Mon, 29 Jun 2020 22:01:02: 7000000 INFO @ Mon, 29 Jun 2020 22:01:07: 2000000 INFO @ Mon, 29 Jun 2020 22:01:07: 8000000 INFO @ Mon, 29 Jun 2020 22:01:12: 3000000 INFO @ Mon, 29 Jun 2020 22:01:13: 9000000 INFO @ Mon, 29 Jun 2020 22:01:18: 4000000 INFO @ Mon, 29 Jun 2020 22:01:19: 10000000 INFO @ Mon, 29 Jun 2020 22:01:23: 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 22:01:24: 11000000 INFO @ Mon, 29 Jun 2020 22:01:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709766/SRX5709766.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709766/SRX5709766.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709766/SRX5709766.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709766/SRX5709766.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, 29 Jun 2020 22:01:26: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:01:26: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:01:29: 6000000 INFO @ Mon, 29 Jun 2020 22:01:30: 12000000 INFO @ Mon, 29 Jun 2020 22:01:32: 1000000 INFO @ Mon, 29 Jun 2020 22:01:35: 7000000 INFO @ Mon, 29 Jun 2020 22:01:36: 13000000 INFO @ Mon, 29 Jun 2020 22:01:39: 2000000 INFO @ Mon, 29 Jun 2020 22:01:40: 8000000 INFO @ Mon, 29 Jun 2020 22:01:42: 14000000 INFO @ Mon, 29 Jun 2020 22:01:46: 3000000 INFO @ Mon, 29 Jun 2020 22:01:46: 9000000 INFO @ Mon, 29 Jun 2020 22:01:47: 15000000 INFO @ Mon, 29 Jun 2020 22:01:52: 10000000 INFO @ Mon, 29 Jun 2020 22:01:52: 4000000 INFO @ Mon, 29 Jun 2020 22:01:53: 16000000 INFO @ Mon, 29 Jun 2020 22:01:58: 11000000 INFO @ Mon, 29 Jun 2020 22:01:59: 5000000 INFO @ Mon, 29 Jun 2020 22:01:59: 17000000 INFO @ Mon, 29 Jun 2020 22:02:04: 12000000 INFO @ Mon, 29 Jun 2020 22:02:05: 18000000 INFO @ Mon, 29 Jun 2020 22:02:06: 6000000 INFO @ Mon, 29 Jun 2020 22:02:09: 13000000 INFO @ Mon, 29 Jun 2020 22:02:11: 19000000 INFO @ Mon, 29 Jun 2020 22:02:12: 7000000 INFO @ Mon, 29 Jun 2020 22:02:15: 14000000 INFO @ Mon, 29 Jun 2020 22:02:16: 20000000 INFO @ Mon, 29 Jun 2020 22:02:19: 8000000 INFO @ Mon, 29 Jun 2020 22:02:21: 15000000 INFO @ Mon, 29 Jun 2020 22:02:22: 21000000 INFO @ Mon, 29 Jun 2020 22:02:25: 9000000 INFO @ Mon, 29 Jun 2020 22:02:27: 16000000 INFO @ Mon, 29 Jun 2020 22:02:28: 22000000 INFO @ Mon, 29 Jun 2020 22:02:32: 10000000 INFO @ Mon, 29 Jun 2020 22:02:32: 17000000 INFO @ Mon, 29 Jun 2020 22:02:34: 23000000 INFO @ Mon, 29 Jun 2020 22:02:38: 18000000 INFO @ Mon, 29 Jun 2020 22:02:39: 11000000 INFO @ Mon, 29 Jun 2020 22:02:39: 24000000 INFO @ Mon, 29 Jun 2020 22:02:44: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 22:02:44: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 22:02:44: #1 total tags in treatment: 24750242 INFO @ Mon, 29 Jun 2020 22:02:44: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:02:44: #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 22:02:44: 19000000 INFO @ Mon, 29 Jun 2020 22:02:44: #1 tags after filtering in treatment: 24750242 INFO @ Mon, 29 Jun 2020 22:02:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:02:44: #1 finished! INFO @ Mon, 29 Jun 2020 22:02:44: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:02:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:02:45: 12000000 INFO @ Mon, 29 Jun 2020 22:02:46: #2 number of paired peaks: 161 WARNING @ Mon, 29 Jun 2020 22:02:46: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Mon, 29 Jun 2020 22:02:46: start model_add_line... INFO @ Mon, 29 Jun 2020 22:02:46: start X-correlation... INFO @ Mon, 29 Jun 2020 22:02:46: end of X-cor INFO @ Mon, 29 Jun 2020 22:02:46: #2 finished! INFO @ Mon, 29 Jun 2020 22:02:46: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 22:02:46: #2 alternative fragment length(s) may be 0,20,546,585,595 bps INFO @ Mon, 29 Jun 2020 22:02:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709766/SRX5709766.05_model.r WARNING @ Mon, 29 Jun 2020 22:02:46: #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 22:02:46: #2 You may need to consider one of the other alternative d(s): 0,20,546,585,595 WARNING @ Mon, 29 Jun 2020 22:02:46: #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 22:02:46: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:02:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:02:50: 20000000 INFO @ Mon, 29 Jun 2020 22:02:52: 13000000 INFO @ Mon, 29 Jun 2020 22:02:55: 21000000 INFO @ Mon, 29 Jun 2020 22:02:58: 14000000 INFO @ Mon, 29 Jun 2020 22:03:01: 22000000 INFO @ Mon, 29 Jun 2020 22:03:05: 15000000 INFO @ Mon, 29 Jun 2020 22:03:07: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:03:11: 16000000 INFO @ Mon, 29 Jun 2020 22:03:12: 24000000 INFO @ Mon, 29 Jun 2020 22:03:17: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 22:03:17: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 22:03:17: #1 total tags in treatment: 24750242 INFO @ Mon, 29 Jun 2020 22:03:17: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:03:17: #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 22:03:17: #1 tags after filtering in treatment: 24750242 INFO @ Mon, 29 Jun 2020 22:03:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:03:17: #1 finished! INFO @ Mon, 29 Jun 2020 22:03:17: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:03:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:03:18: 17000000 INFO @ Mon, 29 Jun 2020 22:03:19: #2 number of paired peaks: 161 WARNING @ Mon, 29 Jun 2020 22:03:19: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Mon, 29 Jun 2020 22:03:19: start model_add_line... INFO @ Mon, 29 Jun 2020 22:03:19: start X-correlation... INFO @ Mon, 29 Jun 2020 22:03:19: end of X-cor INFO @ Mon, 29 Jun 2020 22:03:19: #2 finished! INFO @ Mon, 29 Jun 2020 22:03:19: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 22:03:19: #2 alternative fragment length(s) may be 0,20,546,585,595 bps INFO @ Mon, 29 Jun 2020 22:03:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709766/SRX5709766.10_model.r WARNING @ Mon, 29 Jun 2020 22:03:19: #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 22:03:19: #2 You may need to consider one of the other alternative d(s): 0,20,546,585,595 WARNING @ Mon, 29 Jun 2020 22:03:19: #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 22:03:19: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:03:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:03:24: 18000000 INFO @ Mon, 29 Jun 2020 22:03:30: 19000000 INFO @ Mon, 29 Jun 2020 22:03:36: 20000000 INFO @ Mon, 29 Jun 2020 22:03:42: 21000000 INFO @ Mon, 29 Jun 2020 22:03:48: 22000000 INFO @ Mon, 29 Jun 2020 22:03:55: 23000000 INFO @ Mon, 29 Jun 2020 22:04:01: 24000000 BigWig に変換しました。 /var/spool/uge/at152/job_scripts/6527420: line 293: 56590 Terminated MACS $i /var/spool/uge/at152/job_scripts/6527420: line 293: 59390 Terminated MACS $i /var/spool/uge/at152/job_scripts/6527420: line 293: 62228 Terminated MACS $i ls: cannot access SRX5709766.05.bed: No such file or directory mv: cannot stat ‘SRX5709766.05.bed’: No such file or directory mv: cannot stat ‘SRX5709766.05.bb’: No such file or directory ls: cannot access SRX5709766.10.bed: No such file or directory mv: cannot stat ‘SRX5709766.10.bed’: No such file or directory mv: cannot stat ‘SRX5709766.10.bb’: No such file or directory ls: cannot access SRX5709766.20.bed: No such file or directory mv: cannot stat ‘SRX5709766.20.bed’: No such file or directory mv: cannot stat ‘SRX5709766.20.bb’: No such file or directory