Job ID = 10166121 SRX = SRX9120618 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:07:08 33805134 reads; of these: 33805134 (100.00%) were unpaired; of these: 848157 (2.51%) aligned 0 times 27553351 (81.51%) aligned exactly 1 time 5403626 (15.98%) aligned >1 times 97.49% overall alignment rate Time searching: 00:07:08 Overall time: 00:07:08 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] 5894399 / 32956977 = 0.1789 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 @ Thu, 08 Oct 2020 20:45:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120618/SRX9120618.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120618/SRX9120618.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120618/SRX9120618.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120618/SRX9120618.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 @ Thu, 08 Oct 2020 20:45:02: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:45:02: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:45:06: 1000000 INFO @ Thu, 08 Oct 2020 20:45:11: 2000000 INFO @ Thu, 08 Oct 2020 20:45:15: 3000000 INFO @ Thu, 08 Oct 2020 20:45:20: 4000000 INFO @ Thu, 08 Oct 2020 20:45:24: 5000000 INFO @ Thu, 08 Oct 2020 20:45:28: 6000000 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 @ Thu, 08 Oct 2020 20:45:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120618/SRX9120618.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120618/SRX9120618.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120618/SRX9120618.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120618/SRX9120618.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 @ Thu, 08 Oct 2020 20:45:32: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:45:32: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:45:33: 7000000 INFO @ Thu, 08 Oct 2020 20:45:36: 1000000 INFO @ Thu, 08 Oct 2020 20:45:37: 8000000 INFO @ Thu, 08 Oct 2020 20:45:41: 2000000 INFO @ Thu, 08 Oct 2020 20:45:42: 9000000 INFO @ Thu, 08 Oct 2020 20:45:45: 3000000 INFO @ Thu, 08 Oct 2020 20:45:47: 10000000 INFO @ Thu, 08 Oct 2020 20:45:50: 4000000 INFO @ Thu, 08 Oct 2020 20:45:51: 11000000 INFO @ Thu, 08 Oct 2020 20:45:54: 5000000 INFO @ Thu, 08 Oct 2020 20:45:56: 12000000 INFO @ Thu, 08 Oct 2020 20:45:59: 6000000 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 @ Thu, 08 Oct 2020 20:46:00: 13000000 INFO @ Thu, 08 Oct 2020 20:46:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120618/SRX9120618.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120618/SRX9120618.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120618/SRX9120618.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120618/SRX9120618.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 @ Thu, 08 Oct 2020 20:46:02: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:46:02: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:46:04: 7000000 INFO @ Thu, 08 Oct 2020 20:46:05: 14000000 INFO @ Thu, 08 Oct 2020 20:46:06: 1000000 INFO @ Thu, 08 Oct 2020 20:46:08: 8000000 INFO @ Thu, 08 Oct 2020 20:46:10: 15000000 INFO @ Thu, 08 Oct 2020 20:46:11: 2000000 INFO @ Thu, 08 Oct 2020 20:46:13: 9000000 INFO @ Thu, 08 Oct 2020 20:46:14: 16000000 INFO @ Thu, 08 Oct 2020 20:46:16: 3000000 INFO @ Thu, 08 Oct 2020 20:46:18: 10000000 INFO @ Thu, 08 Oct 2020 20:46:19: 17000000 INFO @ Thu, 08 Oct 2020 20:46:20: 4000000 INFO @ Thu, 08 Oct 2020 20:46:22: 11000000 INFO @ Thu, 08 Oct 2020 20:46:24: 18000000 INFO @ Thu, 08 Oct 2020 20:46:25: 5000000 INFO @ Thu, 08 Oct 2020 20:46:27: 12000000 INFO @ Thu, 08 Oct 2020 20:46:28: 19000000 INFO @ Thu, 08 Oct 2020 20:46:30: 6000000 INFO @ Thu, 08 Oct 2020 20:46:32: 13000000 INFO @ Thu, 08 Oct 2020 20:46:33: 20000000 INFO @ Thu, 08 Oct 2020 20:46:34: 7000000 INFO @ Thu, 08 Oct 2020 20:46:36: 14000000 INFO @ Thu, 08 Oct 2020 20:46:37: 21000000 INFO @ Thu, 08 Oct 2020 20:46:39: 8000000 INFO @ Thu, 08 Oct 2020 20:46:41: 15000000 INFO @ Thu, 08 Oct 2020 20:46:42: 22000000 INFO @ Thu, 08 Oct 2020 20:46:43: 9000000 INFO @ Thu, 08 Oct 2020 20:46:45: 16000000 INFO @ Thu, 08 Oct 2020 20:46:47: 23000000 INFO @ Thu, 08 Oct 2020 20:46:48: 10000000 INFO @ Thu, 08 Oct 2020 20:46:50: 17000000 INFO @ Thu, 08 Oct 2020 20:46:51: 24000000 INFO @ Thu, 08 Oct 2020 20:46:53: 11000000 INFO @ Thu, 08 Oct 2020 20:46:55: 18000000 INFO @ Thu, 08 Oct 2020 20:46:56: 25000000 INFO @ Thu, 08 Oct 2020 20:46:57: 12000000 INFO @ Thu, 08 Oct 2020 20:46:59: 19000000 INFO @ Thu, 08 Oct 2020 20:47:01: 26000000 INFO @ Thu, 08 Oct 2020 20:47:02: 13000000 INFO @ Thu, 08 Oct 2020 20:47:04: 20000000 INFO @ Thu, 08 Oct 2020 20:47:05: 27000000 INFO @ Thu, 08 Oct 2020 20:47:06: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:47:06: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:47:06: #1 total tags in treatment: 27062578 INFO @ Thu, 08 Oct 2020 20:47:06: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:47:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:47:06: #1 tags after filtering in treatment: 27062578 INFO @ Thu, 08 Oct 2020 20:47:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:47:06: #1 finished! INFO @ Thu, 08 Oct 2020 20:47:06: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:47:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:47:07: 14000000 INFO @ Thu, 08 Oct 2020 20:47:08: #2 number of paired peaks: 101 WARNING @ Thu, 08 Oct 2020 20:47:08: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Thu, 08 Oct 2020 20:47:08: start model_add_line... INFO @ Thu, 08 Oct 2020 20:47:08: start X-correlation... INFO @ Thu, 08 Oct 2020 20:47:08: end of X-cor INFO @ Thu, 08 Oct 2020 20:47:08: #2 finished! INFO @ Thu, 08 Oct 2020 20:47:08: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 20:47:08: #2 alternative fragment length(s) may be 0,47,175,191,483,496,518,562,587 bps INFO @ Thu, 08 Oct 2020 20:47:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120618/SRX9120618.05_model.r WARNING @ Thu, 08 Oct 2020 20:47:08: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:47:08: #2 You may need to consider one of the other alternative d(s): 0,47,175,191,483,496,518,562,587 WARNING @ Thu, 08 Oct 2020 20:47:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:47:08: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:47:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:47:09: 21000000 INFO @ Thu, 08 Oct 2020 20:47:11: 15000000 INFO @ Thu, 08 Oct 2020 20:47:13: 22000000 INFO @ Thu, 08 Oct 2020 20:47:16: 16000000 INFO @ Thu, 08 Oct 2020 20:47:18: 23000000 INFO @ Thu, 08 Oct 2020 20:47:20: 17000000 INFO @ Thu, 08 Oct 2020 20:47:23: 24000000 INFO @ Thu, 08 Oct 2020 20:47:25: 18000000 INFO @ Thu, 08 Oct 2020 20:47:27: 25000000 INFO @ Thu, 08 Oct 2020 20:47:29: 19000000 INFO @ Thu, 08 Oct 2020 20:47:32: 26000000 INFO @ Thu, 08 Oct 2020 20:47:34: 20000000 INFO @ Thu, 08 Oct 2020 20:47:36: 27000000 INFO @ Thu, 08 Oct 2020 20:47:37: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:47:37: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:47:37: #1 total tags in treatment: 27062578 INFO @ Thu, 08 Oct 2020 20:47:37: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:47:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:47:37: #1 tags after filtering in treatment: 27062578 INFO @ Thu, 08 Oct 2020 20:47:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:47:37: #1 finished! INFO @ Thu, 08 Oct 2020 20:47:37: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:47:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:47:38: 21000000 INFO @ Thu, 08 Oct 2020 20:47:39: #2 number of paired peaks: 101 WARNING @ Thu, 08 Oct 2020 20:47:39: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Thu, 08 Oct 2020 20:47:39: start model_add_line... INFO @ Thu, 08 Oct 2020 20:47:39: start X-correlation... INFO @ Thu, 08 Oct 2020 20:47:39: end of X-cor INFO @ Thu, 08 Oct 2020 20:47:39: #2 finished! INFO @ Thu, 08 Oct 2020 20:47:39: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 20:47:39: #2 alternative fragment length(s) may be 0,47,175,191,483,496,518,562,587 bps INFO @ Thu, 08 Oct 2020 20:47:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120618/SRX9120618.10_model.r WARNING @ Thu, 08 Oct 2020 20:47:39: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:47:39: #2 You may need to consider one of the other alternative d(s): 0,47,175,191,483,496,518,562,587 WARNING @ Thu, 08 Oct 2020 20:47:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:47:39: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:47:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:47:43: 22000000 INFO @ Thu, 08 Oct 2020 20:47:48: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:47:52: 24000000 INFO @ Thu, 08 Oct 2020 20:47:57: 25000000 INFO @ Thu, 08 Oct 2020 20:48:01: 26000000 INFO @ Thu, 08 Oct 2020 20:48:06: 27000000 INFO @ Thu, 08 Oct 2020 20:48:06: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:48:06: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:48:06: #1 total tags in treatment: 27062578 INFO @ Thu, 08 Oct 2020 20:48:06: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:48:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:48:07: #1 tags after filtering in treatment: 27062578 INFO @ Thu, 08 Oct 2020 20:48:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:48:07: #1 finished! INFO @ Thu, 08 Oct 2020 20:48:07: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:48:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:48:08: #2 number of paired peaks: 101 WARNING @ Thu, 08 Oct 2020 20:48:08: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Thu, 08 Oct 2020 20:48:08: start model_add_line... INFO @ Thu, 08 Oct 2020 20:48:09: start X-correlation... INFO @ Thu, 08 Oct 2020 20:48:09: end of X-cor INFO @ Thu, 08 Oct 2020 20:48:09: #2 finished! INFO @ Thu, 08 Oct 2020 20:48:09: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 20:48:09: #2 alternative fragment length(s) may be 0,47,175,191,483,496,518,562,587 bps INFO @ Thu, 08 Oct 2020 20:48:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120618/SRX9120618.20_model.r WARNING @ Thu, 08 Oct 2020 20:48:09: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:48:09: #2 You may need to consider one of the other alternative d(s): 0,47,175,191,483,496,518,562,587 WARNING @ Thu, 08 Oct 2020 20:48:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:48:09: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:48:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at157/job_scripts/10166121: line 297: 85394 Terminated MACS $i /var/spool/uge/at157/job_scripts/10166121: line 297: 88828 Terminated MACS $i /var/spool/uge/at157/job_scripts/10166121: line 297: 100386 Terminated MACS $i ls: cannot access SRX9120618.05.bed: No such file or directory mv: cannot stat ‘SRX9120618.05.bed’: No such file or directory mv: cannot stat ‘SRX9120618.05.bb’: No such file or directory ls: cannot access SRX9120618.10.bed: No such file or directory mv: cannot stat ‘SRX9120618.10.bed’: No such file or directory mv: cannot stat ‘SRX9120618.10.bb’: No such file or directory ls: cannot access SRX9120618.20.bed: No such file or directory mv: cannot stat ‘SRX9120618.20.bed’: No such file or directory mv: cannot stat ‘SRX9120618.20.bb’: No such file or directory