Job ID = 14160410 SRX = SRX8582559 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 29615542 spots for SRR12054120/SRR12054120.sra Written 29615542 spots for SRR12054120/SRR12054120.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160549 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:09 29615542 reads; of these: 29615542 (100.00%) were unpaired; of these: 510872 (1.73%) aligned 0 times 24140019 (81.51%) aligned exactly 1 time 4964651 (16.76%) aligned >1 times 98.27% overall alignment rate Time searching: 00:07:09 Overall time: 00:07:09 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 12 files... [bam_rmdupse_core] 6091469 / 29104670 = 0.2093 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 02:28:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8582559/SRX8582559.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8582559/SRX8582559.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8582559/SRX8582559.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8582559/SRX8582559.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, 09 Dec 2021 02:28:02: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:28:02: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:28:08: 1000000 INFO @ Thu, 09 Dec 2021 02:28:14: 2000000 INFO @ Thu, 09 Dec 2021 02:28:20: 3000000 INFO @ Thu, 09 Dec 2021 02:28:26: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 02:28:32: 5000000 INFO @ Thu, 09 Dec 2021 02:28:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8582559/SRX8582559.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8582559/SRX8582559.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8582559/SRX8582559.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8582559/SRX8582559.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, 09 Dec 2021 02:28:34: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:28:34: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:28:38: 6000000 INFO @ Thu, 09 Dec 2021 02:28:40: 1000000 INFO @ Thu, 09 Dec 2021 02:28:44: 7000000 INFO @ Thu, 09 Dec 2021 02:28:47: 2000000 INFO @ Thu, 09 Dec 2021 02:28:51: 8000000 INFO @ Thu, 09 Dec 2021 02:28:53: 3000000 INFO @ Thu, 09 Dec 2021 02:28:57: 9000000 INFO @ Thu, 09 Dec 2021 02:29:00: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 02:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8582559/SRX8582559.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8582559/SRX8582559.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8582559/SRX8582559.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8582559/SRX8582559.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, 09 Dec 2021 02:29:02: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:29:02: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:29:03: 10000000 INFO @ Thu, 09 Dec 2021 02:29:06: 5000000 INFO @ Thu, 09 Dec 2021 02:29:08: 1000000 INFO @ Thu, 09 Dec 2021 02:29:09: 11000000 INFO @ Thu, 09 Dec 2021 02:29:12: 6000000 INFO @ Thu, 09 Dec 2021 02:29:13: 2000000 INFO @ Thu, 09 Dec 2021 02:29:15: 12000000 INFO @ Thu, 09 Dec 2021 02:29:19: 7000000 INFO @ Thu, 09 Dec 2021 02:29:19: 3000000 INFO @ Thu, 09 Dec 2021 02:29:22: 13000000 INFO @ Thu, 09 Dec 2021 02:29:25: 8000000 INFO @ Thu, 09 Dec 2021 02:29:25: 4000000 INFO @ Thu, 09 Dec 2021 02:29:28: 14000000 INFO @ Thu, 09 Dec 2021 02:29:31: 9000000 INFO @ Thu, 09 Dec 2021 02:29:31: 5000000 INFO @ Thu, 09 Dec 2021 02:29:34: 15000000 INFO @ Thu, 09 Dec 2021 02:29:37: 6000000 INFO @ Thu, 09 Dec 2021 02:29:37: 10000000 INFO @ Thu, 09 Dec 2021 02:29:40: 16000000 INFO @ Thu, 09 Dec 2021 02:29:43: 7000000 INFO @ Thu, 09 Dec 2021 02:29:44: 11000000 INFO @ Thu, 09 Dec 2021 02:29:46: 17000000 INFO @ Thu, 09 Dec 2021 02:29:49: 8000000 INFO @ Thu, 09 Dec 2021 02:29:50: 12000000 INFO @ Thu, 09 Dec 2021 02:29:52: 18000000 INFO @ Thu, 09 Dec 2021 02:29:55: 9000000 INFO @ Thu, 09 Dec 2021 02:29:56: 13000000 INFO @ Thu, 09 Dec 2021 02:29:59: 19000000 INFO @ Thu, 09 Dec 2021 02:30:00: 10000000 INFO @ Thu, 09 Dec 2021 02:30:02: 14000000 INFO @ Thu, 09 Dec 2021 02:30:05: 20000000 INFO @ Thu, 09 Dec 2021 02:30:06: 11000000 INFO @ Thu, 09 Dec 2021 02:30:08: 15000000 INFO @ Thu, 09 Dec 2021 02:30:11: 21000000 INFO @ Thu, 09 Dec 2021 02:30:12: 12000000 INFO @ Thu, 09 Dec 2021 02:30:15: 16000000 INFO @ Thu, 09 Dec 2021 02:30:17: 22000000 INFO @ Thu, 09 Dec 2021 02:30:18: 13000000 INFO @ Thu, 09 Dec 2021 02:30:21: 17000000 INFO @ Thu, 09 Dec 2021 02:30:23: 23000000 INFO @ Thu, 09 Dec 2021 02:30:24: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 02:30:24: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 02:30:24: #1 total tags in treatment: 23013201 INFO @ Thu, 09 Dec 2021 02:30:24: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:30:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:30:24: 14000000 INFO @ Thu, 09 Dec 2021 02:30:24: #1 tags after filtering in treatment: 23013201 INFO @ Thu, 09 Dec 2021 02:30:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:30:24: #1 finished! INFO @ Thu, 09 Dec 2021 02:30:24: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:30:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:30:25: #2 number of paired peaks: 189 WARNING @ Thu, 09 Dec 2021 02:30:25: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Thu, 09 Dec 2021 02:30:25: start model_add_line... INFO @ Thu, 09 Dec 2021 02:30:26: start X-correlation... INFO @ Thu, 09 Dec 2021 02:30:26: end of X-cor INFO @ Thu, 09 Dec 2021 02:30:26: #2 finished! INFO @ Thu, 09 Dec 2021 02:30:26: #2 predicted fragment length is 0 bps INFO @ Thu, 09 Dec 2021 02:30:26: #2 alternative fragment length(s) may be 0,43,548 bps INFO @ Thu, 09 Dec 2021 02:30:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8582559/SRX8582559.05_model.r WARNING @ Thu, 09 Dec 2021 02:30:26: #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, 09 Dec 2021 02:30:26: #2 You may need to consider one of the other alternative d(s): 0,43,548 WARNING @ Thu, 09 Dec 2021 02:30:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:30:26: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:30:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:30:27: 18000000 INFO @ Thu, 09 Dec 2021 02:30:30: 15000000 INFO @ Thu, 09 Dec 2021 02:30:33: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:30:35: 16000000 INFO @ Thu, 09 Dec 2021 02:30:39: 20000000 INFO @ Thu, 09 Dec 2021 02:30:41: 17000000 INFO @ Thu, 09 Dec 2021 02:30:45: 21000000 INFO @ Thu, 09 Dec 2021 02:30:47: 18000000 INFO @ Thu, 09 Dec 2021 02:30:52: 22000000 INFO @ Thu, 09 Dec 2021 02:30:53: 19000000 INFO @ Thu, 09 Dec 2021 02:30:58: 23000000 INFO @ Thu, 09 Dec 2021 02:30:58: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 02:30:58: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 02:30:58: #1 total tags in treatment: 23013201 INFO @ Thu, 09 Dec 2021 02:30:58: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:30:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:30:58: #1 tags after filtering in treatment: 23013201 INFO @ Thu, 09 Dec 2021 02:30:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:30:58: #1 finished! INFO @ Thu, 09 Dec 2021 02:30:58: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:30:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:30:59: 20000000 INFO @ Thu, 09 Dec 2021 02:31:00: #2 number of paired peaks: 189 WARNING @ Thu, 09 Dec 2021 02:31:00: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Thu, 09 Dec 2021 02:31:00: start model_add_line... INFO @ Thu, 09 Dec 2021 02:31:00: start X-correlation... INFO @ Thu, 09 Dec 2021 02:31:00: end of X-cor INFO @ Thu, 09 Dec 2021 02:31:00: #2 finished! INFO @ Thu, 09 Dec 2021 02:31:00: #2 predicted fragment length is 0 bps INFO @ Thu, 09 Dec 2021 02:31:00: #2 alternative fragment length(s) may be 0,43,548 bps INFO @ Thu, 09 Dec 2021 02:31:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8582559/SRX8582559.10_model.r WARNING @ Thu, 09 Dec 2021 02:31:00: #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, 09 Dec 2021 02:31:00: #2 You may need to consider one of the other alternative d(s): 0,43,548 WARNING @ Thu, 09 Dec 2021 02:31:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:31:00: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:31:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:31:04: 21000000 INFO @ Thu, 09 Dec 2021 02:31:09: 22000000 INFO @ Thu, 09 Dec 2021 02:31:14: 23000000 INFO @ Thu, 09 Dec 2021 02:31:14: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 02:31:14: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 02:31:14: #1 total tags in treatment: 23013201 INFO @ Thu, 09 Dec 2021 02:31:14: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:31:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:31:14: #1 tags after filtering in treatment: 23013201 INFO @ Thu, 09 Dec 2021 02:31:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:31:14: #1 finished! INFO @ Thu, 09 Dec 2021 02:31:14: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:31:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:31:16: #2 number of paired peaks: 189 WARNING @ Thu, 09 Dec 2021 02:31:16: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Thu, 09 Dec 2021 02:31:16: start model_add_line... INFO @ Thu, 09 Dec 2021 02:31:16: start X-correlation... INFO @ Thu, 09 Dec 2021 02:31:16: end of X-cor INFO @ Thu, 09 Dec 2021 02:31:16: #2 finished! INFO @ Thu, 09 Dec 2021 02:31:16: #2 predicted fragment length is 0 bps INFO @ Thu, 09 Dec 2021 02:31:16: #2 alternative fragment length(s) may be 0,43,548 bps INFO @ Thu, 09 Dec 2021 02:31:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8582559/SRX8582559.20_model.r WARNING @ Thu, 09 Dec 2021 02:31:16: #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, 09 Dec 2021 02:31:16: #2 You may need to consider one of the other alternative d(s): 0,43,548 WARNING @ Thu, 09 Dec 2021 02:31:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:31:16: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:31:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at140/job_scripts/14160410: line 297: 2525 Terminated MACS $i /var/spool/uge/at140/job_scripts/14160410: line 297: 3564 Terminated MACS $i /var/spool/uge/at140/job_scripts/14160410: line 297: 3667 Terminated MACS $i ls: cannot access SRX8582559.05.bed: No such file or directory mv: cannot stat ‘SRX8582559.05.bed’: No such file or directory mv: cannot stat ‘SRX8582559.05.bb’: No such file or directory ls: cannot access SRX8582559.10.bed: No such file or directory mv: cannot stat ‘SRX8582559.10.bed’: No such file or directory mv: cannot stat ‘SRX8582559.10.bb’: No such file or directory ls: cannot access SRX8582559.20.bed: No such file or directory mv: cannot stat ‘SRX8582559.20.bed’: No such file or directory mv: cannot stat ‘SRX8582559.20.bb’: No such file or directory