Job ID = 14160714 SRX = SRX10569202 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2021-12-08T18:52:13 prefetch.2.10.7: 1) Downloading 'SRR14202290'... 2021-12-08T18:52:13 prefetch.2.10.7: Downloading via HTTPS... 2021-12-08T18:55:28 prefetch.2.10.7: HTTPS download succeed 2021-12-08T18:55:28 prefetch.2.10.7: 1) 'SRR14202290' was downloaded successfully 2021-12-08T18:55:28 prefetch.2.10.7: 'SRR14202290' has 0 unresolved dependencies Read 22152982 spots for SRR14202290/SRR14202290.sra Written 22152982 spots for SRR14202290/SRR14202290.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160862 ("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: 00:08:50 22152982 reads; of these: 22152982 (100.00%) were unpaired; of these: 8319218 (37.55%) aligned 0 times 9816022 (44.31%) aligned exactly 1 time 4017742 (18.14%) aligned >1 times 62.45% overall alignment rate Time searching: 00:08:50 Overall time: 00:08:50 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] 3020176 / 13833764 = 0.2183 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 04:09:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.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 04:09:56: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:09:56: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:10:02: 1000000 INFO @ Thu, 09 Dec 2021 04:10:07: 2000000 INFO @ Thu, 09 Dec 2021 04:10:12: 3000000 INFO @ Thu, 09 Dec 2021 04:10:17: 4000000 INFO @ Thu, 09 Dec 2021 04:10:22: 5000000 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 04:10:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.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 04:10:26: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:10:26: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:10:27: 6000000 INFO @ Thu, 09 Dec 2021 04:10:32: 1000000 INFO @ Thu, 09 Dec 2021 04:10:32: 7000000 INFO @ Thu, 09 Dec 2021 04:10:37: 2000000 INFO @ Thu, 09 Dec 2021 04:10:38: 8000000 INFO @ Thu, 09 Dec 2021 04:10:42: 3000000 INFO @ Thu, 09 Dec 2021 04:10:43: 9000000 INFO @ Thu, 09 Dec 2021 04:10:47: 4000000 INFO @ Thu, 09 Dec 2021 04:10:48: 10000000 INFO @ Thu, 09 Dec 2021 04:10:52: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:10:52: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:10:52: #1 total tags in treatment: 10813588 INFO @ Thu, 09 Dec 2021 04:10:52: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:10:52: #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 04:10:52: #1 tags after filtering in treatment: 10813588 INFO @ Thu, 09 Dec 2021 04:10:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:10:52: #1 finished! INFO @ Thu, 09 Dec 2021 04:10:52: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:10:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:10:53: 5000000 INFO @ Thu, 09 Dec 2021 04:10:53: #2 number of paired peaks: 382 WARNING @ Thu, 09 Dec 2021 04:10:53: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Thu, 09 Dec 2021 04:10:53: start model_add_line... INFO @ Thu, 09 Dec 2021 04:10:53: start X-correlation... INFO @ Thu, 09 Dec 2021 04:10:53: end of X-cor INFO @ Thu, 09 Dec 2021 04:10:53: #2 finished! INFO @ Thu, 09 Dec 2021 04:10:53: #2 predicted fragment length is 52 bps INFO @ Thu, 09 Dec 2021 04:10:53: #2 alternative fragment length(s) may be 3,52 bps INFO @ Thu, 09 Dec 2021 04:10:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.05_model.r WARNING @ Thu, 09 Dec 2021 04:10:53: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:10:53: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Thu, 09 Dec 2021 04:10:53: #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 04:10:53: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:10:53: #3 Pre-compute pvalue-qvalue table... 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 04:10:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.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 04:10:56: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:10:56: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:10:58: 6000000 INFO @ Thu, 09 Dec 2021 04:11:02: 1000000 INFO @ Thu, 09 Dec 2021 04:11:03: 7000000 INFO @ Thu, 09 Dec 2021 04:11:07: 2000000 INFO @ Thu, 09 Dec 2021 04:11:08: 8000000 INFO @ Thu, 09 Dec 2021 04:11:12: 3000000 INFO @ Thu, 09 Dec 2021 04:11:13: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:11:13: 9000000 INFO @ Thu, 09 Dec 2021 04:11:17: 4000000 INFO @ Thu, 09 Dec 2021 04:11:19: 10000000 INFO @ Thu, 09 Dec 2021 04:11:23: 5000000 INFO @ Thu, 09 Dec 2021 04:11:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:11:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:11:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.05_summits.bed INFO @ Thu, 09 Dec 2021 04:11:23: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (683 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:11:23: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:11:23: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:11:23: #1 total tags in treatment: 10813588 INFO @ Thu, 09 Dec 2021 04:11:23: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:11:23: #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 04:11:23: #1 tags after filtering in treatment: 10813588 INFO @ Thu, 09 Dec 2021 04:11:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:11:23: #1 finished! INFO @ Thu, 09 Dec 2021 04:11:23: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:11:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:11:24: #2 number of paired peaks: 382 WARNING @ Thu, 09 Dec 2021 04:11:24: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Thu, 09 Dec 2021 04:11:24: start model_add_line... INFO @ Thu, 09 Dec 2021 04:11:24: start X-correlation... INFO @ Thu, 09 Dec 2021 04:11:24: end of X-cor INFO @ Thu, 09 Dec 2021 04:11:24: #2 finished! INFO @ Thu, 09 Dec 2021 04:11:24: #2 predicted fragment length is 52 bps INFO @ Thu, 09 Dec 2021 04:11:24: #2 alternative fragment length(s) may be 3,52 bps INFO @ Thu, 09 Dec 2021 04:11:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.10_model.r WARNING @ Thu, 09 Dec 2021 04:11:24: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:11:24: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Thu, 09 Dec 2021 04:11:24: #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 04:11:24: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:11:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:11:28: 6000000 INFO @ Thu, 09 Dec 2021 04:11:33: 7000000 INFO @ Thu, 09 Dec 2021 04:11:38: 8000000 INFO @ Thu, 09 Dec 2021 04:11:43: 9000000 INFO @ Thu, 09 Dec 2021 04:11:44: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:11:48: 10000000 INFO @ Thu, 09 Dec 2021 04:11:53: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:11:53: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:11:53: #1 total tags in treatment: 10813588 INFO @ Thu, 09 Dec 2021 04:11:53: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:11:53: #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 04:11:53: #1 tags after filtering in treatment: 10813588 INFO @ Thu, 09 Dec 2021 04:11:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:11:53: #1 finished! INFO @ Thu, 09 Dec 2021 04:11:53: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:11:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:11:54: #2 number of paired peaks: 382 WARNING @ Thu, 09 Dec 2021 04:11:54: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Thu, 09 Dec 2021 04:11:54: start model_add_line... INFO @ Thu, 09 Dec 2021 04:11:54: start X-correlation... INFO @ Thu, 09 Dec 2021 04:11:54: end of X-cor INFO @ Thu, 09 Dec 2021 04:11:54: #2 finished! INFO @ Thu, 09 Dec 2021 04:11:54: #2 predicted fragment length is 52 bps INFO @ Thu, 09 Dec 2021 04:11:54: #2 alternative fragment length(s) may be 3,52 bps INFO @ Thu, 09 Dec 2021 04:11:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.20_model.r WARNING @ Thu, 09 Dec 2021 04:11:54: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:11:54: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Thu, 09 Dec 2021 04:11:54: #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 04:11:54: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:11:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:11:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:11:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:11:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.10_summits.bed INFO @ Thu, 09 Dec 2021 04:11:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (447 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:12:14: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:12:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:12:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:12:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569202/SRX10569202.20_summits.bed INFO @ Thu, 09 Dec 2021 04:12:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (203 records, 4 fields): 1 millis CompletedMACS2peakCalling