Job ID = 10165671 SRX = SRX8331148 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 63128850 spots for SRR11778461/SRR11778461.sra Written 63128850 spots for SRR11778461/SRR11778461.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166083 ("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: 00:21:45 63128850 reads; of these: 63128850 (100.00%) were unpaired; of these: 798978 (1.27%) aligned 0 times 52255230 (82.78%) aligned exactly 1 time 10074642 (15.96%) aligned >1 times 98.73% overall alignment rate Time searching: 00:21:45 Overall time: 00:21:45 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 28 files... [bam_rmdupse_core] 51853501 / 62329872 = 0.8319 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 20:10:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.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 20:10:14: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:10:14: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:10:20: 1000000 INFO @ Thu, 08 Oct 2020 20:10:25: 2000000 INFO @ Thu, 08 Oct 2020 20:10:31: 3000000 INFO @ Thu, 08 Oct 2020 20:10:36: 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 @ Thu, 08 Oct 2020 20:10:42: 5000000 INFO @ Thu, 08 Oct 2020 20:10:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.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 20:10:44: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:10:44: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:10:48: 6000000 INFO @ Thu, 08 Oct 2020 20:10:50: 1000000 INFO @ Thu, 08 Oct 2020 20:10:53: 7000000 INFO @ Thu, 08 Oct 2020 20:10:57: 2000000 INFO @ Thu, 08 Oct 2020 20:10:59: 8000000 INFO @ Thu, 08 Oct 2020 20:11:03: 3000000 INFO @ Thu, 08 Oct 2020 20:11:06: 9000000 INFO @ Thu, 08 Oct 2020 20:11:10: 4000000 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 20:11:12: 10000000 INFO @ Thu, 08 Oct 2020 20:11:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.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 20:11:14: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:11:14: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:11:15: #1 tag size is determined as 65 bps INFO @ Thu, 08 Oct 2020 20:11:15: #1 tag size = 65 INFO @ Thu, 08 Oct 2020 20:11:15: #1 total tags in treatment: 10476371 INFO @ Thu, 08 Oct 2020 20:11:15: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:11:15: #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 20:11:16: #1 tags after filtering in treatment: 10476371 INFO @ Thu, 08 Oct 2020 20:11:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:11:16: #1 finished! INFO @ Thu, 08 Oct 2020 20:11:16: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:11:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:11:16: 5000000 INFO @ Thu, 08 Oct 2020 20:11:16: #2 number of paired peaks: 762 WARNING @ Thu, 08 Oct 2020 20:11:16: Fewer paired peaks (762) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 762 pairs to build model! INFO @ Thu, 08 Oct 2020 20:11:16: start model_add_line... INFO @ Thu, 08 Oct 2020 20:11:16: start X-correlation... INFO @ Thu, 08 Oct 2020 20:11:16: end of X-cor INFO @ Thu, 08 Oct 2020 20:11:16: #2 finished! INFO @ Thu, 08 Oct 2020 20:11:16: #2 predicted fragment length is 56 bps INFO @ Thu, 08 Oct 2020 20:11:16: #2 alternative fragment length(s) may be 3,56 bps INFO @ Thu, 08 Oct 2020 20:11:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.05_model.r WARNING @ Thu, 08 Oct 2020 20:11:16: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:11:16: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Thu, 08 Oct 2020 20:11:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:11:16: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:11:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:11:21: 1000000 INFO @ Thu, 08 Oct 2020 20:11:22: 6000000 INFO @ Thu, 08 Oct 2020 20:11:28: 7000000 INFO @ Thu, 08 Oct 2020 20:11:28: 2000000 INFO @ Thu, 08 Oct 2020 20:11:34: 8000000 INFO @ Thu, 08 Oct 2020 20:11:35: 3000000 INFO @ Thu, 08 Oct 2020 20:11:38: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:11:40: 9000000 INFO @ Thu, 08 Oct 2020 20:11:41: 4000000 INFO @ Thu, 08 Oct 2020 20:11:46: 5000000 INFO @ Thu, 08 Oct 2020 20:11:47: 10000000 INFO @ Thu, 08 Oct 2020 20:11:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:11:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:11:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.05_summits.bed INFO @ Thu, 08 Oct 2020 20:11:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2241 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:11:50: #1 tag size is determined as 65 bps INFO @ Thu, 08 Oct 2020 20:11:50: #1 tag size = 65 INFO @ Thu, 08 Oct 2020 20:11:50: #1 total tags in treatment: 10476371 INFO @ Thu, 08 Oct 2020 20:11:50: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:11:50: #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 20:11:50: #1 tags after filtering in treatment: 10476371 INFO @ Thu, 08 Oct 2020 20:11:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:11:50: #1 finished! INFO @ Thu, 08 Oct 2020 20:11:50: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:11:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:11:51: #2 number of paired peaks: 762 WARNING @ Thu, 08 Oct 2020 20:11:51: Fewer paired peaks (762) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 762 pairs to build model! INFO @ Thu, 08 Oct 2020 20:11:51: start model_add_line... INFO @ Thu, 08 Oct 2020 20:11:51: start X-correlation... INFO @ Thu, 08 Oct 2020 20:11:51: end of X-cor INFO @ Thu, 08 Oct 2020 20:11:51: #2 finished! INFO @ Thu, 08 Oct 2020 20:11:51: #2 predicted fragment length is 56 bps INFO @ Thu, 08 Oct 2020 20:11:51: #2 alternative fragment length(s) may be 3,56 bps INFO @ Thu, 08 Oct 2020 20:11:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.10_model.r WARNING @ Thu, 08 Oct 2020 20:11:51: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:11:51: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Thu, 08 Oct 2020 20:11:51: #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 20:11:51: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:11:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:11:52: 6000000 INFO @ Thu, 08 Oct 2020 20:11:58: 7000000 INFO @ Thu, 08 Oct 2020 20:12:03: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:12:09: 9000000 INFO @ Thu, 08 Oct 2020 20:12:11: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:12:14: 10000000 INFO @ Thu, 08 Oct 2020 20:12:17: #1 tag size is determined as 65 bps INFO @ Thu, 08 Oct 2020 20:12:17: #1 tag size = 65 INFO @ Thu, 08 Oct 2020 20:12:17: #1 total tags in treatment: 10476371 INFO @ Thu, 08 Oct 2020 20:12:17: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:12:17: #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 20:12:17: #1 tags after filtering in treatment: 10476371 INFO @ Thu, 08 Oct 2020 20:12:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:12:17: #1 finished! INFO @ Thu, 08 Oct 2020 20:12:17: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:12:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:12:18: #2 number of paired peaks: 762 WARNING @ Thu, 08 Oct 2020 20:12:18: Fewer paired peaks (762) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 762 pairs to build model! INFO @ Thu, 08 Oct 2020 20:12:18: start model_add_line... INFO @ Thu, 08 Oct 2020 20:12:18: start X-correlation... INFO @ Thu, 08 Oct 2020 20:12:18: end of X-cor INFO @ Thu, 08 Oct 2020 20:12:18: #2 finished! INFO @ Thu, 08 Oct 2020 20:12:18: #2 predicted fragment length is 56 bps INFO @ Thu, 08 Oct 2020 20:12:18: #2 alternative fragment length(s) may be 3,56 bps INFO @ Thu, 08 Oct 2020 20:12:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.20_model.r WARNING @ Thu, 08 Oct 2020 20:12:18: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:12:18: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Thu, 08 Oct 2020 20:12:18: #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 20:12:18: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:12:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:12:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:12:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:12:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.10_summits.bed INFO @ Thu, 08 Oct 2020 20:12:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (968 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:12:38: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:12:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:12:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:12:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331148/SRX8331148.20_summits.bed INFO @ Thu, 08 Oct 2020 20:12:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (373 records, 4 fields): 22 millis CompletedMACS2peakCalling