Job ID = 6626359 SRX = SRX7262199 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6646167 spots for SRR10581822/SRR10581822.sra Written 6646167 spots for SRR10581822/SRR10581822.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626417 ("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: 00:01:41 6646167 reads; of these: 6646167 (100.00%) were unpaired; of these: 207670 (3.12%) aligned 0 times 4961934 (74.66%) aligned exactly 1 time 1476563 (22.22%) aligned >1 times 96.88% overall alignment rate Time searching: 00:01:41 Overall time: 00:01:41 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_rmdupse_core] 596276 / 6438497 = 0.0926 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 @ Tue, 14 Jul 2020 06:59:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.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 @ Tue, 14 Jul 2020 06:59:32: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:59:32: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 06:59:37: 1000000 INFO @ Tue, 14 Jul 2020 06:59:42: 2000000 INFO @ Tue, 14 Jul 2020 06:59:47: 3000000 INFO @ Tue, 14 Jul 2020 06:59:52: 4000000 INFO @ Tue, 14 Jul 2020 06:59:57: 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 @ Tue, 14 Jul 2020 07:00:01: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:00:01: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:00:01: #1 total tags in treatment: 5842221 INFO @ Tue, 14 Jul 2020 07:00:01: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:00:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:00:01: #1 tags after filtering in treatment: 5842221 INFO @ Tue, 14 Jul 2020 07:00:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:00:01: #1 finished! INFO @ Tue, 14 Jul 2020 07:00:01: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:00:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:00:02: #2 number of paired peaks: 509 WARNING @ Tue, 14 Jul 2020 07:00:02: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 14 Jul 2020 07:00:02: start model_add_line... INFO @ Tue, 14 Jul 2020 07:00:02: start X-correlation... INFO @ Tue, 14 Jul 2020 07:00:02: end of X-cor INFO @ Tue, 14 Jul 2020 07:00:02: #2 finished! INFO @ Tue, 14 Jul 2020 07:00:02: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 07:00:02: #2 alternative fragment length(s) may be 4,46 bps INFO @ Tue, 14 Jul 2020 07:00:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.05_model.r WARNING @ Tue, 14 Jul 2020 07:00:02: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:00:02: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Tue, 14 Jul 2020 07:00:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:00:02: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:00:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:00:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.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 @ Tue, 14 Jul 2020 07:00:02: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:00:02: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:00:07: 1000000 INFO @ Tue, 14 Jul 2020 07:00:12: 2000000 INFO @ Tue, 14 Jul 2020 07:00:14: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:00:17: 3000000 INFO @ Tue, 14 Jul 2020 07:00:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:00:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:00:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.05_summits.bed INFO @ Tue, 14 Jul 2020 07:00:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (612 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:00:21: 4000000 INFO @ Tue, 14 Jul 2020 07:00:26: 5000000 INFO @ Tue, 14 Jul 2020 07:00:30: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:00:30: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:00:30: #1 total tags in treatment: 5842221 INFO @ Tue, 14 Jul 2020 07:00:30: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:00:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:00:30: #1 tags after filtering in treatment: 5842221 INFO @ Tue, 14 Jul 2020 07:00:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:00:30: #1 finished! INFO @ Tue, 14 Jul 2020 07:00:30: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:00:30: #2 looking for paired plus/minus strand peaks... 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 @ Tue, 14 Jul 2020 07:00:31: #2 number of paired peaks: 509 WARNING @ Tue, 14 Jul 2020 07:00:31: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 14 Jul 2020 07:00:31: start model_add_line... INFO @ Tue, 14 Jul 2020 07:00:31: start X-correlation... INFO @ Tue, 14 Jul 2020 07:00:31: end of X-cor INFO @ Tue, 14 Jul 2020 07:00:31: #2 finished! INFO @ Tue, 14 Jul 2020 07:00:31: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 07:00:31: #2 alternative fragment length(s) may be 4,46 bps INFO @ Tue, 14 Jul 2020 07:00:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.10_model.r WARNING @ Tue, 14 Jul 2020 07:00:31: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:00:31: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Tue, 14 Jul 2020 07:00:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:00:31: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:00:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:00:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.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 @ Tue, 14 Jul 2020 07:00:32: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:00:32: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:00:37: 1000000 INFO @ Tue, 14 Jul 2020 07:00:42: 2000000 INFO @ Tue, 14 Jul 2020 07:00:43: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:00:47: 3000000 INFO @ Tue, 14 Jul 2020 07:00:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:00:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:00:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.10_summits.bed INFO @ Tue, 14 Jul 2020 07:00:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (391 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:00:51: 4000000 INFO @ Tue, 14 Jul 2020 07:00:56: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:01:00: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:01:00: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:01:00: #1 total tags in treatment: 5842221 INFO @ Tue, 14 Jul 2020 07:01:00: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:01:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:01:00: #1 tags after filtering in treatment: 5842221 INFO @ Tue, 14 Jul 2020 07:01:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:01:00: #1 finished! INFO @ Tue, 14 Jul 2020 07:01:00: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:01:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:01:01: #2 number of paired peaks: 509 WARNING @ Tue, 14 Jul 2020 07:01:01: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 14 Jul 2020 07:01:01: start model_add_line... INFO @ Tue, 14 Jul 2020 07:01:01: start X-correlation... INFO @ Tue, 14 Jul 2020 07:01:01: end of X-cor INFO @ Tue, 14 Jul 2020 07:01:01: #2 finished! INFO @ Tue, 14 Jul 2020 07:01:01: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 07:01:01: #2 alternative fragment length(s) may be 4,46 bps INFO @ Tue, 14 Jul 2020 07:01:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.20_model.r WARNING @ Tue, 14 Jul 2020 07:01:01: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:01:01: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Tue, 14 Jul 2020 07:01:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:01:01: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:01:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:01:13: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:01:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:01:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:01:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262199/SRX7262199.20_summits.bed INFO @ Tue, 14 Jul 2020 07:01:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (144 records, 4 fields): 10 millis CompletedMACS2peakCalling