Job ID = 16434814 SRX = SRX11633403 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 10732127 spots for SRR15329112/SRR15329112.sra Written 10732127 spots for SRR15329112/SRR15329112.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434858 ("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: 00:03:55 10732127 reads; of these: 10732127 (100.00%) were unpaired; of these: 1091486 (10.17%) aligned 0 times 8169667 (76.12%) aligned exactly 1 time 1470974 (13.71%) aligned >1 times 89.83% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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] 980927 / 9640641 = 0.1017 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:05:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.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, 02 Aug 2022 10:05:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:05:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:06:00: 1000000 INFO @ Tue, 02 Aug 2022 10:06:08: 2000000 INFO @ Tue, 02 Aug 2022 10:06:16: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:06:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.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, 02 Aug 2022 10:06:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:06:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:06:24: 4000000 INFO @ Tue, 02 Aug 2022 10:06:27: 1000000 INFO @ Tue, 02 Aug 2022 10:06:32: 5000000 INFO @ Tue, 02 Aug 2022 10:06:33: 2000000 INFO @ Tue, 02 Aug 2022 10:06:39: 3000000 INFO @ Tue, 02 Aug 2022 10:06:40: 6000000 INFO @ Tue, 02 Aug 2022 10:06:45: 4000000 INFO @ Tue, 02 Aug 2022 10:06:48: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:06:50: 5000000 INFO @ Tue, 02 Aug 2022 10:06:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.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, 02 Aug 2022 10:06:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:06:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:06:56: 8000000 INFO @ Tue, 02 Aug 2022 10:06:56: 6000000 INFO @ Tue, 02 Aug 2022 10:07:00: 1000000 INFO @ Tue, 02 Aug 2022 10:07:01: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:07:01: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:07:01: #1 total tags in treatment: 8659714 INFO @ Tue, 02 Aug 2022 10:07:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:07:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:07:02: #1 tags after filtering in treatment: 8659714 INFO @ Tue, 02 Aug 2022 10:07:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:07:02: #1 finished! INFO @ Tue, 02 Aug 2022 10:07:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:07:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:07:02: 7000000 INFO @ Tue, 02 Aug 2022 10:07:02: #2 number of paired peaks: 317 WARNING @ Tue, 02 Aug 2022 10:07:02: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Tue, 02 Aug 2022 10:07:02: start model_add_line... INFO @ Tue, 02 Aug 2022 10:07:02: start X-correlation... INFO @ Tue, 02 Aug 2022 10:07:02: end of X-cor INFO @ Tue, 02 Aug 2022 10:07:02: #2 finished! INFO @ Tue, 02 Aug 2022 10:07:02: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 10:07:02: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 02 Aug 2022 10:07:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.05_model.r WARNING @ Tue, 02 Aug 2022 10:07:03: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:07:03: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 02 Aug 2022 10:07:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:07:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:07:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:07:07: 2000000 INFO @ Tue, 02 Aug 2022 10:07:08: 8000000 INFO @ Tue, 02 Aug 2022 10:07:12: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:07:12: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:07:12: #1 total tags in treatment: 8659714 INFO @ Tue, 02 Aug 2022 10:07:12: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:07:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:07:12: #1 tags after filtering in treatment: 8659714 INFO @ Tue, 02 Aug 2022 10:07:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:07:12: #1 finished! INFO @ Tue, 02 Aug 2022 10:07:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:07:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:07:12: #2 number of paired peaks: 317 WARNING @ Tue, 02 Aug 2022 10:07:12: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Tue, 02 Aug 2022 10:07:12: start model_add_line... INFO @ Tue, 02 Aug 2022 10:07:13: start X-correlation... INFO @ Tue, 02 Aug 2022 10:07:13: end of X-cor INFO @ Tue, 02 Aug 2022 10:07:13: #2 finished! INFO @ Tue, 02 Aug 2022 10:07:13: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 10:07:13: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 02 Aug 2022 10:07:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.10_model.r WARNING @ Tue, 02 Aug 2022 10:07:13: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:07:13: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 02 Aug 2022 10:07:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:07:13: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:07:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:07:15: 3000000 INFO @ Tue, 02 Aug 2022 10:07:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:07:22: 4000000 INFO @ Tue, 02 Aug 2022 10:07:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:07:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:07:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.05_summits.bed INFO @ Tue, 02 Aug 2022 10:07:27: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (494 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:07:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:07:29: 5000000 INFO @ Tue, 02 Aug 2022 10:07:36: 6000000 INFO @ Tue, 02 Aug 2022 10:07:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:07:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:07:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.10_summits.bed INFO @ Tue, 02 Aug 2022 10:07:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (319 records, 4 fields): 427 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:07:43: 7000000 INFO @ Tue, 02 Aug 2022 10:07:50: 8000000 INFO @ Tue, 02 Aug 2022 10:07:55: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:07:55: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:07:55: #1 total tags in treatment: 8659714 INFO @ Tue, 02 Aug 2022 10:07:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:07:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:07:55: #1 tags after filtering in treatment: 8659714 INFO @ Tue, 02 Aug 2022 10:07:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:07:55: #1 finished! INFO @ Tue, 02 Aug 2022 10:07:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:07:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:07:55: #2 number of paired peaks: 317 WARNING @ Tue, 02 Aug 2022 10:07:55: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Tue, 02 Aug 2022 10:07:55: start model_add_line... INFO @ Tue, 02 Aug 2022 10:07:55: start X-correlation... INFO @ Tue, 02 Aug 2022 10:07:55: end of X-cor INFO @ Tue, 02 Aug 2022 10:07:55: #2 finished! INFO @ Tue, 02 Aug 2022 10:07:55: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 10:07:55: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 02 Aug 2022 10:07:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.20_model.r WARNING @ Tue, 02 Aug 2022 10:07:56: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:07:56: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 02 Aug 2022 10:07:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:07:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:07:56: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:08:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:08:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:08:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:08:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633403/SRX11633403.20_summits.bed INFO @ Tue, 02 Aug 2022 10:08:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。