Job ID = 6626400 SRX = SRX7262233 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 3996761 spots for SRR10581856/SRR10581856.sra Written 3996761 spots for SRR10581856/SRR10581856.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626447 ("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: 00:00:48 3996761 reads; of these: 3996761 (100.00%) were unpaired; of these: 321583 (8.05%) aligned 0 times 2873581 (71.90%) aligned exactly 1 time 801597 (20.06%) aligned >1 times 91.95% overall alignment rate Time searching: 00:00:48 Overall time: 00:00:48 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] 578304 / 3675178 = 0.1574 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 06:59:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.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 06:59:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:59:55: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:00:00: 1000000 INFO @ Tue, 14 Jul 2020 07:00:06: 2000000 INFO @ Tue, 14 Jul 2020 07:00:11: 3000000 INFO @ Tue, 14 Jul 2020 07:00:12: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:00:12: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:00:12: #1 total tags in treatment: 3096874 INFO @ Tue, 14 Jul 2020 07:00:12: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:00:12: #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 07:00:12: #1 tags after filtering in treatment: 3096874 INFO @ Tue, 14 Jul 2020 07:00:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:00:12: #1 finished! INFO @ Tue, 14 Jul 2020 07:00:12: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:00:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:00:12: #2 number of paired peaks: 502 WARNING @ Tue, 14 Jul 2020 07:00:12: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Tue, 14 Jul 2020 07:00:12: start model_add_line... INFO @ Tue, 14 Jul 2020 07:00:12: start X-correlation... INFO @ Tue, 14 Jul 2020 07:00:12: end of X-cor INFO @ Tue, 14 Jul 2020 07:00:12: #2 finished! INFO @ Tue, 14 Jul 2020 07:00:12: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 07:00:12: #2 alternative fragment length(s) may be 50,468 bps INFO @ Tue, 14 Jul 2020 07:00:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.05_model.r WARNING @ Tue, 14 Jul 2020 07:00:12: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:00:12: #2 You may need to consider one of the other alternative d(s): 50,468 WARNING @ Tue, 14 Jul 2020 07:00:12: #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 07:00:12: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:00:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:00:19: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:00:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:00:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:00:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.05_summits.bed INFO @ Tue, 14 Jul 2020 07:00:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (509 records, 4 fields): 15 millis CompletedMACS2peakCalling 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 07:00:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.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 07:00:25: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:00:25: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:00:31: 1000000 INFO @ Tue, 14 Jul 2020 07:00:36: 2000000 INFO @ Tue, 14 Jul 2020 07:00:42: 3000000 INFO @ Tue, 14 Jul 2020 07:00:42: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:00:42: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:00:42: #1 total tags in treatment: 3096874 INFO @ Tue, 14 Jul 2020 07:00:42: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:00:42: #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 07:00:42: #1 tags after filtering in treatment: 3096874 INFO @ Tue, 14 Jul 2020 07:00:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:00:42: #1 finished! INFO @ Tue, 14 Jul 2020 07:00:42: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:00:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:00:43: #2 number of paired peaks: 502 WARNING @ Tue, 14 Jul 2020 07:00:43: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Tue, 14 Jul 2020 07:00:43: start model_add_line... INFO @ Tue, 14 Jul 2020 07:00:43: start X-correlation... INFO @ Tue, 14 Jul 2020 07:00:43: end of X-cor INFO @ Tue, 14 Jul 2020 07:00:43: #2 finished! INFO @ Tue, 14 Jul 2020 07:00:43: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 07:00:43: #2 alternative fragment length(s) may be 50,468 bps INFO @ Tue, 14 Jul 2020 07:00:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.10_model.r WARNING @ Tue, 14 Jul 2020 07:00:43: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:00:43: #2 You may need to consider one of the other alternative d(s): 50,468 WARNING @ Tue, 14 Jul 2020 07:00:43: #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 07:00:43: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:00:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:00:49: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:00:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:00:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:00:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.10_summits.bed INFO @ Tue, 14 Jul 2020 07:00:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (312 records, 4 fields): 16 millis CompletedMACS2peakCalling 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 07:00:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.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 07:00:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:00:55: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:01:01: 1000000 INFO @ Tue, 14 Jul 2020 07:01:06: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:01:12: 3000000 INFO @ Tue, 14 Jul 2020 07:01:13: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:01:13: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:01:13: #1 total tags in treatment: 3096874 INFO @ Tue, 14 Jul 2020 07:01:13: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:01:13: #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 07:01:13: #1 tags after filtering in treatment: 3096874 INFO @ Tue, 14 Jul 2020 07:01:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:01:13: #1 finished! INFO @ Tue, 14 Jul 2020 07:01:13: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:01:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:01:13: #2 number of paired peaks: 502 WARNING @ Tue, 14 Jul 2020 07:01:13: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Tue, 14 Jul 2020 07:01:13: start model_add_line... INFO @ Tue, 14 Jul 2020 07:01:13: start X-correlation... INFO @ Tue, 14 Jul 2020 07:01:13: end of X-cor INFO @ Tue, 14 Jul 2020 07:01:13: #2 finished! INFO @ Tue, 14 Jul 2020 07:01:13: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 07:01:13: #2 alternative fragment length(s) may be 50,468 bps INFO @ Tue, 14 Jul 2020 07:01:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.20_model.r WARNING @ Tue, 14 Jul 2020 07:01:13: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:01:13: #2 You may need to consider one of the other alternative d(s): 50,468 WARNING @ Tue, 14 Jul 2020 07:01:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:01:13: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:01:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:01:20: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:01:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:01:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:01:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262233/SRX7262233.20_summits.bed INFO @ Tue, 14 Jul 2020 07:01:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (121 records, 4 fields): 19 millis CompletedMACS2peakCalling