Job ID = 12264755 SRX = SRX2969573 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 41403819 spots for SRR5772136/SRR5772136.sra Written 41403819 spots for SRR5772136/SRR5772136.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265164 ("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: 00:11:12 41403819 reads; of these: 41403819 (100.00%) were unpaired; of these: 3080397 (7.44%) aligned 0 times 33829727 (81.71%) aligned exactly 1 time 4493695 (10.85%) aligned >1 times 92.56% overall alignment rate Time searching: 00:11:12 Overall time: 00:11:12 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 16 files... [bam_rmdupse_core] 27988693 / 38323422 = 0.7303 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:14:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.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 @ Sat, 03 Apr 2021 06:14:24: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:14:24: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:14:33: 1000000 INFO @ Sat, 03 Apr 2021 06:14:42: 2000000 INFO @ Sat, 03 Apr 2021 06:14:50: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:14:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.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 @ Sat, 03 Apr 2021 06:14:54: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:14:54: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:14:59: 4000000 INFO @ Sat, 03 Apr 2021 06:15:03: 1000000 INFO @ Sat, 03 Apr 2021 06:15:07: 5000000 INFO @ Sat, 03 Apr 2021 06:15:12: 2000000 INFO @ Sat, 03 Apr 2021 06:15:16: 6000000 INFO @ Sat, 03 Apr 2021 06:15:20: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:15:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.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 @ Sat, 03 Apr 2021 06:15:24: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:15:24: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:15:25: 7000000 INFO @ Sat, 03 Apr 2021 06:15:29: 4000000 INFO @ Sat, 03 Apr 2021 06:15:33: 1000000 INFO @ Sat, 03 Apr 2021 06:15:33: 8000000 INFO @ Sat, 03 Apr 2021 06:15:37: 5000000 INFO @ Sat, 03 Apr 2021 06:15:41: 9000000 INFO @ Sat, 03 Apr 2021 06:15:42: 2000000 INFO @ Sat, 03 Apr 2021 06:15:46: 6000000 INFO @ Sat, 03 Apr 2021 06:15:50: 10000000 INFO @ Sat, 03 Apr 2021 06:15:50: 3000000 INFO @ Sat, 03 Apr 2021 06:15:53: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:15:53: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:15:53: #1 total tags in treatment: 10334729 INFO @ Sat, 03 Apr 2021 06:15:53: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:15:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:15:54: #1 tags after filtering in treatment: 10334729 INFO @ Sat, 03 Apr 2021 06:15:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:15:54: #1 finished! INFO @ Sat, 03 Apr 2021 06:15:54: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:15:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:15:54: #2 number of paired peaks: 522 WARNING @ Sat, 03 Apr 2021 06:15:54: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Sat, 03 Apr 2021 06:15:54: start model_add_line... INFO @ Sat, 03 Apr 2021 06:15:55: start X-correlation... INFO @ Sat, 03 Apr 2021 06:15:55: end of X-cor INFO @ Sat, 03 Apr 2021 06:15:55: #2 finished! INFO @ Sat, 03 Apr 2021 06:15:55: #2 predicted fragment length is 68 bps INFO @ Sat, 03 Apr 2021 06:15:55: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 03 Apr 2021 06:15:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.05_model.r WARNING @ Sat, 03 Apr 2021 06:15:55: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:15:55: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 03 Apr 2021 06:15:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:15:55: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:15:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:15:55: 7000000 INFO @ Sat, 03 Apr 2021 06:15:59: 4000000 INFO @ Sat, 03 Apr 2021 06:16:04: 8000000 INFO @ Sat, 03 Apr 2021 06:16:08: 5000000 INFO @ Sat, 03 Apr 2021 06:16:14: 9000000 INFO @ Sat, 03 Apr 2021 06:16:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:16:18: 6000000 INFO @ Sat, 03 Apr 2021 06:16:23: 10000000 INFO @ Sat, 03 Apr 2021 06:16:26: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:16:26: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:16:26: #1 total tags in treatment: 10334729 INFO @ Sat, 03 Apr 2021 06:16:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:16:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:16:26: #1 tags after filtering in treatment: 10334729 INFO @ Sat, 03 Apr 2021 06:16:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:16:26: #1 finished! INFO @ Sat, 03 Apr 2021 06:16:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:16:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:16:26: 7000000 INFO @ Sat, 03 Apr 2021 06:16:27: #2 number of paired peaks: 522 WARNING @ Sat, 03 Apr 2021 06:16:27: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Sat, 03 Apr 2021 06:16:27: start model_add_line... INFO @ Sat, 03 Apr 2021 06:16:27: start X-correlation... INFO @ Sat, 03 Apr 2021 06:16:27: end of X-cor INFO @ Sat, 03 Apr 2021 06:16:27: #2 finished! INFO @ Sat, 03 Apr 2021 06:16:27: #2 predicted fragment length is 68 bps INFO @ Sat, 03 Apr 2021 06:16:27: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 03 Apr 2021 06:16:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.10_model.r WARNING @ Sat, 03 Apr 2021 06:16:27: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:16:27: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 03 Apr 2021 06:16:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:16:27: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:16:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:16:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:16:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:16:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.05_summits.bed INFO @ Sat, 03 Apr 2021 06:16:31: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (8388 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:16:35: 8000000 INFO @ Sat, 03 Apr 2021 06:16:43: 9000000 INFO @ Sat, 03 Apr 2021 06:16:48: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:16:51: 10000000 INFO @ Sat, 03 Apr 2021 06:16:54: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:16:54: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:16:54: #1 total tags in treatment: 10334729 INFO @ Sat, 03 Apr 2021 06:16:54: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:16:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:16:54: #1 tags after filtering in treatment: 10334729 INFO @ Sat, 03 Apr 2021 06:16:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:16:54: #1 finished! INFO @ Sat, 03 Apr 2021 06:16:54: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:16:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:16:55: #2 number of paired peaks: 522 WARNING @ Sat, 03 Apr 2021 06:16:55: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Sat, 03 Apr 2021 06:16:55: start model_add_line... INFO @ Sat, 03 Apr 2021 06:16:55: start X-correlation... INFO @ Sat, 03 Apr 2021 06:16:55: end of X-cor INFO @ Sat, 03 Apr 2021 06:16:55: #2 finished! INFO @ Sat, 03 Apr 2021 06:16:55: #2 predicted fragment length is 68 bps INFO @ Sat, 03 Apr 2021 06:16:55: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 03 Apr 2021 06:16:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.20_model.r WARNING @ Sat, 03 Apr 2021 06:16:55: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:16:55: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 03 Apr 2021 06:16:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:16:55: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:16:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:17:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:17:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:17:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.10_summits.bed INFO @ Sat, 03 Apr 2021 06:17:00: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5134 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:17:16: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:17:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:17:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:17:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2969573/SRX2969573.20_summits.bed INFO @ Sat, 03 Apr 2021 06:17:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2353 records, 4 fields): 4 millis CompletedMACS2peakCalling