Job ID = 6366957 SRX = SRX2576657 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:10:31 prefetch.2.10.7: 1) Downloading 'SRR5272614'... 2020-06-15T23:10:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:11:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:11:30 prefetch.2.10.7: 'SRR5272614' is valid 2020-06-15T23:11:30 prefetch.2.10.7: 1) 'SRR5272614' was downloaded successfully 2020-06-15T23:11:30 prefetch.2.10.7: 'SRR5272614' has 0 unresolved dependencies Read 20456193 spots for SRR5272614/SRR5272614.sra Written 20456193 spots for SRR5272614/SRR5272614.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:33 20456193 reads; of these: 20456193 (100.00%) were unpaired; of these: 1727558 (8.45%) aligned 0 times 15381200 (75.19%) aligned exactly 1 time 3347435 (16.36%) aligned >1 times 91.55% overall alignment rate Time searching: 00:04:34 Overall time: 00:04:34 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 8 files... [bam_rmdupse_core] 13196976 / 18728635 = 0.7046 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, 16 Jun 2020 08:20:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.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, 16 Jun 2020 08:20:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:15: 1000000 INFO @ Tue, 16 Jun 2020 08:20:20: 2000000 INFO @ Tue, 16 Jun 2020 08:20:26: 3000000 INFO @ Tue, 16 Jun 2020 08:20:31: 4000000 INFO @ Tue, 16 Jun 2020 08:20:36: 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, 16 Jun 2020 08:20:39: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:20:39: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:20:39: #1 total tags in treatment: 5531659 INFO @ Tue, 16 Jun 2020 08:20:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:20:39: #1 tags after filtering in treatment: 5531659 INFO @ Tue, 16 Jun 2020 08:20:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.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, 16 Jun 2020 08:20:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:40: #2 number of paired peaks: 794 WARNING @ Tue, 16 Jun 2020 08:20:40: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:40: #2 predicted fragment length is 93 bps INFO @ Tue, 16 Jun 2020 08:20:40: #2 alternative fragment length(s) may be 93 bps INFO @ Tue, 16 Jun 2020 08:20:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.05_model.r WARNING @ Tue, 16 Jun 2020 08:20:40: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:40: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Tue, 16 Jun 2020 08:20:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:20:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:45: 1000000 INFO @ Tue, 16 Jun 2020 08:20:50: 2000000 INFO @ Tue, 16 Jun 2020 08:20:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:55: 3000000 INFO @ Tue, 16 Jun 2020 08:20:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.05_summits.bed INFO @ Tue, 16 Jun 2020 08:20:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1464 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:21:00: 4000000 INFO @ Tue, 16 Jun 2020 08:21:06: 5000000 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, 16 Jun 2020 08:21:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:21:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:21:08: #1 total tags in treatment: 5531659 INFO @ Tue, 16 Jun 2020 08:21:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:21:08: #1 tags after filtering in treatment: 5531659 INFO @ Tue, 16 Jun 2020 08:21:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:09: #2 number of paired peaks: 794 WARNING @ Tue, 16 Jun 2020 08:21:09: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:09: #2 predicted fragment length is 93 bps INFO @ Tue, 16 Jun 2020 08:21:09: #2 alternative fragment length(s) may be 93 bps INFO @ Tue, 16 Jun 2020 08:21:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.10_model.r WARNING @ Tue, 16 Jun 2020 08:21:09: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:21:09: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Tue, 16 Jun 2020 08:21:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:21:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.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, 16 Jun 2020 08:21:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:15: 1000000 INFO @ Tue, 16 Jun 2020 08:21:21: 2000000 INFO @ Tue, 16 Jun 2020 08:21:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:26: 3000000 INFO @ Tue, 16 Jun 2020 08:21:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.10_summits.bed INFO @ Tue, 16 Jun 2020 08:21:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (980 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:21:32: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:21:37: 5000000 INFO @ Tue, 16 Jun 2020 08:21:40: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:21:40: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:21:40: #1 total tags in treatment: 5531659 INFO @ Tue, 16 Jun 2020 08:21:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:21:40: #1 tags after filtering in treatment: 5531659 INFO @ Tue, 16 Jun 2020 08:21:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:40: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:40: #2 number of paired peaks: 794 WARNING @ Tue, 16 Jun 2020 08:21:40: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:40: #2 predicted fragment length is 93 bps INFO @ Tue, 16 Jun 2020 08:21:40: #2 alternative fragment length(s) may be 93 bps INFO @ Tue, 16 Jun 2020 08:21:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.20_model.r WARNING @ Tue, 16 Jun 2020 08:21:40: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:21:40: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Tue, 16 Jun 2020 08:21:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:21:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:21:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576657/SRX2576657.20_summits.bed INFO @ Tue, 16 Jun 2020 08:21:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (566 records, 4 fields): 1 millis CompletedMACS2peakCalling