Job ID = 6366951 SRX = SRX2576651 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:18:46 prefetch.2.10.7: 1) Downloading 'SRR5272608'... 2020-06-15T23:18:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:20:01 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:20:02 prefetch.2.10.7: 'SRR5272608' is valid 2020-06-15T23:20:02 prefetch.2.10.7: 1) 'SRR5272608' was downloaded successfully 2020-06-15T23:20:02 prefetch.2.10.7: 'SRR5272608' has 0 unresolved dependencies Read 29253295 spots for SRR5272608/SRR5272608.sra Written 29253295 spots for SRR5272608/SRR5272608.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:38 29253295 reads; of these: 29253295 (100.00%) were unpaired; of these: 8703972 (29.75%) aligned 0 times 16755843 (57.28%) aligned exactly 1 time 3793480 (12.97%) aligned >1 times 70.25% overall alignment rate Time searching: 00:05:38 Overall time: 00:05:38 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 12 files... [bam_rmdupse_core] 13586970 / 20549323 = 0.6612 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 08:30:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.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 08:30:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:31: 1000000 INFO @ Tue, 16 Jun 2020 08:30:38: 2000000 INFO @ Tue, 16 Jun 2020 08:30:45: 3000000 INFO @ Tue, 16 Jun 2020 08:30:51: 4000000 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 08:30:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.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 08:30:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:58: 5000000 INFO @ Tue, 16 Jun 2020 08:31:02: 1000000 INFO @ Tue, 16 Jun 2020 08:31:06: 6000000 INFO @ Tue, 16 Jun 2020 08:31:09: 2000000 INFO @ Tue, 16 Jun 2020 08:31:13: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:31:13: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:31:13: #1 total tags in treatment: 6962353 INFO @ Tue, 16 Jun 2020 08:31:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:13: #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 08:31:13: #1 tags after filtering in treatment: 6962353 INFO @ Tue, 16 Jun 2020 08:31:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:14: #2 number of paired peaks: 704 WARNING @ Tue, 16 Jun 2020 08:31:14: Fewer paired peaks (704) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 704 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:14: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:14: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:14: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:14: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 08:31:14: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 16 Jun 2020 08:31:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.05_model.r WARNING @ Tue, 16 Jun 2020 08:31:14: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:14: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 16 Jun 2020 08:31:14: #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 08:31:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:31:16: 3000000 INFO @ Tue, 16 Jun 2020 08:31:22: 4000000 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 08:31:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.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 08:31:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:29: 5000000 INFO @ Tue, 16 Jun 2020 08:31:33: 1000000 INFO @ Tue, 16 Jun 2020 08:31:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.05_summits.bed INFO @ Tue, 16 Jun 2020 08:31:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1442 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:31:36: 6000000 INFO @ Tue, 16 Jun 2020 08:31:42: 2000000 INFO @ Tue, 16 Jun 2020 08:31:43: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:31:43: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:31:43: #1 total tags in treatment: 6962353 INFO @ Tue, 16 Jun 2020 08:31:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:43: #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 08:31:43: #1 tags after filtering in treatment: 6962353 INFO @ Tue, 16 Jun 2020 08:31:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:44: #2 number of paired peaks: 704 WARNING @ Tue, 16 Jun 2020 08:31:44: Fewer paired peaks (704) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 704 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:44: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:44: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:44: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:44: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:44: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 08:31:44: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 16 Jun 2020 08:31:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.10_model.r WARNING @ Tue, 16 Jun 2020 08:31:44: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:44: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 16 Jun 2020 08:31:44: #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 08:31:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:31:49: 3000000 INFO @ Tue, 16 Jun 2020 08:31:57: 4000000 INFO @ Tue, 16 Jun 2020 08:31:58: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:32:04: 5000000 INFO @ Tue, 16 Jun 2020 08:32:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.10_summits.bed INFO @ Tue, 16 Jun 2020 08:32:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (891 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:32:12: 6000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:32:18: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:32:18: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:32:18: #1 total tags in treatment: 6962353 INFO @ Tue, 16 Jun 2020 08:32:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:18: #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 08:32:19: #1 tags after filtering in treatment: 6962353 INFO @ Tue, 16 Jun 2020 08:32:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:19: #2 number of paired peaks: 704 WARNING @ Tue, 16 Jun 2020 08:32:19: Fewer paired peaks (704) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 704 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:19: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 08:32:19: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 16 Jun 2020 08:32:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.20_model.r WARNING @ Tue, 16 Jun 2020 08:32:19: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:32:19: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 16 Jun 2020 08:32:19: #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 08:32:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576651/SRX2576651.20_summits.bed INFO @ Tue, 16 Jun 2020 08:32:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (397 records, 4 fields): 1 millis CompletedMACS2peakCalling