Job ID = 6366968 SRX = SRX257667 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:20:01 prefetch.2.10.7: 1) Downloading 'SRR800678'... 2020-06-15T23:20:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:22:20 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:22:20 prefetch.2.10.7: 1) 'SRR800678' was downloaded successfully Read 21688641 spots for SRR800678/SRR800678.sra Written 21688641 spots for SRR800678/SRR800678.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: 00:05:07 21688641 reads; of these: 21688641 (100.00%) were unpaired; of these: 1604061 (7.40%) aligned 0 times 16552678 (76.32%) aligned exactly 1 time 3531902 (16.28%) aligned >1 times 92.60% overall alignment rate Time searching: 00:05:07 Overall time: 00:05:07 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] 12061530 / 20084580 = 0.6005 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 08:33:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.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 08:33:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:24: 1000000 INFO @ Tue, 16 Jun 2020 08:33:30: 2000000 INFO @ Tue, 16 Jun 2020 08:33:37: 3000000 INFO @ Tue, 16 Jun 2020 08:33:43: 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 08:33:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.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 08:33:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:49: 5000000 INFO @ Tue, 16 Jun 2020 08:33:54: 1000000 INFO @ Tue, 16 Jun 2020 08:33:56: 6000000 INFO @ Tue, 16 Jun 2020 08:34:01: 2000000 INFO @ Tue, 16 Jun 2020 08:34:02: 7000000 INFO @ Tue, 16 Jun 2020 08:34:07: 3000000 INFO @ Tue, 16 Jun 2020 08:34:09: 8000000 INFO @ Tue, 16 Jun 2020 08:34:09: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:34:09: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:34:09: #1 total tags in treatment: 8023050 INFO @ Tue, 16 Jun 2020 08:34:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:09: #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 08:34:09: #1 tags after filtering in treatment: 8023050 INFO @ Tue, 16 Jun 2020 08:34:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:10: #2 number of paired peaks: 616 WARNING @ Tue, 16 Jun 2020 08:34:10: Fewer paired peaks (616) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 616 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:10: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 08:34:10: #2 alternative fragment length(s) may be 4,69 bps INFO @ Tue, 16 Jun 2020 08:34:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.05_model.r WARNING @ Tue, 16 Jun 2020 08:34:10: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:34:10: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Tue, 16 Jun 2020 08:34:10: #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 08:34:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:13: 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 08:34:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.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 08:34:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:20: 5000000 INFO @ Tue, 16 Jun 2020 08:34:25: 1000000 INFO @ Tue, 16 Jun 2020 08:34:27: 6000000 INFO @ Tue, 16 Jun 2020 08:34:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:33: 2000000 INFO @ Tue, 16 Jun 2020 08:34:34: 7000000 INFO @ Tue, 16 Jun 2020 08:34:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.05_summits.bed INFO @ Tue, 16 Jun 2020 08:34:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1395 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:34:41: 3000000 INFO @ Tue, 16 Jun 2020 08:34:41: 8000000 INFO @ Tue, 16 Jun 2020 08:34:42: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:34:42: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:34:42: #1 total tags in treatment: 8023050 INFO @ Tue, 16 Jun 2020 08:34:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:42: #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 08:34:42: #1 tags after filtering in treatment: 8023050 INFO @ Tue, 16 Jun 2020 08:34:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:42: #2 number of paired peaks: 616 WARNING @ Tue, 16 Jun 2020 08:34:42: Fewer paired peaks (616) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 616 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:42: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:42: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:43: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 08:34:43: #2 alternative fragment length(s) may be 4,69 bps INFO @ Tue, 16 Jun 2020 08:34:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.10_model.r WARNING @ Tue, 16 Jun 2020 08:34:43: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:34:43: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Tue, 16 Jun 2020 08:34:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:34:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:48: 4000000 INFO @ Tue, 16 Jun 2020 08:34:55: 5000000 INFO @ Tue, 16 Jun 2020 08:35:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:35:02: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:35:09: 7000000 INFO @ Tue, 16 Jun 2020 08:35:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.10_summits.bed INFO @ Tue, 16 Jun 2020 08:35:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (810 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:35:16: 8000000 INFO @ Tue, 16 Jun 2020 08:35:16: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:35:16: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:35:16: #1 total tags in treatment: 8023050 INFO @ Tue, 16 Jun 2020 08:35:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:16: #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 08:35:16: #1 tags after filtering in treatment: 8023050 INFO @ Tue, 16 Jun 2020 08:35:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:17: #2 number of paired peaks: 616 WARNING @ Tue, 16 Jun 2020 08:35:17: Fewer paired peaks (616) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 616 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:17: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 08:35:17: #2 alternative fragment length(s) may be 4,69 bps INFO @ Tue, 16 Jun 2020 08:35:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.20_model.r WARNING @ Tue, 16 Jun 2020 08:35:17: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:35:17: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Tue, 16 Jun 2020 08:35:17: #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 08:35:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:35:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:35:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257667/SRX257667.20_summits.bed INFO @ Tue, 16 Jun 2020 08:35:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (384 records, 4 fields): 1 millis CompletedMACS2peakCalling