Job ID = 6366397 SRX = SRX1388771 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:45:52 prefetch.2.10.7: 1) Downloading 'SRR2832487'... 2020-06-15T22:45:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:46:42 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:46:43 prefetch.2.10.7: 'SRR2832487' is valid 2020-06-15T22:46:43 prefetch.2.10.7: 1) 'SRR2832487' was downloaded successfully Read 8786527 spots for SRR2832487/SRR2832487.sra Written 8786527 spots for SRR2832487/SRR2832487.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: 00:02:05 8786527 reads; of these: 8786527 (100.00%) were unpaired; of these: 312126 (3.55%) aligned 0 times 6255972 (71.20%) aligned exactly 1 time 2218429 (25.25%) aligned >1 times 96.45% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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] 989410 / 8474401 = 0.1168 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 07:51:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.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 07:51:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:41: 1000000 INFO @ Tue, 16 Jun 2020 07:51:46: 2000000 INFO @ Tue, 16 Jun 2020 07:51:52: 3000000 INFO @ Tue, 16 Jun 2020 07:51:58: 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 07:52:04: 5000000 INFO @ Tue, 16 Jun 2020 07:52:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.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 07:52:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:10: 6000000 INFO @ Tue, 16 Jun 2020 07:52:10: 1000000 INFO @ Tue, 16 Jun 2020 07:52:15: 2000000 INFO @ Tue, 16 Jun 2020 07:52:15: 7000000 INFO @ Tue, 16 Jun 2020 07:52:18: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:52:18: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:52:18: #1 total tags in treatment: 7484991 INFO @ Tue, 16 Jun 2020 07:52:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:18: #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 07:52:18: #1 tags after filtering in treatment: 7484991 INFO @ Tue, 16 Jun 2020 07:52:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:18: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:19: #2 number of paired peaks: 756 WARNING @ Tue, 16 Jun 2020 07:52:19: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Tue, 16 Jun 2020 07:52:19: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:19: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:19: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:19: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:19: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 07:52:19: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 16 Jun 2020 07:52:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.05_model.r WARNING @ Tue, 16 Jun 2020 07:52:19: #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, 16 Jun 2020 07:52:19: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 16 Jun 2020 07:52:19: #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 07:52:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:52:20: 3000000 INFO @ Tue, 16 Jun 2020 07:52:24: 4000000 INFO @ Tue, 16 Jun 2020 07:52:29: 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 07:52:34: 6000000 INFO @ Tue, 16 Jun 2020 07:52:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.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 07:52:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:52:39: 7000000 INFO @ Tue, 16 Jun 2020 07:52:40: 1000000 INFO @ Tue, 16 Jun 2020 07:52:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:52:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:52:41: #1 total tags in treatment: 7484991 INFO @ Tue, 16 Jun 2020 07:52:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:41: #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 07:52:42: #1 tags after filtering in treatment: 7484991 INFO @ Tue, 16 Jun 2020 07:52:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:42: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:42: #2 number of paired peaks: 756 WARNING @ Tue, 16 Jun 2020 07:52:42: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Tue, 16 Jun 2020 07:52:42: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:42: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:42: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:42: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:42: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 07:52:42: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 16 Jun 2020 07:52:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.10_model.r WARNING @ Tue, 16 Jun 2020 07:52:42: #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, 16 Jun 2020 07:52:42: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 16 Jun 2020 07:52:42: #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 07:52:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:52:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.05_summits.bed INFO @ Tue, 16 Jun 2020 07:52:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (707 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:52:45: 2000000 INFO @ Tue, 16 Jun 2020 07:52:50: 3000000 INFO @ Tue, 16 Jun 2020 07:52:55: 4000000 INFO @ Tue, 16 Jun 2020 07:52:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:52:59: 5000000 INFO @ Tue, 16 Jun 2020 07:53:04: 6000000 INFO @ Tue, 16 Jun 2020 07:53:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.10_summits.bed INFO @ Tue, 16 Jun 2020 07:53:07: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (437 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:53:09: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:53:11: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:53:11: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:53:11: #1 total tags in treatment: 7484991 INFO @ Tue, 16 Jun 2020 07:53:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:11: #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 07:53:12: #1 tags after filtering in treatment: 7484991 INFO @ Tue, 16 Jun 2020 07:53:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:12: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:12: #2 number of paired peaks: 756 WARNING @ Tue, 16 Jun 2020 07:53:12: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Tue, 16 Jun 2020 07:53:12: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:12: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:12: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:12: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:12: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 07:53:12: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 16 Jun 2020 07:53:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.20_model.r WARNING @ Tue, 16 Jun 2020 07:53:12: #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, 16 Jun 2020 07:53:12: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 16 Jun 2020 07:53:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:53:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:53:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388771/SRX1388771.20_summits.bed INFO @ Tue, 16 Jun 2020 07:53:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (170 records, 4 fields): 1 millis CompletedMACS2peakCalling