Job ID = 6369034 SRX = SRX982098 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T01:08:24 prefetch.2.10.7: 1) Downloading 'SRR1956585'... 2020-06-16T01:08:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T01:10:05 prefetch.2.10.7: HTTPS download succeed 2020-06-16T01:10:05 prefetch.2.10.7: 'SRR1956585' is valid 2020-06-16T01:10:05 prefetch.2.10.7: 1) 'SRR1956585' was downloaded successfully Read 6722011 spots for SRR1956585/SRR1956585.sra Written 6722011 spots for SRR1956585/SRR1956585.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: 00:01:29 6722011 reads; of these: 6722011 (100.00%) were unpaired; of these: 301449 (4.48%) aligned 0 times 5375946 (79.98%) aligned exactly 1 time 1044616 (15.54%) aligned >1 times 95.52% overall alignment rate Time searching: 00:01:29 Overall time: 00:01:29 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] 326889 / 6420562 = 0.0509 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 10:14:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.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 10:14:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:14:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:14:40: 1000000 INFO @ Tue, 16 Jun 2020 10:14:47: 2000000 INFO @ Tue, 16 Jun 2020 10:14:54: 3000000 INFO @ Tue, 16 Jun 2020 10:15:00: 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 10:15:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.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 10:15:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:15:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:15:07: 5000000 INFO @ Tue, 16 Jun 2020 10:15:11: 1000000 INFO @ Tue, 16 Jun 2020 10:15:14: 6000000 INFO @ Tue, 16 Jun 2020 10:15:14: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:15:14: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:15:14: #1 total tags in treatment: 6093673 INFO @ Tue, 16 Jun 2020 10:15:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:15:14: #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 10:15:14: #1 tags after filtering in treatment: 6093673 INFO @ Tue, 16 Jun 2020 10:15:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:15:14: #1 finished! INFO @ Tue, 16 Jun 2020 10:15:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:15:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:15:15: #2 number of paired peaks: 352 WARNING @ Tue, 16 Jun 2020 10:15:15: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Tue, 16 Jun 2020 10:15:15: start model_add_line... INFO @ Tue, 16 Jun 2020 10:15:15: start X-correlation... INFO @ Tue, 16 Jun 2020 10:15:15: end of X-cor INFO @ Tue, 16 Jun 2020 10:15:15: #2 finished! INFO @ Tue, 16 Jun 2020 10:15:15: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 10:15:15: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 16 Jun 2020 10:15:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.05_model.r WARNING @ Tue, 16 Jun 2020 10:15:15: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:15:15: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 16 Jun 2020 10:15:15: #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 10:15:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:15:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:15:18: 2000000 INFO @ Tue, 16 Jun 2020 10:15:24: 3000000 INFO @ Tue, 16 Jun 2020 10:15:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:15:31: 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 10:15:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:15:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:15:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.05_summits.bed INFO @ Tue, 16 Jun 2020 10:15:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (461 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:15:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.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 10:15:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:15:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:15:37: 5000000 INFO @ Tue, 16 Jun 2020 10:15:43: 1000000 INFO @ Tue, 16 Jun 2020 10:15:44: 6000000 INFO @ Tue, 16 Jun 2020 10:15:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:15:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:15:45: #1 total tags in treatment: 6093673 INFO @ Tue, 16 Jun 2020 10:15:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:15:45: #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 10:15:45: #1 tags after filtering in treatment: 6093673 INFO @ Tue, 16 Jun 2020 10:15:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:15:45: #1 finished! INFO @ Tue, 16 Jun 2020 10:15:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:15:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:15:45: #2 number of paired peaks: 352 WARNING @ Tue, 16 Jun 2020 10:15:45: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Tue, 16 Jun 2020 10:15:45: start model_add_line... INFO @ Tue, 16 Jun 2020 10:15:45: start X-correlation... INFO @ Tue, 16 Jun 2020 10:15:45: end of X-cor INFO @ Tue, 16 Jun 2020 10:15:45: #2 finished! INFO @ Tue, 16 Jun 2020 10:15:45: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 10:15:45: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 16 Jun 2020 10:15:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.10_model.r WARNING @ Tue, 16 Jun 2020 10:15:45: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:15:45: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 16 Jun 2020 10:15:45: #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 10:15:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:15:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:15:52: 2000000 INFO @ Tue, 16 Jun 2020 10:15:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:16:02: 3000000 INFO @ Tue, 16 Jun 2020 10:16:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:16:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:16:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.10_summits.bed INFO @ Tue, 16 Jun 2020 10:16:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (302 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:16:11: 4000000 INFO @ Tue, 16 Jun 2020 10:16:20: 5000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:16:29: 6000000 INFO @ Tue, 16 Jun 2020 10:16:30: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:16:30: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:16:30: #1 total tags in treatment: 6093673 INFO @ Tue, 16 Jun 2020 10:16:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:16:30: #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 10:16:30: #1 tags after filtering in treatment: 6093673 INFO @ Tue, 16 Jun 2020 10:16:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:16:30: #1 finished! INFO @ Tue, 16 Jun 2020 10:16:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:16:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:16:30: #2 number of paired peaks: 352 WARNING @ Tue, 16 Jun 2020 10:16:30: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Tue, 16 Jun 2020 10:16:30: start model_add_line... INFO @ Tue, 16 Jun 2020 10:16:30: start X-correlation... INFO @ Tue, 16 Jun 2020 10:16:30: end of X-cor INFO @ Tue, 16 Jun 2020 10:16:30: #2 finished! INFO @ Tue, 16 Jun 2020 10:16:30: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 10:16:30: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 16 Jun 2020 10:16:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.20_model.r WARNING @ Tue, 16 Jun 2020 10:16:30: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:16:30: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 16 Jun 2020 10:16:30: #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 10:16:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:16:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:16:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:16:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:16:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:16:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982098/SRX982098.20_summits.bed INFO @ Tue, 16 Jun 2020 10:16:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (124 records, 4 fields): 1 millis CompletedMACS2peakCalling