Job ID = 6367739 SRX = SRX4082353 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:47:14 prefetch.2.10.7: 1) Downloading 'SRR7164171'... 2020-06-15T23:47:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:53 prefetch.2.10.7: 'SRR7164171' is valid 2020-06-15T23:48:53 prefetch.2.10.7: 1) 'SRR7164171' was downloaded successfully Read 10874584 spots for SRR7164171/SRR7164171.sra Written 10874584 spots for SRR7164171/SRR7164171.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: 00:02:29 10874584 reads; of these: 10874584 (100.00%) were unpaired; of these: 340707 (3.13%) aligned 0 times 9186668 (84.48%) aligned exactly 1 time 1347209 (12.39%) aligned >1 times 96.87% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2290281 / 10533877 = 0.2174 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 08:54:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.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 08:54:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:54:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:54:52: 1000000 INFO @ Tue, 16 Jun 2020 08:54:58: 2000000 INFO @ Tue, 16 Jun 2020 08:55:05: 3000000 INFO @ Tue, 16 Jun 2020 08:55:11: 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 08:55:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.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 08:55:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:18: 5000000 INFO @ Tue, 16 Jun 2020 08:55:22: 1000000 INFO @ Tue, 16 Jun 2020 08:55:25: 6000000 INFO @ Tue, 16 Jun 2020 08:55:30: 2000000 INFO @ Tue, 16 Jun 2020 08:55:32: 7000000 INFO @ Tue, 16 Jun 2020 08:55:37: 3000000 INFO @ Tue, 16 Jun 2020 08:55:40: 8000000 INFO @ Tue, 16 Jun 2020 08:55:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:55:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:55:41: #1 total tags in treatment: 8243596 INFO @ Tue, 16 Jun 2020 08:55:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:55:41: #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 08:55:42: #1 tags after filtering in treatment: 8243596 INFO @ Tue, 16 Jun 2020 08:55:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:55:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:55:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:55:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:55:42: #2 number of paired peaks: 156 WARNING @ Tue, 16 Jun 2020 08:55:42: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Tue, 16 Jun 2020 08:55:42: start model_add_line... INFO @ Tue, 16 Jun 2020 08:55:42: start X-correlation... INFO @ Tue, 16 Jun 2020 08:55:42: end of X-cor INFO @ Tue, 16 Jun 2020 08:55:42: #2 finished! INFO @ Tue, 16 Jun 2020 08:55:42: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:55:42: #2 alternative fragment length(s) may be 4,48,520 bps INFO @ Tue, 16 Jun 2020 08:55:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.05_model.r WARNING @ Tue, 16 Jun 2020 08:55:42: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:55:42: #2 You may need to consider one of the other alternative d(s): 4,48,520 WARNING @ Tue, 16 Jun 2020 08:55:42: #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 08:55:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:55:42: #3 Pre-compute pvalue-qvalue table... 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 08:55:44: 4000000 INFO @ Tue, 16 Jun 2020 08:55:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.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 08:55:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:51: 5000000 INFO @ Tue, 16 Jun 2020 08:55:52: 1000000 INFO @ Tue, 16 Jun 2020 08:55:59: 6000000 INFO @ Tue, 16 Jun 2020 08:55:59: 2000000 INFO @ Tue, 16 Jun 2020 08:56:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:56:06: 7000000 INFO @ Tue, 16 Jun 2020 08:56:06: 3000000 INFO @ Tue, 16 Jun 2020 08:56:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:56:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:56:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.05_summits.bed INFO @ Tue, 16 Jun 2020 08:56:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (356 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:56:13: 8000000 INFO @ Tue, 16 Jun 2020 08:56:13: 4000000 INFO @ Tue, 16 Jun 2020 08:56:15: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:56:15: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:56:15: #1 total tags in treatment: 8243596 INFO @ Tue, 16 Jun 2020 08:56:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:56:15: #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 08:56:15: #1 tags after filtering in treatment: 8243596 INFO @ Tue, 16 Jun 2020 08:56:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:56:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:56:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:56:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:56:16: #2 number of paired peaks: 156 WARNING @ Tue, 16 Jun 2020 08:56:16: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Tue, 16 Jun 2020 08:56:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:56:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:56:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:56:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:56:16: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:56:16: #2 alternative fragment length(s) may be 4,48,520 bps INFO @ Tue, 16 Jun 2020 08:56:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.10_model.r WARNING @ Tue, 16 Jun 2020 08:56:16: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:56:16: #2 You may need to consider one of the other alternative d(s): 4,48,520 WARNING @ Tue, 16 Jun 2020 08:56:16: #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 08:56:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:56:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:56:20: 5000000 INFO @ Tue, 16 Jun 2020 08:56:27: 6000000 INFO @ Tue, 16 Jun 2020 08:56:34: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:56:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:56:40: 8000000 INFO @ Tue, 16 Jun 2020 08:56:42: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:56:42: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:56:42: #1 total tags in treatment: 8243596 INFO @ Tue, 16 Jun 2020 08:56:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:56:42: #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 08:56:42: #1 tags after filtering in treatment: 8243596 INFO @ Tue, 16 Jun 2020 08:56:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:56:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:56:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:56:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:56:43: #2 number of paired peaks: 156 WARNING @ Tue, 16 Jun 2020 08:56:43: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Tue, 16 Jun 2020 08:56:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:56:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:56:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:56:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:56:43: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:56:43: #2 alternative fragment length(s) may be 4,48,520 bps INFO @ Tue, 16 Jun 2020 08:56:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.20_model.r WARNING @ Tue, 16 Jun 2020 08:56:43: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:56:43: #2 You may need to consider one of the other alternative d(s): 4,48,520 WARNING @ Tue, 16 Jun 2020 08:56:43: #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 08:56:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:56:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:56:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:56:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:56:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.10_summits.bed INFO @ Tue, 16 Jun 2020 08:56:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (203 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:57:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082353/SRX4082353.20_summits.bed INFO @ Tue, 16 Jun 2020 08:57:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (73 records, 4 fields): 1 millis CompletedMACS2peakCalling