Job ID = 6366841 SRX = SRX2350740 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:03:38 prefetch.2.10.7: 1) Downloading 'SRR5024049'... 2020-06-15T23:03:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:04:44 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:04:45 prefetch.2.10.7: 'SRR5024049' is valid 2020-06-15T23:04:45 prefetch.2.10.7: 1) 'SRR5024049' was downloaded successfully Read 11618832 spots for SRR5024049/SRR5024049.sra Written 11618832 spots for SRR5024049/SRR5024049.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: 00:02:30 11618832 reads; of these: 11618832 (100.00%) were unpaired; of these: 99747 (0.86%) aligned 0 times 10113887 (87.05%) aligned exactly 1 time 1405198 (12.09%) aligned >1 times 99.14% overall alignment rate Time searching: 00:02:30 Overall time: 00:02:30 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] 1347521 / 11519085 = 0.1170 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 08:10:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.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 08:10:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:03: 1000000 INFO @ Tue, 16 Jun 2020 08:11:10: 2000000 INFO @ Tue, 16 Jun 2020 08:11:17: 3000000 INFO @ Tue, 16 Jun 2020 08:11:24: 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 08:11:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.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 08:11:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:31: 5000000 INFO @ Tue, 16 Jun 2020 08:11:34: 1000000 INFO @ Tue, 16 Jun 2020 08:11:39: 6000000 INFO @ Tue, 16 Jun 2020 08:11:42: 2000000 INFO @ Tue, 16 Jun 2020 08:11:47: 7000000 INFO @ Tue, 16 Jun 2020 08:11:50: 3000000 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 08:11:55: 8000000 INFO @ Tue, 16 Jun 2020 08:11:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.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 08:11:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:58: 4000000 INFO @ Tue, 16 Jun 2020 08:12:03: 9000000 INFO @ Tue, 16 Jun 2020 08:12:04: 1000000 INFO @ Tue, 16 Jun 2020 08:12:06: 5000000 INFO @ Tue, 16 Jun 2020 08:12:11: 10000000 INFO @ Tue, 16 Jun 2020 08:12:12: 2000000 INFO @ Tue, 16 Jun 2020 08:12:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:12:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:12:12: #1 total tags in treatment: 10171564 INFO @ Tue, 16 Jun 2020 08:12:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:12: #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 08:12:12: #1 tags after filtering in treatment: 10171564 INFO @ Tue, 16 Jun 2020 08:12:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:13: #2 number of paired peaks: 140 WARNING @ Tue, 16 Jun 2020 08:12:13: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 16 Jun 2020 08:12:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:13: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:12:13: #2 alternative fragment length(s) may be 3,47,206,434,438,468 bps INFO @ Tue, 16 Jun 2020 08:12:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.05_model.r WARNING @ Tue, 16 Jun 2020 08:12:13: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:12:13: #2 You may need to consider one of the other alternative d(s): 3,47,206,434,438,468 WARNING @ Tue, 16 Jun 2020 08:12:13: #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 08:12:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:12:14: 6000000 INFO @ Tue, 16 Jun 2020 08:12:20: 3000000 INFO @ Tue, 16 Jun 2020 08:12:22: 7000000 INFO @ Tue, 16 Jun 2020 08:12:28: 4000000 INFO @ Tue, 16 Jun 2020 08:12:30: 8000000 INFO @ Tue, 16 Jun 2020 08:12:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:36: 5000000 INFO @ Tue, 16 Jun 2020 08:12:38: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:12:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.05_summits.bed INFO @ Tue, 16 Jun 2020 08:12:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (468 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:12:44: 6000000 INFO @ Tue, 16 Jun 2020 08:12:46: 10000000 INFO @ Tue, 16 Jun 2020 08:12:48: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:12:48: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:12:48: #1 total tags in treatment: 10171564 INFO @ Tue, 16 Jun 2020 08:12:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:48: #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 08:12:48: #1 tags after filtering in treatment: 10171564 INFO @ Tue, 16 Jun 2020 08:12:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:48: #2 number of paired peaks: 140 WARNING @ Tue, 16 Jun 2020 08:12:48: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 16 Jun 2020 08:12:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:49: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:12:49: #2 alternative fragment length(s) may be 3,47,206,434,438,468 bps INFO @ Tue, 16 Jun 2020 08:12:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.10_model.r WARNING @ Tue, 16 Jun 2020 08:12:49: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:12:49: #2 You may need to consider one of the other alternative d(s): 3,47,206,434,438,468 WARNING @ Tue, 16 Jun 2020 08:12:49: #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 08:12:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:12:51: 7000000 INFO @ Tue, 16 Jun 2020 08:12:59: 8000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:13:06: 9000000 INFO @ Tue, 16 Jun 2020 08:13:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:13: 10000000 INFO @ Tue, 16 Jun 2020 08:13:14: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:13:14: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:13:14: #1 total tags in treatment: 10171564 INFO @ Tue, 16 Jun 2020 08:13:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:14: #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 08:13:14: #1 tags after filtering in treatment: 10171564 INFO @ Tue, 16 Jun 2020 08:13:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:15: #2 number of paired peaks: 140 WARNING @ Tue, 16 Jun 2020 08:13:15: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:15: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:13:15: #2 alternative fragment length(s) may be 3,47,206,434,438,468 bps INFO @ Tue, 16 Jun 2020 08:13:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.20_model.r WARNING @ Tue, 16 Jun 2020 08:13:15: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:13:15: #2 You may need to consider one of the other alternative d(s): 3,47,206,434,438,468 WARNING @ Tue, 16 Jun 2020 08:13:15: #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 08:13:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.10_summits.bed INFO @ Tue, 16 Jun 2020 08:13:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (215 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:13:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350740/SRX2350740.20_summits.bed INFO @ Tue, 16 Jun 2020 08:13:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (80 records, 4 fields): 1 millis CompletedMACS2peakCalling