Job ID = 6366853 SRX = SRX2350752 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:13:01 prefetch.2.10.7: 1) Downloading 'SRR5024061'... 2020-06-15T23:13:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:14:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:14:14 prefetch.2.10.7: 1) 'SRR5024061' was downloaded successfully Read 12454882 spots for SRR5024061/SRR5024061.sra Written 12454882 spots for SRR5024061/SRR5024061.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: 00:02:45 12454882 reads; of these: 12454882 (100.00%) were unpaired; of these: 161246 (1.29%) aligned 0 times 10796582 (86.69%) aligned exactly 1 time 1497054 (12.02%) aligned >1 times 98.71% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 1622794 / 12293636 = 0.1320 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 08:20:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.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 08:20:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:04: 1000000 INFO @ Tue, 16 Jun 2020 08:21:10: 2000000 INFO @ Tue, 16 Jun 2020 08:21:17: 3000000 INFO @ Tue, 16 Jun 2020 08:21:23: 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 08:21:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.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 08:21:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:30: 5000000 INFO @ Tue, 16 Jun 2020 08:21:34: 1000000 INFO @ Tue, 16 Jun 2020 08:21:36: 6000000 INFO @ Tue, 16 Jun 2020 08:21:41: 2000000 INFO @ Tue, 16 Jun 2020 08:21:43: 7000000 INFO @ Tue, 16 Jun 2020 08:21:48: 3000000 INFO @ Tue, 16 Jun 2020 08:21:50: 8000000 INFO @ Tue, 16 Jun 2020 08:21:55: 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 08:21:57: 9000000 INFO @ Tue, 16 Jun 2020 08:21:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.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 08:21:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:22:02: 5000000 INFO @ Tue, 16 Jun 2020 08:22:04: 10000000 INFO @ Tue, 16 Jun 2020 08:22:05: 1000000 INFO @ Tue, 16 Jun 2020 08:22:09: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:22:09: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:22:09: #1 total tags in treatment: 10670842 INFO @ Tue, 16 Jun 2020 08:22:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:09: #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 08:22:09: #1 tags after filtering in treatment: 10670842 INFO @ Tue, 16 Jun 2020 08:22:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:09: 6000000 INFO @ Tue, 16 Jun 2020 08:22:10: #2 number of paired peaks: 161 WARNING @ Tue, 16 Jun 2020 08:22:10: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:10: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:22:10: #2 alternative fragment length(s) may be 3,50,181,207,241,256,403,487 bps INFO @ Tue, 16 Jun 2020 08:22:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.05_model.r WARNING @ Tue, 16 Jun 2020 08:22:10: #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 08:22:10: #2 You may need to consider one of the other alternative d(s): 3,50,181,207,241,256,403,487 WARNING @ Tue, 16 Jun 2020 08:22:10: #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 08:22:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:11: 2000000 INFO @ Tue, 16 Jun 2020 08:22:16: 7000000 INFO @ Tue, 16 Jun 2020 08:22:17: 3000000 INFO @ Tue, 16 Jun 2020 08:22:23: 8000000 INFO @ Tue, 16 Jun 2020 08:22:24: 4000000 INFO @ Tue, 16 Jun 2020 08:22:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:30: 5000000 INFO @ Tue, 16 Jun 2020 08:22:30: 9000000 INFO @ Tue, 16 Jun 2020 08:22:36: 6000000 INFO @ Tue, 16 Jun 2020 08:22:37: 10000000 INFO @ Tue, 16 Jun 2020 08:22:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.05_summits.bed INFO @ Tue, 16 Jun 2020 08:22:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (776 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:22:42: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:22:42: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:22:42: #1 total tags in treatment: 10670842 INFO @ Tue, 16 Jun 2020 08:22:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:42: #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 08:22:42: #1 tags after filtering in treatment: 10670842 INFO @ Tue, 16 Jun 2020 08:22:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:42: 7000000 INFO @ Tue, 16 Jun 2020 08:22:43: #2 number of paired peaks: 161 WARNING @ Tue, 16 Jun 2020 08:22:43: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:43: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:22:43: #2 alternative fragment length(s) may be 3,50,181,207,241,256,403,487 bps INFO @ Tue, 16 Jun 2020 08:22:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.10_model.r WARNING @ Tue, 16 Jun 2020 08:22:43: #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 08:22:43: #2 You may need to consider one of the other alternative d(s): 3,50,181,207,241,256,403,487 WARNING @ Tue, 16 Jun 2020 08:22:43: #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 08:22:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:43: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:22:48: 8000000 INFO @ Tue, 16 Jun 2020 08:22:54: 9000000 INFO @ Tue, 16 Jun 2020 08:22:59: 10000000 INFO @ Tue, 16 Jun 2020 08:23:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:23:03: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:23:03: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:23:03: #1 total tags in treatment: 10670842 INFO @ Tue, 16 Jun 2020 08:23:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:03: #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 08:23:03: #1 tags after filtering in treatment: 10670842 INFO @ Tue, 16 Jun 2020 08:23:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:04: #2 number of paired peaks: 161 WARNING @ Tue, 16 Jun 2020 08:23:04: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 16 Jun 2020 08:23:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:04: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:23:04: #2 alternative fragment length(s) may be 3,50,181,207,241,256,403,487 bps INFO @ Tue, 16 Jun 2020 08:23:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.20_model.r WARNING @ Tue, 16 Jun 2020 08:23:04: #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 08:23:04: #2 You may need to consider one of the other alternative d(s): 3,50,181,207,241,256,403,487 WARNING @ Tue, 16 Jun 2020 08:23:04: #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 08:23:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:23:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.10_summits.bed INFO @ Tue, 16 Jun 2020 08:23:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (203 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:23:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:23:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350752/SRX2350752.20_summits.bed INFO @ Tue, 16 Jun 2020 08:23:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (65 records, 4 fields): 1 millis CompletedMACS2peakCalling