Job ID = 6366845 SRX = SRX2350744 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:02:53 prefetch.2.10.7: 1) Downloading 'SRR5024053'... 2020-06-15T23:02:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:04:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:04:01 prefetch.2.10.7: 'SRR5024053' is valid 2020-06-15T23:04:01 prefetch.2.10.7: 1) 'SRR5024053' was downloaded successfully Read 10506268 spots for SRR5024053/SRR5024053.sra Written 10506268 spots for SRR5024053/SRR5024053.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: 00:02:12 10506268 reads; of these: 10506268 (100.00%) were unpaired; of these: 140891 (1.34%) aligned 0 times 9031824 (85.97%) aligned exactly 1 time 1333553 (12.69%) aligned >1 times 98.66% overall alignment rate Time searching: 00:02:12 Overall time: 00:02:12 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] 682704 / 10365377 = 0.0659 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 08:10:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.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 08:10:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:23: 1000000 INFO @ Tue, 16 Jun 2020 08:10:28: 2000000 INFO @ Tue, 16 Jun 2020 08:10:33: 3000000 INFO @ Tue, 16 Jun 2020 08:10:37: 4000000 INFO @ Tue, 16 Jun 2020 08:10:42: 5000000 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 08:10:47: 6000000 INFO @ Tue, 16 Jun 2020 08:10:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.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 08:10:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:53: 7000000 INFO @ Tue, 16 Jun 2020 08:10:53: 1000000 INFO @ Tue, 16 Jun 2020 08:10:58: 8000000 INFO @ Tue, 16 Jun 2020 08:10:59: 2000000 INFO @ Tue, 16 Jun 2020 08:11:04: 9000000 INFO @ Tue, 16 Jun 2020 08:11:04: 3000000 INFO @ Tue, 16 Jun 2020 08:11:07: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:11:07: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:11:07: #1 total tags in treatment: 9682673 INFO @ Tue, 16 Jun 2020 08:11:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:07: #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 08:11:08: #1 tags after filtering in treatment: 9682673 INFO @ Tue, 16 Jun 2020 08:11:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:08: #2 number of paired peaks: 202 WARNING @ Tue, 16 Jun 2020 08:11:08: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:08: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:11:08: #2 alternative fragment length(s) may be 3,49,446 bps INFO @ Tue, 16 Jun 2020 08:11:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.05_model.r WARNING @ Tue, 16 Jun 2020 08:11:08: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:11:08: #2 You may need to consider one of the other alternative d(s): 3,49,446 WARNING @ Tue, 16 Jun 2020 08:11:08: #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 08:11:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:11:10: 4000000 INFO @ Tue, 16 Jun 2020 08:11:14: 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 08:11:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.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 08:11:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:19: 6000000 INFO @ Tue, 16 Jun 2020 08:11:23: 1000000 INFO @ Tue, 16 Jun 2020 08:11:24: 7000000 INFO @ Tue, 16 Jun 2020 08:11:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:27: 2000000 INFO @ Tue, 16 Jun 2020 08:11:29: 8000000 INFO @ Tue, 16 Jun 2020 08:11:32: 3000000 INFO @ Tue, 16 Jun 2020 08:11:35: 9000000 INFO @ Tue, 16 Jun 2020 08:11:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.05_summits.bed INFO @ Tue, 16 Jun 2020 08:11:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (527 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:11:37: 4000000 INFO @ Tue, 16 Jun 2020 08:11:38: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:11:38: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:11:38: #1 total tags in treatment: 9682673 INFO @ Tue, 16 Jun 2020 08:11:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:38: #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 08:11:38: #1 tags after filtering in treatment: 9682673 INFO @ Tue, 16 Jun 2020 08:11:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:39: #2 number of paired peaks: 202 WARNING @ Tue, 16 Jun 2020 08:11:39: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:39: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:11:39: #2 alternative fragment length(s) may be 3,49,446 bps INFO @ Tue, 16 Jun 2020 08:11:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.10_model.r WARNING @ Tue, 16 Jun 2020 08:11:39: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:11:39: #2 You may need to consider one of the other alternative d(s): 3,49,446 WARNING @ Tue, 16 Jun 2020 08:11:39: #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 08:11:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:11:42: 5000000 INFO @ Tue, 16 Jun 2020 08:11:48: 6000000 INFO @ Tue, 16 Jun 2020 08:11:53: 7000000 INFO @ Tue, 16 Jun 2020 08:11:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:58: 8000000 INFO @ Tue, 16 Jun 2020 08:12:03: 9000000 INFO @ Tue, 16 Jun 2020 08:12:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.10_summits.bed INFO @ Tue, 16 Jun 2020 08:12:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (223 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:12:07: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:12:07: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:12:07: #1 total tags in treatment: 9682673 INFO @ Tue, 16 Jun 2020 08:12:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:07: #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 08:12:07: #1 tags after filtering in treatment: 9682673 INFO @ Tue, 16 Jun 2020 08:12:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:08: #2 number of paired peaks: 202 WARNING @ Tue, 16 Jun 2020 08:12:08: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Tue, 16 Jun 2020 08:12:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:08: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:12:08: #2 alternative fragment length(s) may be 3,49,446 bps INFO @ Tue, 16 Jun 2020 08:12:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.20_model.r BedGraph に変換しました。 BigWig に変換中... WARNING @ Tue, 16 Jun 2020 08:12:08: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:12:08: #2 You may need to consider one of the other alternative d(s): 3,49,446 WARNING @ Tue, 16 Jun 2020 08:12:08: #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 08:12:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:12:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:12:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350744/SRX2350744.20_summits.bed INFO @ Tue, 16 Jun 2020 08:12:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (81 records, 4 fields): 1 millis CompletedMACS2peakCalling