Job ID = 6366155 SRX = SRX065680 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:40:36 prefetch.2.10.7: 1) Downloading 'SRR217386'... 2020-06-15T22:40:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:41:13 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:41:13 prefetch.2.10.7: 'SRR217386' is valid 2020-06-15T22:41:13 prefetch.2.10.7: 1) 'SRR217386' was downloaded successfully Read 5624697 spots for SRR217386/SRR217386.sra Written 5624697 spots for SRR217386/SRR217386.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: 00:00:54 5624697 reads; of these: 5624697 (100.00%) were unpaired; of these: 110107 (1.96%) aligned 0 times 4552693 (80.94%) aligned exactly 1 time 961897 (17.10%) aligned >1 times 98.04% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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] 564537 / 5514590 = 0.1024 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 07:43:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.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 07:43:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:54: 1000000 INFO @ Tue, 16 Jun 2020 07:43:59: 2000000 INFO @ Tue, 16 Jun 2020 07:44:04: 3000000 INFO @ Tue, 16 Jun 2020 07:44:09: 4000000 INFO @ Tue, 16 Jun 2020 07:44:13: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:44:13: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:44:13: #1 total tags in treatment: 4950053 INFO @ Tue, 16 Jun 2020 07:44:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:13: #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 07:44:13: #1 tags after filtering in treatment: 4950053 INFO @ Tue, 16 Jun 2020 07:44:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:13: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:14: #2 number of paired peaks: 504 WARNING @ Tue, 16 Jun 2020 07:44:14: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Tue, 16 Jun 2020 07:44:14: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:14: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:14: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:14: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:14: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 07:44:14: #2 alternative fragment length(s) may be 2,35,593,596 bps INFO @ Tue, 16 Jun 2020 07:44:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.05_model.r WARNING @ Tue, 16 Jun 2020 07:44:14: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:44:14: #2 You may need to consider one of the other alternative d(s): 2,35,593,596 WARNING @ Tue, 16 Jun 2020 07:44:14: #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 07:44:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:14: #3 Pre-compute pvalue-qvalue table... 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 07:44:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.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 07:44:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:24: 1000000 INFO @ Tue, 16 Jun 2020 07:44:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:29: 2000000 INFO @ Tue, 16 Jun 2020 07:44:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.05_summits.bed INFO @ Tue, 16 Jun 2020 07:44:30: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (537 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:44:33: 3000000 INFO @ Tue, 16 Jun 2020 07:44:38: 4000000 INFO @ Tue, 16 Jun 2020 07:44:43: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:44:43: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:44:43: #1 total tags in treatment: 4950053 INFO @ Tue, 16 Jun 2020 07:44:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:43: #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 07:44:43: #1 tags after filtering in treatment: 4950053 INFO @ Tue, 16 Jun 2020 07:44:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:43: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:43: #2 number of paired peaks: 504 WARNING @ Tue, 16 Jun 2020 07:44:43: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Tue, 16 Jun 2020 07:44:43: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:43: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:43: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:43: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:43: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 07:44:43: #2 alternative fragment length(s) may be 2,35,593,596 bps INFO @ Tue, 16 Jun 2020 07:44:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.10_model.r WARNING @ Tue, 16 Jun 2020 07:44:43: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:44:43: #2 You may need to consider one of the other alternative d(s): 2,35,593,596 WARNING @ Tue, 16 Jun 2020 07:44:43: #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 07:44:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:43: #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 07:44:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.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 07:44:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:54: 1000000 INFO @ Tue, 16 Jun 2020 07:44:59: 2000000 INFO @ Tue, 16 Jun 2020 07:44:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.10_summits.bed INFO @ Tue, 16 Jun 2020 07:44:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (262 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:45:04: 3000000 INFO @ Tue, 16 Jun 2020 07:45:08: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:45:13: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:45:13: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:45:13: #1 total tags in treatment: 4950053 INFO @ Tue, 16 Jun 2020 07:45:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:13: #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 07:45:13: #1 tags after filtering in treatment: 4950053 INFO @ Tue, 16 Jun 2020 07:45:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:13: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:13: #2 number of paired peaks: 504 WARNING @ Tue, 16 Jun 2020 07:45:13: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Tue, 16 Jun 2020 07:45:13: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:13: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:13: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:13: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:13: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 07:45:13: #2 alternative fragment length(s) may be 2,35,593,596 bps INFO @ Tue, 16 Jun 2020 07:45:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.20_model.r WARNING @ Tue, 16 Jun 2020 07:45:13: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:45:13: #2 You may need to consider one of the other alternative d(s): 2,35,593,596 WARNING @ Tue, 16 Jun 2020 07:45:13: #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 07:45:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:45:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065680/SRX065680.20_summits.bed INFO @ Tue, 16 Jun 2020 07:45:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (71 records, 4 fields): 1 millis CompletedMACS2peakCalling