Job ID = 6366411 SRX = SRX146418 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:46:37 prefetch.2.10.7: 1) Downloading 'SRR494579'... 2020-06-15T22:46:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:47:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:47:14 prefetch.2.10.7: 'SRR494579' is valid 2020-06-15T22:47:14 prefetch.2.10.7: 1) 'SRR494579' was downloaded successfully Read 5513164 spots for SRR494579/SRR494579.sra Written 5513164 spots for SRR494579/SRR494579.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:52 5513164 reads; of these: 5513164 (100.00%) were unpaired; of these: 542908 (9.85%) aligned 0 times 4167114 (75.58%) aligned exactly 1 time 803142 (14.57%) aligned >1 times 90.15% overall alignment rate Time searching: 00:00:53 Overall time: 00:00:53 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] 349810 / 4970256 = 0.0704 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 07:49:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.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 07:49:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:49:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:50:01: 1000000 INFO @ Tue, 16 Jun 2020 07:50:07: 2000000 INFO @ Tue, 16 Jun 2020 07:50:13: 3000000 INFO @ Tue, 16 Jun 2020 07:50:19: 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 07:50:23: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:50:23: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:50:23: #1 total tags in treatment: 4620446 INFO @ Tue, 16 Jun 2020 07:50:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:50:23: #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 07:50:23: #1 tags after filtering in treatment: 4620446 INFO @ Tue, 16 Jun 2020 07:50:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:50:23: #1 finished! INFO @ Tue, 16 Jun 2020 07:50:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:50:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:50:23: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 07:50:23: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 07:50:23: start model_add_line... INFO @ Tue, 16 Jun 2020 07:50:23: start X-correlation... INFO @ Tue, 16 Jun 2020 07:50:23: end of X-cor INFO @ Tue, 16 Jun 2020 07:50:23: #2 finished! INFO @ Tue, 16 Jun 2020 07:50:23: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 07:50:23: #2 alternative fragment length(s) may be 3,42,568 bps INFO @ Tue, 16 Jun 2020 07:50:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.05_model.r WARNING @ Tue, 16 Jun 2020 07:50:23: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:50:23: #2 You may need to consider one of the other alternative d(s): 3,42,568 WARNING @ Tue, 16 Jun 2020 07:50:23: #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 07:50:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:50:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:50:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.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 07:50:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:50:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:50:30: 1000000 INFO @ Tue, 16 Jun 2020 07:50:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:50:35: 2000000 INFO @ Tue, 16 Jun 2020 07:50:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:50:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:50:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.05_summits.bed INFO @ Tue, 16 Jun 2020 07:50:38: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (523 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:50:40: 3000000 INFO @ Tue, 16 Jun 2020 07:50:45: 4000000 INFO @ Tue, 16 Jun 2020 07:50:48: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:50:48: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:50:48: #1 total tags in treatment: 4620446 INFO @ Tue, 16 Jun 2020 07:50:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:50:48: #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 07:50:48: #1 tags after filtering in treatment: 4620446 INFO @ Tue, 16 Jun 2020 07:50:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:50:48: #1 finished! INFO @ Tue, 16 Jun 2020 07:50:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:50:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:50:49: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 07:50:49: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 07:50:49: start model_add_line... INFO @ Tue, 16 Jun 2020 07:50:49: start X-correlation... INFO @ Tue, 16 Jun 2020 07:50:49: end of X-cor INFO @ Tue, 16 Jun 2020 07:50:49: #2 finished! INFO @ Tue, 16 Jun 2020 07:50:49: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 07:50:49: #2 alternative fragment length(s) may be 3,42,568 bps INFO @ Tue, 16 Jun 2020 07:50:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.10_model.r WARNING @ Tue, 16 Jun 2020 07:50:49: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:50:49: #2 You may need to consider one of the other alternative d(s): 3,42,568 WARNING @ Tue, 16 Jun 2020 07:50:49: #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 07:50:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:50:49: #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 07:50:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.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 07:50:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:50:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:50:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:51:00: 1000000 INFO @ Tue, 16 Jun 2020 07:51:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:51:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:51:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.10_summits.bed INFO @ Tue, 16 Jun 2020 07:51:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (211 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:51:05: 2000000 INFO @ Tue, 16 Jun 2020 07:51:10: 3000000 INFO @ Tue, 16 Jun 2020 07:51:15: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:51:18: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:51:18: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:51:18: #1 total tags in treatment: 4620446 INFO @ Tue, 16 Jun 2020 07:51:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:51:18: #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 07:51:18: #1 tags after filtering in treatment: 4620446 INFO @ Tue, 16 Jun 2020 07:51:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:51:18: #1 finished! INFO @ Tue, 16 Jun 2020 07:51:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:51:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:51:18: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 07:51:18: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 07:51:18: start model_add_line... INFO @ Tue, 16 Jun 2020 07:51:18: start X-correlation... INFO @ Tue, 16 Jun 2020 07:51:19: end of X-cor INFO @ Tue, 16 Jun 2020 07:51:19: #2 finished! INFO @ Tue, 16 Jun 2020 07:51:19: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 07:51:19: #2 alternative fragment length(s) may be 3,42,568 bps INFO @ Tue, 16 Jun 2020 07:51:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.20_model.r WARNING @ Tue, 16 Jun 2020 07:51:19: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:51:19: #2 You may need to consider one of the other alternative d(s): 3,42,568 WARNING @ Tue, 16 Jun 2020 07:51:19: #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 07:51:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:51:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:51:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:51:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:51:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:51:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX146418/SRX146418.20_summits.bed INFO @ Tue, 16 Jun 2020 07:51:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (69 records, 4 fields): 1 millis CompletedMACS2peakCalling