Job ID = 6365850 SRX = SRX003816 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:23:14 prefetch.2.10.7: 1) Downloading 'SRR015056'... 2020-06-15T22:23:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:32:42 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:32:42 prefetch.2.10.7: 1) 'SRR015056' was downloaded successfully Read 11736857 spots for SRR015056/SRR015056.sra Written 11736857 spots for SRR015056/SRR015056.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: 00:01:26 11736857 reads; of these: 11736857 (100.00%) were unpaired; of these: 5158814 (43.95%) aligned 0 times 5412472 (46.12%) aligned exactly 1 time 1165571 (9.93%) aligned >1 times 56.05% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 450298 / 6578043 = 0.0685 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 07:36:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.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 07:36:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:36:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:36:52: 1000000 INFO @ Tue, 16 Jun 2020 07:36:56: 2000000 INFO @ Tue, 16 Jun 2020 07:37:01: 3000000 INFO @ Tue, 16 Jun 2020 07:37:06: 4000000 INFO @ Tue, 16 Jun 2020 07:37:11: 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 07:37:16: 6000000 INFO @ Tue, 16 Jun 2020 07:37:16: #1 tag size is determined as 33 bps INFO @ Tue, 16 Jun 2020 07:37:16: #1 tag size = 33 INFO @ Tue, 16 Jun 2020 07:37:16: #1 total tags in treatment: 6127745 INFO @ Tue, 16 Jun 2020 07:37:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:37:16: #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 07:37:16: #1 tags after filtering in treatment: 6127745 INFO @ Tue, 16 Jun 2020 07:37:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:37:16: #1 finished! INFO @ Tue, 16 Jun 2020 07:37:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:37:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:37:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.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 07:37:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:37:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:37:17: #2 number of paired peaks: 346 WARNING @ Tue, 16 Jun 2020 07:37:17: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Tue, 16 Jun 2020 07:37:17: start model_add_line... INFO @ Tue, 16 Jun 2020 07:37:17: start X-correlation... INFO @ Tue, 16 Jun 2020 07:37:17: end of X-cor INFO @ Tue, 16 Jun 2020 07:37:17: #2 finished! INFO @ Tue, 16 Jun 2020 07:37:17: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 07:37:17: #2 alternative fragment length(s) may be 4,31,520,546 bps INFO @ Tue, 16 Jun 2020 07:37:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.05_model.r WARNING @ Tue, 16 Jun 2020 07:37:17: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:37:17: #2 You may need to consider one of the other alternative d(s): 4,31,520,546 WARNING @ Tue, 16 Jun 2020 07:37:17: #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 07:37:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:37:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:37:22: 1000000 INFO @ Tue, 16 Jun 2020 07:37:27: 2000000 INFO @ Tue, 16 Jun 2020 07:37:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:37:32: 3000000 INFO @ Tue, 16 Jun 2020 07:37:37: 4000000 INFO @ Tue, 16 Jun 2020 07:37:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:37:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:37:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.05_summits.bed INFO @ Tue, 16 Jun 2020 07:37:37: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (486 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:37:42: 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 07:37:47: 6000000 INFO @ Tue, 16 Jun 2020 07:37:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.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 07:37:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:37:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:37:48: #1 tag size is determined as 33 bps INFO @ Tue, 16 Jun 2020 07:37:48: #1 tag size = 33 INFO @ Tue, 16 Jun 2020 07:37:48: #1 total tags in treatment: 6127745 INFO @ Tue, 16 Jun 2020 07:37:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:37:48: #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 07:37:48: #1 tags after filtering in treatment: 6127745 INFO @ Tue, 16 Jun 2020 07:37:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:37:48: #1 finished! INFO @ Tue, 16 Jun 2020 07:37:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:37:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:37:48: #2 number of paired peaks: 346 WARNING @ Tue, 16 Jun 2020 07:37:48: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Tue, 16 Jun 2020 07:37:48: start model_add_line... INFO @ Tue, 16 Jun 2020 07:37:48: start X-correlation... INFO @ Tue, 16 Jun 2020 07:37:48: end of X-cor INFO @ Tue, 16 Jun 2020 07:37:48: #2 finished! INFO @ Tue, 16 Jun 2020 07:37:48: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 07:37:48: #2 alternative fragment length(s) may be 4,31,520,546 bps INFO @ Tue, 16 Jun 2020 07:37:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.10_model.r WARNING @ Tue, 16 Jun 2020 07:37:48: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:37:48: #2 You may need to consider one of the other alternative d(s): 4,31,520,546 WARNING @ Tue, 16 Jun 2020 07:37:48: #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 07:37:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:37:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:37:52: 1000000 INFO @ Tue, 16 Jun 2020 07:37:57: 2000000 INFO @ Tue, 16 Jun 2020 07:38:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:38:02: 3000000 INFO @ Tue, 16 Jun 2020 07:38:07: 4000000 INFO @ Tue, 16 Jun 2020 07:38:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:38:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:38:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.10_summits.bed INFO @ Tue, 16 Jun 2020 07:38:09: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (208 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:38:12: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:38:17: 6000000 INFO @ Tue, 16 Jun 2020 07:38:18: #1 tag size is determined as 33 bps INFO @ Tue, 16 Jun 2020 07:38:18: #1 tag size = 33 INFO @ Tue, 16 Jun 2020 07:38:18: #1 total tags in treatment: 6127745 INFO @ Tue, 16 Jun 2020 07:38:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:38:18: #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 07:38:18: #1 tags after filtering in treatment: 6127745 INFO @ Tue, 16 Jun 2020 07:38:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:38:18: #1 finished! INFO @ Tue, 16 Jun 2020 07:38:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:38:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:38:18: #2 number of paired peaks: 346 WARNING @ Tue, 16 Jun 2020 07:38:18: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Tue, 16 Jun 2020 07:38:18: start model_add_line... INFO @ Tue, 16 Jun 2020 07:38:18: start X-correlation... INFO @ Tue, 16 Jun 2020 07:38:18: end of X-cor INFO @ Tue, 16 Jun 2020 07:38:18: #2 finished! INFO @ Tue, 16 Jun 2020 07:38:18: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 07:38:18: #2 alternative fragment length(s) may be 4,31,520,546 bps INFO @ Tue, 16 Jun 2020 07:38:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.20_model.r WARNING @ Tue, 16 Jun 2020 07:38:18: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:38:18: #2 You may need to consider one of the other alternative d(s): 4,31,520,546 WARNING @ Tue, 16 Jun 2020 07:38:18: #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 07:38:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:38:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:38:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:38:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:38:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:38:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX003816/SRX003816.20_summits.bed INFO @ Tue, 16 Jun 2020 07:38:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (54 records, 4 fields): 1 millis CompletedMACS2peakCalling