Job ID = 6369053 SRX = SRX997752 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:38:01 prefetch.2.10.7: 1) Downloading 'SRR1977499'... 2020-06-16T00:38:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:42:07 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:42:07 prefetch.2.10.7: 1) 'SRR1977499' was downloaded successfully Read 36880923 spots for SRR1977499/SRR1977499.sra Written 36880923 spots for SRR1977499/SRR1977499.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: 00:05:31 36880923 reads; of these: 36880923 (100.00%) were unpaired; of these: 7915665 (21.46%) aligned 0 times 22901941 (62.10%) aligned exactly 1 time 6063317 (16.44%) aligned >1 times 78.54% overall alignment rate Time searching: 00:05:31 Overall time: 00:05:31 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] 25611832 / 28965258 = 0.8842 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 09:53:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.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 09:53:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:18: 1000000 INFO @ Tue, 16 Jun 2020 09:53:23: 2000000 INFO @ Tue, 16 Jun 2020 09:53:28: 3000000 INFO @ Tue, 16 Jun 2020 09:53:30: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:53:30: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:53:30: #1 total tags in treatment: 3353426 INFO @ Tue, 16 Jun 2020 09:53:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:30: #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 09:53:30: #1 tags after filtering in treatment: 3353426 INFO @ Tue, 16 Jun 2020 09:53:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:30: #2 number of paired peaks: 991 WARNING @ Tue, 16 Jun 2020 09:53:30: Fewer paired peaks (991) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 991 pairs to build model! INFO @ Tue, 16 Jun 2020 09:53:30: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:30: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 09:53:30: #2 alternative fragment length(s) may be 3,37 bps INFO @ Tue, 16 Jun 2020 09:53:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.05_model.r WARNING @ Tue, 16 Jun 2020 09:53:30: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:53:30: #2 You may need to consider one of the other alternative d(s): 3,37 WARNING @ Tue, 16 Jun 2020 09:53:30: #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 09:53:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:37: #3 Call peaks for each chromosome... 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 09:53:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.05_summits.bed INFO @ Tue, 16 Jun 2020 09:53:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2790 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:53:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.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 09:53:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:48: 1000000 INFO @ Tue, 16 Jun 2020 09:53:53: 2000000 INFO @ Tue, 16 Jun 2020 09:53:58: 3000000 INFO @ Tue, 16 Jun 2020 09:54:00: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:54:00: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:54:00: #1 total tags in treatment: 3353426 INFO @ Tue, 16 Jun 2020 09:54:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:00: #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 09:54:00: #1 tags after filtering in treatment: 3353426 INFO @ Tue, 16 Jun 2020 09:54:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:00: #2 number of paired peaks: 991 WARNING @ Tue, 16 Jun 2020 09:54:00: Fewer paired peaks (991) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 991 pairs to build model! INFO @ Tue, 16 Jun 2020 09:54:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:00: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 09:54:00: #2 alternative fragment length(s) may be 3,37 bps INFO @ Tue, 16 Jun 2020 09:54:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.10_model.r WARNING @ Tue, 16 Jun 2020 09:54:00: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:54:00: #2 You may need to consider one of the other alternative d(s): 3,37 WARNING @ Tue, 16 Jun 2020 09:54:00: #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 09:54:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:07: #3 Call peaks for each chromosome... 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 09:54:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.10_summits.bed INFO @ Tue, 16 Jun 2020 09:54:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (886 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:54:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.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 09:54:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:54:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:54:18: 1000000 INFO @ Tue, 16 Jun 2020 09:54:25: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:54:31: 3000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:54:33: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:54:33: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:54:33: #1 total tags in treatment: 3353426 INFO @ Tue, 16 Jun 2020 09:54:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:33: #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 09:54:33: #1 tags after filtering in treatment: 3353426 INFO @ Tue, 16 Jun 2020 09:54:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:34: #2 number of paired peaks: 991 WARNING @ Tue, 16 Jun 2020 09:54:34: Fewer paired peaks (991) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 991 pairs to build model! INFO @ Tue, 16 Jun 2020 09:54:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:34: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 09:54:34: #2 alternative fragment length(s) may be 3,37 bps INFO @ Tue, 16 Jun 2020 09:54:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.20_model.r WARNING @ Tue, 16 Jun 2020 09:54:34: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:54:34: #2 You may need to consider one of the other alternative d(s): 3,37 WARNING @ Tue, 16 Jun 2020 09:54:34: #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 09:54:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:54:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX997752/SRX997752.20_summits.bed INFO @ Tue, 16 Jun 2020 09:54:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (251 records, 4 fields): 2 millis CompletedMACS2peakCalling