Job ID = 6459122 SRX = SRX6420686 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:58:20 prefetch.2.10.7: 1) Downloading 'SRR9659706'... 2020-06-21T12:58:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:58:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:58:56 prefetch.2.10.7: 'SRR9659706' is valid 2020-06-21T12:58:56 prefetch.2.10.7: 1) 'SRR9659706' was downloaded successfully 2020-06-21T12:58:56 prefetch.2.10.7: 'SRR9659706' has 0 unresolved dependencies Read 3194173 spots for SRR9659706/SRR9659706.sra Written 3194173 spots for SRR9659706/SRR9659706.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: 00:00:51 3194173 reads; of these: 3194173 (100.00%) were unpaired; of these: 538 (0.02%) aligned 0 times 2394837 (74.98%) aligned exactly 1 time 798798 (25.01%) aligned >1 times 99.98% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 168953 / 3193635 = 0.0529 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 @ Sun, 21 Jun 2020 22:01:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 22:01:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:01:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:01:17: 1000000 INFO @ Sun, 21 Jun 2020 22:01:22: 2000000 INFO @ Sun, 21 Jun 2020 22:01:28: 3000000 INFO @ Sun, 21 Jun 2020 22:01:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:01:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:01:28: #1 total tags in treatment: 3024682 INFO @ Sun, 21 Jun 2020 22:01:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:01:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:01:28: #1 tags after filtering in treatment: 3024430 INFO @ Sun, 21 Jun 2020 22:01:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:01:28: #1 finished! INFO @ Sun, 21 Jun 2020 22:01:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:01:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:01:29: #2 number of paired peaks: 540 WARNING @ Sun, 21 Jun 2020 22:01:29: Fewer paired peaks (540) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 540 pairs to build model! INFO @ Sun, 21 Jun 2020 22:01:29: start model_add_line... INFO @ Sun, 21 Jun 2020 22:01:29: start X-correlation... INFO @ Sun, 21 Jun 2020 22:01:29: end of X-cor INFO @ Sun, 21 Jun 2020 22:01:29: #2 finished! INFO @ Sun, 21 Jun 2020 22:01:29: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 22:01:29: #2 alternative fragment length(s) may be 52,475,501,546,592 bps INFO @ Sun, 21 Jun 2020 22:01:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.05_model.r WARNING @ Sun, 21 Jun 2020 22:01:29: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:01:29: #2 You may need to consider one of the other alternative d(s): 52,475,501,546,592 WARNING @ Sun, 21 Jun 2020 22:01:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:01:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:01:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:01:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:01:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:01:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:01:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.05_summits.bed INFO @ Sun, 21 Jun 2020 22:01:40: Done! pass1 - making usageList (178 chroms): 1 millis 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 pass2 - checking and writing primary data (391 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:01:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 22:01:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:01:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:01:48: 1000000 INFO @ Sun, 21 Jun 2020 22:01:54: 2000000 INFO @ Sun, 21 Jun 2020 22:02:00: 3000000 INFO @ Sun, 21 Jun 2020 22:02:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:02:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:02:00: #1 total tags in treatment: 3024682 INFO @ Sun, 21 Jun 2020 22:02:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:02:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:02:01: #1 tags after filtering in treatment: 3024430 INFO @ Sun, 21 Jun 2020 22:02:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:02:01: #1 finished! INFO @ Sun, 21 Jun 2020 22:02:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:02:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:02:01: #2 number of paired peaks: 540 WARNING @ Sun, 21 Jun 2020 22:02:01: Fewer paired peaks (540) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 540 pairs to build model! INFO @ Sun, 21 Jun 2020 22:02:01: start model_add_line... INFO @ Sun, 21 Jun 2020 22:02:01: start X-correlation... INFO @ Sun, 21 Jun 2020 22:02:01: end of X-cor INFO @ Sun, 21 Jun 2020 22:02:01: #2 finished! INFO @ Sun, 21 Jun 2020 22:02:01: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 22:02:01: #2 alternative fragment length(s) may be 52,475,501,546,592 bps INFO @ Sun, 21 Jun 2020 22:02:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.10_model.r WARNING @ Sun, 21 Jun 2020 22:02:01: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:02:01: #2 You may need to consider one of the other alternative d(s): 52,475,501,546,592 WARNING @ Sun, 21 Jun 2020 22:02:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:02:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:02:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:02:08: #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 @ Sun, 21 Jun 2020 22:02:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:02:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:02:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.10_summits.bed INFO @ Sun, 21 Jun 2020 22:02:11: Done! pass1 - making usageList (93 chroms): 0 millis pass2 - checking and writing primary data (190 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:02:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 22:02:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:02:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:02:18: 1000000 INFO @ Sun, 21 Jun 2020 22:02:23: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:02:28: 3000000 INFO @ Sun, 21 Jun 2020 22:02:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:02:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:02:29: #1 total tags in treatment: 3024682 INFO @ Sun, 21 Jun 2020 22:02:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:02:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:02:29: #1 tags after filtering in treatment: 3024430 INFO @ Sun, 21 Jun 2020 22:02:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:02:29: #1 finished! INFO @ Sun, 21 Jun 2020 22:02:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:02:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:02:29: #2 number of paired peaks: 540 WARNING @ Sun, 21 Jun 2020 22:02:29: Fewer paired peaks (540) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 540 pairs to build model! INFO @ Sun, 21 Jun 2020 22:02:29: start model_add_line... INFO @ Sun, 21 Jun 2020 22:02:29: start X-correlation... INFO @ Sun, 21 Jun 2020 22:02:29: end of X-cor INFO @ Sun, 21 Jun 2020 22:02:29: #2 finished! INFO @ Sun, 21 Jun 2020 22:02:29: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 22:02:29: #2 alternative fragment length(s) may be 52,475,501,546,592 bps INFO @ Sun, 21 Jun 2020 22:02:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.20_model.r WARNING @ Sun, 21 Jun 2020 22:02:29: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:02:29: #2 You may need to consider one of the other alternative d(s): 52,475,501,546,592 WARNING @ Sun, 21 Jun 2020 22:02:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:02:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:02:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:02:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:02:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:02:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:02:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6420686/SRX6420686.20_summits.bed INFO @ Sun, 21 Jun 2020 22:02:40: Done! pass1 - making usageList (50 chroms): 1 millis pass2 - checking and writing primary data (72 records, 4 fields): 3 millis CompletedMACS2peakCalling