Job ID = 6453373 SRX = SRX1120704 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:24:32 prefetch.2.10.7: 1) Downloading 'SRR2129936'... 2020-06-21T08:24:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:27:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:27:49 prefetch.2.10.7: 'SRR2129936' is valid 2020-06-21T08:27:49 prefetch.2.10.7: 1) 'SRR2129936' was downloaded successfully Read 10383971 spots for SRR2129936/SRR2129936.sra Written 10383971 spots for SRR2129936/SRR2129936.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: 00:03:42 10383971 reads; of these: 10383971 (100.00%) were unpaired; of these: 2490585 (23.98%) aligned 0 times 6595815 (63.52%) aligned exactly 1 time 1297571 (12.50%) aligned >1 times 76.02% overall alignment rate Time searching: 00:03:42 Overall time: 00:03:42 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] 3665819 / 7893386 = 0.4644 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 17:35:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.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 17:35:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:35:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:35:45: 1000000 INFO @ Sun, 21 Jun 2020 17:35:52: 2000000 INFO @ Sun, 21 Jun 2020 17:35:59: 3000000 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 17:36:06: 4000000 INFO @ Sun, 21 Jun 2020 17:36:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.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 17:36:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:36:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:36:08: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:36:08: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:36:08: #1 total tags in treatment: 4227567 INFO @ Sun, 21 Jun 2020 17:36:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:36:08: #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 17:36:09: #1 tags after filtering in treatment: 4227338 INFO @ Sun, 21 Jun 2020 17:36:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:36:09: #1 finished! INFO @ Sun, 21 Jun 2020 17:36:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:36:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:36:09: #2 number of paired peaks: 544 WARNING @ Sun, 21 Jun 2020 17:36:09: Fewer paired peaks (544) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 544 pairs to build model! INFO @ Sun, 21 Jun 2020 17:36:09: start model_add_line... INFO @ Sun, 21 Jun 2020 17:36:09: start X-correlation... INFO @ Sun, 21 Jun 2020 17:36:09: end of X-cor INFO @ Sun, 21 Jun 2020 17:36:09: #2 finished! INFO @ Sun, 21 Jun 2020 17:36:09: #2 predicted fragment length is 70 bps INFO @ Sun, 21 Jun 2020 17:36:09: #2 alternative fragment length(s) may be 4,70,574 bps INFO @ Sun, 21 Jun 2020 17:36:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.05_model.r WARNING @ Sun, 21 Jun 2020 17:36:09: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:36:09: #2 You may need to consider one of the other alternative d(s): 4,70,574 WARNING @ Sun, 21 Jun 2020 17:36:09: #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 17:36:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:36:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:36:14: 1000000 INFO @ Sun, 21 Jun 2020 17:36:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:36:21: 2000000 INFO @ Sun, 21 Jun 2020 17:36:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:36:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:36:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.05_summits.bed INFO @ Sun, 21 Jun 2020 17:36:23: Done! pass1 - making usageList (350 chroms): 1 millis pass2 - checking and writing primary data (918 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:36:27: 3000000 INFO @ Sun, 21 Jun 2020 17:36:33: 4000000 INFO @ Sun, 21 Jun 2020 17:36:35: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:36:35: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:36:35: #1 total tags in treatment: 4227567 INFO @ Sun, 21 Jun 2020 17:36:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:36:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 17:36:36: #1 tags after filtering in treatment: 4227338 INFO @ Sun, 21 Jun 2020 17:36:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:36:36: #1 finished! INFO @ Sun, 21 Jun 2020 17:36:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:36:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:36:36: #2 number of paired peaks: 544 WARNING @ Sun, 21 Jun 2020 17:36:36: Fewer paired peaks (544) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 544 pairs to build model! INFO @ Sun, 21 Jun 2020 17:36:36: start model_add_line... INFO @ Sun, 21 Jun 2020 17:36:36: start X-correlation... INFO @ Sun, 21 Jun 2020 17:36:36: end of X-cor INFO @ Sun, 21 Jun 2020 17:36:36: #2 finished! INFO @ Sun, 21 Jun 2020 17:36:36: #2 predicted fragment length is 70 bps INFO @ Sun, 21 Jun 2020 17:36:36: #2 alternative fragment length(s) may be 4,70,574 bps INFO @ Sun, 21 Jun 2020 17:36:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.10_model.r WARNING @ Sun, 21 Jun 2020 17:36:36: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:36:36: #2 You may need to consider one of the other alternative d(s): 4,70,574 WARNING @ Sun, 21 Jun 2020 17:36:36: #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 17:36:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:36:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:36:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.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 17:36:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:36:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:36:45: 1000000 INFO @ Sun, 21 Jun 2020 17:36:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:36:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:36:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:36:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.10_summits.bed INFO @ Sun, 21 Jun 2020 17:36:50: Done! pass1 - making usageList (244 chroms): 1 millis pass2 - checking and writing primary data (472 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:36:52: 2000000 INFO @ Sun, 21 Jun 2020 17:36:59: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:37:07: 4000000 INFO @ Sun, 21 Jun 2020 17:37:09: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:37:09: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:37:09: #1 total tags in treatment: 4227567 INFO @ Sun, 21 Jun 2020 17:37:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:37:09: #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 17:37:09: #1 tags after filtering in treatment: 4227338 INFO @ Sun, 21 Jun 2020 17:37:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:37:09: #1 finished! INFO @ Sun, 21 Jun 2020 17:37:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:37:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:37:10: #2 number of paired peaks: 544 WARNING @ Sun, 21 Jun 2020 17:37:10: Fewer paired peaks (544) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 544 pairs to build model! INFO @ Sun, 21 Jun 2020 17:37:10: start model_add_line... INFO @ Sun, 21 Jun 2020 17:37:10: start X-correlation... INFO @ Sun, 21 Jun 2020 17:37:10: end of X-cor INFO @ Sun, 21 Jun 2020 17:37:10: #2 finished! INFO @ Sun, 21 Jun 2020 17:37:10: #2 predicted fragment length is 70 bps INFO @ Sun, 21 Jun 2020 17:37:10: #2 alternative fragment length(s) may be 4,70,574 bps INFO @ Sun, 21 Jun 2020 17:37:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.20_model.r WARNING @ Sun, 21 Jun 2020 17:37:10: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:37:10: #2 You may need to consider one of the other alternative d(s): 4,70,574 WARNING @ Sun, 21 Jun 2020 17:37:10: #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 17:37:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:37:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:37:19: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:37:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:37:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:37:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120704/SRX1120704.20_summits.bed INFO @ Sun, 21 Jun 2020 17:37:24: Done! pass1 - making usageList (116 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 8 millis CompletedMACS2peakCalling