Job ID = 6455446 SRX = SRX287796 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:03:59 prefetch.2.10.7: 1) Downloading 'SRR869985'... 2020-06-21T10:03:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:05:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:05:32 prefetch.2.10.7: 'SRR869985' is valid 2020-06-21T10:05:32 prefetch.2.10.7: 1) 'SRR869985' was downloaded successfully Read 12708439 spots for SRR869985/SRR869985.sra Written 12708439 spots for SRR869985/SRR869985.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: 00:03:38 12708439 reads; of these: 12708439 (100.00%) were unpaired; of these: 1566722 (12.33%) aligned 0 times 8433520 (66.36%) aligned exactly 1 time 2708197 (21.31%) aligned >1 times 87.67% overall alignment rate Time searching: 00:03:38 Overall time: 00:03:38 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1429267 / 11141717 = 0.1283 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 19:12:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.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 19:12:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:12:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:05: 1000000 INFO @ Sun, 21 Jun 2020 19:13:12: 2000000 INFO @ Sun, 21 Jun 2020 19:13:19: 3000000 INFO @ Sun, 21 Jun 2020 19:13:26: 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 @ Sun, 21 Jun 2020 19:13:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.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 19:13:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:33: 5000000 INFO @ Sun, 21 Jun 2020 19:13:36: 1000000 INFO @ Sun, 21 Jun 2020 19:13:41: 6000000 INFO @ Sun, 21 Jun 2020 19:13:43: 2000000 INFO @ Sun, 21 Jun 2020 19:13:48: 7000000 INFO @ Sun, 21 Jun 2020 19:13:50: 3000000 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 19:13:56: 8000000 INFO @ Sun, 21 Jun 2020 19:13:57: 4000000 INFO @ Sun, 21 Jun 2020 19:13:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.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 19:13:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:04: 9000000 INFO @ Sun, 21 Jun 2020 19:14:04: 5000000 INFO @ Sun, 21 Jun 2020 19:14:05: 1000000 INFO @ Sun, 21 Jun 2020 19:14:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:10: #1 total tags in treatment: 9712450 INFO @ Sun, 21 Jun 2020 19:14:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:10: #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 19:14:10: #1 tags after filtering in treatment: 9712446 INFO @ Sun, 21 Jun 2020 19:14:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:10: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:11: #2 number of paired peaks: 632 WARNING @ Sun, 21 Jun 2020 19:14:11: Fewer paired peaks (632) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 632 pairs to build model! INFO @ Sun, 21 Jun 2020 19:14:11: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:11: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:11: 6000000 INFO @ Sun, 21 Jun 2020 19:14:11: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:11: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:11: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 19:14:11: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sun, 21 Jun 2020 19:14:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.05_model.r WARNING @ Sun, 21 Jun 2020 19:14:11: #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 19:14:11: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sun, 21 Jun 2020 19:14:11: #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 19:14:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:11: 2000000 INFO @ Sun, 21 Jun 2020 19:14:18: 7000000 INFO @ Sun, 21 Jun 2020 19:14:18: 3000000 INFO @ Sun, 21 Jun 2020 19:14:24: 8000000 INFO @ Sun, 21 Jun 2020 19:14:25: 4000000 INFO @ Sun, 21 Jun 2020 19:14:31: 9000000 INFO @ Sun, 21 Jun 2020 19:14:31: 5000000 INFO @ Sun, 21 Jun 2020 19:14:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:36: #1 total tags in treatment: 9712450 INFO @ Sun, 21 Jun 2020 19:14:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:36: #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 19:14:37: #1 tags after filtering in treatment: 9712446 INFO @ Sun, 21 Jun 2020 19:14:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:37: #2 number of paired peaks: 632 WARNING @ Sun, 21 Jun 2020 19:14:37: Fewer paired peaks (632) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 632 pairs to build model! INFO @ Sun, 21 Jun 2020 19:14:37: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:37: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:37: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:37: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:37: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 19:14:37: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sun, 21 Jun 2020 19:14:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.10_model.r WARNING @ Sun, 21 Jun 2020 19:14:37: #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 19:14:37: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sun, 21 Jun 2020 19:14:37: #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 19:14:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:38: 6000000 INFO @ Sun, 21 Jun 2020 19:14:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.05_summits.bed INFO @ Sun, 21 Jun 2020 19:14:42: Done! pass1 - making usageList (553 chroms): 1 millis pass2 - checking and writing primary data (2106 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:14:44: 7000000 INFO @ Sun, 21 Jun 2020 19:14:50: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:14:56: 9000000 INFO @ Sun, 21 Jun 2020 19:14:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:00: #1 total tags in treatment: 9712450 INFO @ Sun, 21 Jun 2020 19:15:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:00: #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 19:15:00: #1 tags after filtering in treatment: 9712446 INFO @ Sun, 21 Jun 2020 19:15:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:01: #2 number of paired peaks: 632 WARNING @ Sun, 21 Jun 2020 19:15:01: Fewer paired peaks (632) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 632 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:01: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:01: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:01: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:01: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:01: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 19:15:01: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sun, 21 Jun 2020 19:15:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.20_model.r WARNING @ Sun, 21 Jun 2020 19:15:01: #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 19:15:01: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sun, 21 Jun 2020 19:15:01: #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 19:15:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:15:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.10_summits.bed INFO @ Sun, 21 Jun 2020 19:15:06: Done! pass1 - making usageList (453 chroms): 1 millis pass2 - checking and writing primary data (1506 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:15:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287796/SRX287796.20_summits.bed INFO @ Sun, 21 Jun 2020 19:15:30: Done! pass1 - making usageList (255 chroms): 1 millis pass2 - checking and writing primary data (456 records, 4 fields): 7 millis CompletedMACS2peakCalling