Job ID = 6458901 SRX = SRX5775910 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:48:55 prefetch.2.10.7: 1) Downloading 'SRR8997113'... 2020-06-21T12:48:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:51:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:51:05 prefetch.2.10.7: 'SRR8997113' is valid 2020-06-21T12:51:05 prefetch.2.10.7: 1) 'SRR8997113' was downloaded successfully Read 11188385 spots for SRR8997113/SRR8997113.sra Written 11188385 spots for SRR8997113/SRR8997113.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: 00:04:21 11188385 reads; of these: 11188385 (100.00%) were unpaired; of these: 446455 (3.99%) aligned 0 times 7821305 (69.91%) aligned exactly 1 time 2920625 (26.10%) aligned >1 times 96.01% overall alignment rate Time searching: 00:04:21 Overall time: 00:04:21 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] 2989122 / 10741930 = 0.2783 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 21:59:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.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 21:59:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:06: 1000000 INFO @ Sun, 21 Jun 2020 21:59:11: 2000000 INFO @ Sun, 21 Jun 2020 21:59:16: 3000000 INFO @ Sun, 21 Jun 2020 21:59:21: 4000000 INFO @ Sun, 21 Jun 2020 21:59:26: 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 @ Sun, 21 Jun 2020 21:59:31: 6000000 INFO @ Sun, 21 Jun 2020 21:59:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.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 21:59:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:37: 7000000 INFO @ Sun, 21 Jun 2020 21:59:37: 1000000 INFO @ Sun, 21 Jun 2020 21:59:41: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:59:41: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:59:41: #1 total tags in treatment: 7752808 INFO @ Sun, 21 Jun 2020 21:59:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:59:41: #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 21:59:41: #1 tags after filtering in treatment: 7752804 INFO @ Sun, 21 Jun 2020 21:59:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:59:41: #1 finished! INFO @ Sun, 21 Jun 2020 21:59:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:59:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:59:42: #2 number of paired peaks: 884 WARNING @ Sun, 21 Jun 2020 21:59:42: Fewer paired peaks (884) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 884 pairs to build model! INFO @ Sun, 21 Jun 2020 21:59:42: start model_add_line... INFO @ Sun, 21 Jun 2020 21:59:42: start X-correlation... INFO @ Sun, 21 Jun 2020 21:59:42: end of X-cor INFO @ Sun, 21 Jun 2020 21:59:42: #2 finished! INFO @ Sun, 21 Jun 2020 21:59:42: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 21:59:42: #2 alternative fragment length(s) may be 4,72 bps INFO @ Sun, 21 Jun 2020 21:59:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.05_model.r WARNING @ Sun, 21 Jun 2020 21:59:42: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:59:42: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Sun, 21 Jun 2020 21:59:42: #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 21:59:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:59:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:59:43: 2000000 INFO @ Sun, 21 Jun 2020 21:59:49: 3000000 INFO @ Sun, 21 Jun 2020 21:59:54: 4000000 INFO @ Sun, 21 Jun 2020 21:59:58: #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 22:00:00: 5000000 INFO @ Sun, 21 Jun 2020 22:00:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.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 22:00:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:06: 6000000 INFO @ Sun, 21 Jun 2020 22:00:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.05_summits.bed INFO @ Sun, 21 Jun 2020 22:00:06: Done! INFO @ Sun, 21 Jun 2020 22:00:06: 1000000 pass1 - making usageList (632 chroms): 1 millis pass2 - checking and writing primary data (1818 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:00:12: 2000000 INFO @ Sun, 21 Jun 2020 22:00:12: 7000000 INFO @ Sun, 21 Jun 2020 22:00:17: 3000000 INFO @ Sun, 21 Jun 2020 22:00:17: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:00:17: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:00:17: #1 total tags in treatment: 7752808 INFO @ Sun, 21 Jun 2020 22:00:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:00:17: #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 22:00:17: #1 tags after filtering in treatment: 7752804 INFO @ Sun, 21 Jun 2020 22:00:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:00:17: #1 finished! INFO @ Sun, 21 Jun 2020 22:00:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:00:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:00:18: #2 number of paired peaks: 884 WARNING @ Sun, 21 Jun 2020 22:00:18: Fewer paired peaks (884) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 884 pairs to build model! INFO @ Sun, 21 Jun 2020 22:00:18: start model_add_line... INFO @ Sun, 21 Jun 2020 22:00:18: start X-correlation... INFO @ Sun, 21 Jun 2020 22:00:18: end of X-cor INFO @ Sun, 21 Jun 2020 22:00:18: #2 finished! INFO @ Sun, 21 Jun 2020 22:00:18: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 22:00:18: #2 alternative fragment length(s) may be 4,72 bps INFO @ Sun, 21 Jun 2020 22:00:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.10_model.r WARNING @ Sun, 21 Jun 2020 22:00:18: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:00:18: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Sun, 21 Jun 2020 22:00:18: #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 22:00:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:00:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:00:22: 4000000 INFO @ Sun, 21 Jun 2020 22:00:27: 5000000 INFO @ Sun, 21 Jun 2020 22:00:32: 6000000 INFO @ Sun, 21 Jun 2020 22:00:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:00:38: 7000000 INFO @ Sun, 21 Jun 2020 22:00:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.10_summits.bed INFO @ Sun, 21 Jun 2020 22:00:42: Done! INFO @ Sun, 21 Jun 2020 22:00:42: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:00:42: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:00:42: #1 total tags in treatment: 7752808 INFO @ Sun, 21 Jun 2020 22:00:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:00:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (482 chroms): 1 millis pass2 - checking and writing primary data (1331 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:00:42: #1 tags after filtering in treatment: 7752804 INFO @ Sun, 21 Jun 2020 22:00:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:00:42: #1 finished! INFO @ Sun, 21 Jun 2020 22:00:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:00:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:00:43: #2 number of paired peaks: 884 WARNING @ Sun, 21 Jun 2020 22:00:43: Fewer paired peaks (884) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 884 pairs to build model! INFO @ Sun, 21 Jun 2020 22:00:43: start model_add_line... INFO @ Sun, 21 Jun 2020 22:00:43: start X-correlation... INFO @ Sun, 21 Jun 2020 22:00:43: end of X-cor INFO @ Sun, 21 Jun 2020 22:00:43: #2 finished! INFO @ Sun, 21 Jun 2020 22:00:43: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 22:00:43: #2 alternative fragment length(s) may be 4,72 bps INFO @ Sun, 21 Jun 2020 22:00:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.20_model.r WARNING @ Sun, 21 Jun 2020 22:00:43: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:00:43: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Sun, 21 Jun 2020 22:00:43: #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 22:00:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:00:43: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:01:00: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:01:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:01:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:01:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775910/SRX5775910.20_summits.bed INFO @ Sun, 21 Jun 2020 22:01:08: Done! pass1 - making usageList (381 chroms): 1 millis pass2 - checking and writing primary data (821 records, 4 fields): 11 millis CompletedMACS2peakCalling