Job ID = 6455200 SRX = SRX2832095 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:01:14 prefetch.2.10.7: 1) Downloading 'SRR5573759'... 2020-06-21T10:01:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:02:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:02:36 prefetch.2.10.7: 'SRR5573759' is valid 2020-06-21T10:02:36 prefetch.2.10.7: 1) 'SRR5573759' was downloaded successfully Read 9010367 spots for SRR5573759/SRR5573759.sra Written 9010367 spots for SRR5573759/SRR5573759.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: 00:02:29 9010367 reads; of these: 9010367 (100.00%) were unpaired; of these: 579210 (6.43%) aligned 0 times 4614679 (51.22%) aligned exactly 1 time 3816478 (42.36%) aligned >1 times 93.57% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 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] 1598589 / 8431157 = 0.1896 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 19:08:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.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 19:08:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:09: 1000000 INFO @ Sun, 21 Jun 2020 19:08:15: 2000000 INFO @ Sun, 21 Jun 2020 19:08:20: 3000000 INFO @ Sun, 21 Jun 2020 19:08:25: 4000000 INFO @ Sun, 21 Jun 2020 19:08:31: 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 19:08:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.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 19:08:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:37: 6000000 INFO @ Sun, 21 Jun 2020 19:08:39: 1000000 INFO @ Sun, 21 Jun 2020 19:08:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:08:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:08:42: #1 total tags in treatment: 6832568 INFO @ Sun, 21 Jun 2020 19:08:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:08:42: #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 19:08:42: #1 tags after filtering in treatment: 6832494 INFO @ Sun, 21 Jun 2020 19:08:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:08:42: #1 finished! INFO @ Sun, 21 Jun 2020 19:08:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:08:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:08:43: #2 number of paired peaks: 1578 INFO @ Sun, 21 Jun 2020 19:08:43: start model_add_line... INFO @ Sun, 21 Jun 2020 19:08:43: start X-correlation... INFO @ Sun, 21 Jun 2020 19:08:43: end of X-cor INFO @ Sun, 21 Jun 2020 19:08:43: #2 finished! INFO @ Sun, 21 Jun 2020 19:08:43: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 19:08:43: #2 alternative fragment length(s) may be 4,55,102 bps INFO @ Sun, 21 Jun 2020 19:08:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.05_model.r WARNING @ Sun, 21 Jun 2020 19:08:43: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:08:43: #2 You may need to consider one of the other alternative d(s): 4,55,102 WARNING @ Sun, 21 Jun 2020 19:08:43: #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 19:08:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:08:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:08:45: 2000000 INFO @ Sun, 21 Jun 2020 19:08:51: 3000000 INFO @ Sun, 21 Jun 2020 19:08:57: 4000000 INFO @ Sun, 21 Jun 2020 19:08:58: #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 19:09:02: 5000000 INFO @ Sun, 21 Jun 2020 19:09:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.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 19:09:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:09:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:09:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.05_summits.bed INFO @ Sun, 21 Jun 2020 19:09:06: Done! pass1 - making usageList (785 chroms): 2 millis pass2 - checking and writing primary data (3920 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:09:09: 6000000 INFO @ Sun, 21 Jun 2020 19:09:10: 1000000 INFO @ Sun, 21 Jun 2020 19:09:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:09:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:09:14: #1 total tags in treatment: 6832568 INFO @ Sun, 21 Jun 2020 19:09:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:14: #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 19:09:14: #1 tags after filtering in treatment: 6832494 INFO @ Sun, 21 Jun 2020 19:09:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:14: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:15: #2 number of paired peaks: 1578 INFO @ Sun, 21 Jun 2020 19:09:15: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:15: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:15: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:15: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:15: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 19:09:15: #2 alternative fragment length(s) may be 4,55,102 bps INFO @ Sun, 21 Jun 2020 19:09:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.10_model.r WARNING @ Sun, 21 Jun 2020 19:09:15: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:09:15: #2 You may need to consider one of the other alternative d(s): 4,55,102 WARNING @ Sun, 21 Jun 2020 19:09:15: #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 19:09:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:09:17: 2000000 INFO @ Sun, 21 Jun 2020 19:09:24: 3000000 INFO @ Sun, 21 Jun 2020 19:09:31: 4000000 INFO @ Sun, 21 Jun 2020 19:09:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:09:37: 5000000 INFO @ Sun, 21 Jun 2020 19:09:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:09:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:09:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.10_summits.bed INFO @ Sun, 21 Jun 2020 19:09:38: Done! pass1 - making usageList (626 chroms): 1 millis pass2 - checking and writing primary data (2276 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:09:43: 6000000 INFO @ Sun, 21 Jun 2020 19:09:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:09:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:09:48: #1 total tags in treatment: 6832568 INFO @ Sun, 21 Jun 2020 19:09:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:48: #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 19:09:49: #1 tags after filtering in treatment: 6832494 INFO @ Sun, 21 Jun 2020 19:09:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:50: #2 number of paired peaks: 1578 INFO @ Sun, 21 Jun 2020 19:09:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:50: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 19:09:50: #2 alternative fragment length(s) may be 4,55,102 bps INFO @ Sun, 21 Jun 2020 19:09:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.20_model.r WARNING @ Sun, 21 Jun 2020 19:09:50: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:09:50: #2 You may need to consider one of the other alternative d(s): 4,55,102 WARNING @ Sun, 21 Jun 2020 19:09:50: #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 19:09:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:10:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:10:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:10:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2832095/SRX2832095.20_summits.bed INFO @ Sun, 21 Jun 2020 19:10:14: Done! pass1 - making usageList (362 chroms): 1 millis pass2 - checking and writing primary data (722 records, 4 fields): 12 millis CompletedMACS2peakCalling