Job ID = 10166567 SRX = SRX7723702 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:40 34021743 reads; of these: 34021743 (100.00%) were unpaired; of these: 15324828 (45.04%) aligned 0 times 14757809 (43.38%) aligned exactly 1 time 3939106 (11.58%) aligned >1 times 54.96% overall alignment rate Time searching: 00:08:41 Overall time: 00:08:41 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] 9977170 / 18696915 = 0.5336 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 @ Thu, 08 Oct 2020 22:01:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.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 @ Thu, 08 Oct 2020 22:01:22: #1 read tag files... INFO @ Thu, 08 Oct 2020 22:01:22: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 22:01:27: 1000000 INFO @ Thu, 08 Oct 2020 22:01:32: 2000000 INFO @ Thu, 08 Oct 2020 22:01:37: 3000000 INFO @ Thu, 08 Oct 2020 22:01:42: 4000000 INFO @ Thu, 08 Oct 2020 22:01:48: 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 @ Thu, 08 Oct 2020 22:01:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.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 @ Thu, 08 Oct 2020 22:01:52: #1 read tag files... INFO @ Thu, 08 Oct 2020 22:01:52: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 22:01:52: 6000000 INFO @ Thu, 08 Oct 2020 22:01:57: 1000000 INFO @ Thu, 08 Oct 2020 22:01:58: 7000000 INFO @ Thu, 08 Oct 2020 22:02:03: 2000000 INFO @ Thu, 08 Oct 2020 22:02:03: 8000000 INFO @ Thu, 08 Oct 2020 22:02:07: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 22:02:07: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 22:02:07: #1 total tags in treatment: 8719745 INFO @ Thu, 08 Oct 2020 22:02:07: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 22:02:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 22:02:07: #1 tags after filtering in treatment: 8719579 INFO @ Thu, 08 Oct 2020 22:02:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 22:02:07: #1 finished! INFO @ Thu, 08 Oct 2020 22:02:07: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 22:02:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 22:02:08: 3000000 INFO @ Thu, 08 Oct 2020 22:02:08: #2 number of paired peaks: 8004 INFO @ Thu, 08 Oct 2020 22:02:08: start model_add_line... INFO @ Thu, 08 Oct 2020 22:02:08: start X-correlation... INFO @ Thu, 08 Oct 2020 22:02:08: end of X-cor INFO @ Thu, 08 Oct 2020 22:02:08: #2 finished! INFO @ Thu, 08 Oct 2020 22:02:08: #2 predicted fragment length is 130 bps INFO @ Thu, 08 Oct 2020 22:02:08: #2 alternative fragment length(s) may be 130 bps INFO @ Thu, 08 Oct 2020 22:02:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.05_model.r WARNING @ Thu, 08 Oct 2020 22:02:08: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 22:02:08: #2 You may need to consider one of the other alternative d(s): 130 WARNING @ Thu, 08 Oct 2020 22:02:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 22:02:08: #3 Call peaks... INFO @ Thu, 08 Oct 2020 22:02:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 22:02:13: 4000000 INFO @ Thu, 08 Oct 2020 22:02:18: 5000000 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 @ Thu, 08 Oct 2020 22:02:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.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 @ Thu, 08 Oct 2020 22:02:22: #1 read tag files... INFO @ Thu, 08 Oct 2020 22:02:22: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 22:02:23: 6000000 INFO @ Thu, 08 Oct 2020 22:02:28: 1000000 INFO @ Thu, 08 Oct 2020 22:02:28: 7000000 INFO @ Thu, 08 Oct 2020 22:02:29: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 22:02:33: 8000000 INFO @ Thu, 08 Oct 2020 22:02:34: 2000000 INFO @ Thu, 08 Oct 2020 22:02:37: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 22:02:37: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 22:02:37: #1 total tags in treatment: 8719745 INFO @ Thu, 08 Oct 2020 22:02:37: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 22:02:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 22:02:38: #1 tags after filtering in treatment: 8719579 INFO @ Thu, 08 Oct 2020 22:02:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 22:02:38: #1 finished! INFO @ Thu, 08 Oct 2020 22:02:38: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 22:02:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 22:02:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.05_peaks.xls INFO @ Thu, 08 Oct 2020 22:02:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 22:02:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.05_summits.bed INFO @ Thu, 08 Oct 2020 22:02:38: Done! pass1 - making usageList (702 chroms): 2 millis pass2 - checking and writing primary data (8748 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 22:02:39: #2 number of paired peaks: 8004 INFO @ Thu, 08 Oct 2020 22:02:39: start model_add_line... INFO @ Thu, 08 Oct 2020 22:02:39: start X-correlation... INFO @ Thu, 08 Oct 2020 22:02:39: end of X-cor INFO @ Thu, 08 Oct 2020 22:02:39: #2 finished! INFO @ Thu, 08 Oct 2020 22:02:39: #2 predicted fragment length is 130 bps INFO @ Thu, 08 Oct 2020 22:02:39: #2 alternative fragment length(s) may be 130 bps INFO @ Thu, 08 Oct 2020 22:02:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.10_model.r WARNING @ Thu, 08 Oct 2020 22:02:39: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 22:02:39: #2 You may need to consider one of the other alternative d(s): 130 WARNING @ Thu, 08 Oct 2020 22:02:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 22:02:39: #3 Call peaks... INFO @ Thu, 08 Oct 2020 22:02:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 22:02:41: 3000000 INFO @ Thu, 08 Oct 2020 22:02:47: 4000000 INFO @ Thu, 08 Oct 2020 22:02:53: 5000000 INFO @ Thu, 08 Oct 2020 22:02:59: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 22:02:59: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 22:03:06: 7000000 INFO @ Thu, 08 Oct 2020 22:03:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.10_peaks.xls INFO @ Thu, 08 Oct 2020 22:03:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 22:03:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.10_summits.bed INFO @ Thu, 08 Oct 2020 22:03:09: Done! pass1 - making usageList (584 chroms): 2 millis pass2 - checking and writing primary data (6859 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 22:03:12: 8000000 INFO @ Thu, 08 Oct 2020 22:03:16: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 22:03:16: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 22:03:16: #1 total tags in treatment: 8719745 INFO @ Thu, 08 Oct 2020 22:03:16: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 22:03:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 22:03:17: #1 tags after filtering in treatment: 8719579 INFO @ Thu, 08 Oct 2020 22:03:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 22:03:17: #1 finished! INFO @ Thu, 08 Oct 2020 22:03:17: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 22:03:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 22:03:18: #2 number of paired peaks: 8004 INFO @ Thu, 08 Oct 2020 22:03:18: start model_add_line... INFO @ Thu, 08 Oct 2020 22:03:18: start X-correlation... INFO @ Thu, 08 Oct 2020 22:03:18: end of X-cor INFO @ Thu, 08 Oct 2020 22:03:18: #2 finished! INFO @ Thu, 08 Oct 2020 22:03:18: #2 predicted fragment length is 130 bps INFO @ Thu, 08 Oct 2020 22:03:18: #2 alternative fragment length(s) may be 130 bps INFO @ Thu, 08 Oct 2020 22:03:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.20_model.r WARNING @ Thu, 08 Oct 2020 22:03:18: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 22:03:18: #2 You may need to consider one of the other alternative d(s): 130 WARNING @ Thu, 08 Oct 2020 22:03:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 22:03:18: #3 Call peaks... INFO @ Thu, 08 Oct 2020 22:03:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 22:03:40: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 22:03:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.20_peaks.xls INFO @ Thu, 08 Oct 2020 22:03:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 22:03:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723702/SRX7723702.20_summits.bed INFO @ Thu, 08 Oct 2020 22:03:51: Done! pass1 - making usageList (451 chroms): 1 millis pass2 - checking and writing primary data (4604 records, 4 fields): 15 millis CompletedMACS2peakCalling