Job ID = 14168456 SRX = SRX11078132 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-10T09:30:31 prefetch.2.10.7: 1) Downloading 'SRR14743560'... 2021-12-10T09:30:31 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T09:30:45 prefetch.2.10.7: HTTPS download succeed 2021-12-10T09:30:46 prefetch.2.10.7: 'SRR14743560' is valid 2021-12-10T09:30:46 prefetch.2.10.7: 1) 'SRR14743560' was downloaded successfully 2021-12-10T09:30:46 prefetch.2.10.7: 'SRR14743560' has 0 unresolved dependencies Read 7605630 spots for SRR14743560/SRR14743560.sra Written 7605630 spots for SRR14743560/SRR14743560.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169589 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:26 7605630 reads; of these: 7605630 (100.00%) were paired; of these: 7242844 (95.23%) aligned concordantly 0 times 268725 (3.53%) aligned concordantly exactly 1 time 94061 (1.24%) aligned concordantly >1 times ---- 7242844 pairs aligned concordantly 0 times; of these: 670 (0.01%) aligned discordantly 1 time ---- 7242174 pairs aligned 0 times concordantly or discordantly; of these: 14484348 mates make up the pairs; of these: 14428396 (99.61%) aligned 0 times 18694 (0.13%) aligned exactly 1 time 37258 (0.26%) aligned >1 times 5.15% overall alignment rate Time searching: 00:01:26 Overall time: 00:01:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 9267 / 363185 = 0.0255 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 18:33:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.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 @ Fri, 10 Dec 2021 18:33:35: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:33:35: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:33:40: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:33:40: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:33:40: #1 total tags in treatment: 353526 INFO @ Fri, 10 Dec 2021 18:33:40: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:33:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:33:40: #1 tags after filtering in treatment: 349388 INFO @ Fri, 10 Dec 2021 18:33:40: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 10 Dec 2021 18:33:40: #1 finished! INFO @ Fri, 10 Dec 2021 18:33:40: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:33:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:33:40: #2 number of paired peaks: 983 WARNING @ Fri, 10 Dec 2021 18:33:40: Fewer paired peaks (983) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 983 pairs to build model! INFO @ Fri, 10 Dec 2021 18:33:40: start model_add_line... INFO @ Fri, 10 Dec 2021 18:33:40: start X-correlation... INFO @ Fri, 10 Dec 2021 18:33:40: end of X-cor INFO @ Fri, 10 Dec 2021 18:33:40: #2 finished! INFO @ Fri, 10 Dec 2021 18:33:40: #2 predicted fragment length is 94 bps INFO @ Fri, 10 Dec 2021 18:33:40: #2 alternative fragment length(s) may be 94,598 bps INFO @ Fri, 10 Dec 2021 18:33:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.05_model.r INFO @ Fri, 10 Dec 2021 18:33:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:33:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:33:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:33:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:33:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:33:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.05_summits.bed INFO @ Fri, 10 Dec 2021 18:33:41: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (68 records, 4 fields): 2 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 18:34:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.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 @ Fri, 10 Dec 2021 18:34:05: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:34:05: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:34:10: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:34:10: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:34:10: #1 total tags in treatment: 353526 INFO @ Fri, 10 Dec 2021 18:34:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:34:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:34:10: #1 tags after filtering in treatment: 349388 INFO @ Fri, 10 Dec 2021 18:34:10: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 10 Dec 2021 18:34:10: #1 finished! INFO @ Fri, 10 Dec 2021 18:34:10: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:34:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:34:11: #2 number of paired peaks: 983 WARNING @ Fri, 10 Dec 2021 18:34:11: Fewer paired peaks (983) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 983 pairs to build model! INFO @ Fri, 10 Dec 2021 18:34:11: start model_add_line... INFO @ Fri, 10 Dec 2021 18:34:11: start X-correlation... INFO @ Fri, 10 Dec 2021 18:34:11: end of X-cor INFO @ Fri, 10 Dec 2021 18:34:11: #2 finished! INFO @ Fri, 10 Dec 2021 18:34:11: #2 predicted fragment length is 94 bps INFO @ Fri, 10 Dec 2021 18:34:11: #2 alternative fragment length(s) may be 94,598 bps INFO @ Fri, 10 Dec 2021 18:34:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.10_model.r INFO @ Fri, 10 Dec 2021 18:34:11: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:34:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:34:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:34:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:34:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:34:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.10_summits.bed INFO @ Fri, 10 Dec 2021 18:34:12: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (42 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 18:34:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.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 @ Fri, 10 Dec 2021 18:34:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:34:36: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:34:41: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:34:41: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:34:41: #1 total tags in treatment: 353526 INFO @ Fri, 10 Dec 2021 18:34:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:34:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:34:41: #1 tags after filtering in treatment: 349388 INFO @ Fri, 10 Dec 2021 18:34:41: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 10 Dec 2021 18:34:41: #1 finished! INFO @ Fri, 10 Dec 2021 18:34:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:34:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:34:42: #2 number of paired peaks: 983 WARNING @ Fri, 10 Dec 2021 18:34:42: Fewer paired peaks (983) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 983 pairs to build model! INFO @ Fri, 10 Dec 2021 18:34:42: start model_add_line... INFO @ Fri, 10 Dec 2021 18:34:42: start X-correlation... INFO @ Fri, 10 Dec 2021 18:34:42: end of X-cor INFO @ Fri, 10 Dec 2021 18:34:42: #2 finished! INFO @ Fri, 10 Dec 2021 18:34:42: #2 predicted fragment length is 94 bps INFO @ Fri, 10 Dec 2021 18:34:42: #2 alternative fragment length(s) may be 94,598 bps INFO @ Fri, 10 Dec 2021 18:34:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.20_model.r INFO @ Fri, 10 Dec 2021 18:34:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:34:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:34:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:34:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:34:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:34:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078132/SRX11078132.20_summits.bed INFO @ Fri, 10 Dec 2021 18:34:43: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (31 records, 4 fields): 4 millis CompletedMACS2peakCalling