Job ID = 14168348 SRX = SRX11078121 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-10T08:54:47 prefetch.2.10.7: 1) Downloading 'SRR14743549'... 2021-12-10T08:54:47 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T08:55:42 prefetch.2.10.7: HTTPS download succeed 2021-12-10T08:55:42 prefetch.2.10.7: 1) 'SRR14743549' was downloaded successfully 2021-12-10T08:55:42 prefetch.2.10.7: 'SRR14743549' has 0 unresolved dependencies Read 32048993 spots for SRR14743549/SRR14743549.sra Written 32048993 spots for SRR14743549/SRR14743549.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169523 ("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: 00:10:01 32048993 reads; of these: 32048993 (100.00%) were paired; of these: 26731677 (83.41%) aligned concordantly 0 times 4119737 (12.85%) aligned concordantly exactly 1 time 1197579 (3.74%) aligned concordantly >1 times ---- 26731677 pairs aligned concordantly 0 times; of these: 7870 (0.03%) aligned discordantly 1 time ---- 26723807 pairs aligned 0 times concordantly or discordantly; of these: 53447614 mates make up the pairs; of these: 53056286 (99.27%) aligned 0 times 198281 (0.37%) aligned exactly 1 time 193047 (0.36%) aligned >1 times 17.23% overall alignment rate Time searching: 00:10:01 Overall time: 00:10:01 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] 375375 / 5321911 = 0.0705 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 18:10:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.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 18:10:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:10:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:10:56: 1000000 INFO @ Fri, 10 Dec 2021 18:11:00: 2000000 INFO @ Fri, 10 Dec 2021 18:11:04: 3000000 INFO @ Fri, 10 Dec 2021 18:11:08: 4000000 INFO @ Fri, 10 Dec 2021 18:11:12: 5000000 INFO @ Fri, 10 Dec 2021 18:11:16: 6000000 INFO @ Fri, 10 Dec 2021 18:11:20: 7000000 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 18:11:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.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 18:11:22: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:11:22: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:11:24: 8000000 INFO @ Fri, 10 Dec 2021 18:11:27: 1000000 INFO @ Fri, 10 Dec 2021 18:11:28: 9000000 INFO @ Fri, 10 Dec 2021 18:11:32: 2000000 INFO @ Fri, 10 Dec 2021 18:11:33: 10000000 INFO @ Fri, 10 Dec 2021 18:11:34: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:11:34: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:11:34: #1 total tags in treatment: 4942148 INFO @ Fri, 10 Dec 2021 18:11:34: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:11:34: #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 18:11:34: #1 tags after filtering in treatment: 4580094 INFO @ Fri, 10 Dec 2021 18:11:34: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 18:11:34: #1 finished! INFO @ Fri, 10 Dec 2021 18:11:34: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:11:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:11:34: #2 number of paired peaks: 617 WARNING @ Fri, 10 Dec 2021 18:11:34: Fewer paired peaks (617) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 617 pairs to build model! INFO @ Fri, 10 Dec 2021 18:11:34: start model_add_line... INFO @ Fri, 10 Dec 2021 18:11:34: start X-correlation... INFO @ Fri, 10 Dec 2021 18:11:34: end of X-cor INFO @ Fri, 10 Dec 2021 18:11:34: #2 finished! INFO @ Fri, 10 Dec 2021 18:11:34: #2 predicted fragment length is 110 bps INFO @ Fri, 10 Dec 2021 18:11:34: #2 alternative fragment length(s) may be 4,110 bps INFO @ Fri, 10 Dec 2021 18:11:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.05_model.r INFO @ Fri, 10 Dec 2021 18:11:34: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:11:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:11:37: 3000000 INFO @ Fri, 10 Dec 2021 18:11:42: 4000000 INFO @ Fri, 10 Dec 2021 18:11:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:11:47: 5000000 INFO @ Fri, 10 Dec 2021 18:11:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:11:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:11:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.05_summits.bed INFO @ Fri, 10 Dec 2021 18:11:50: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (481 records, 4 fields): 2 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 18:11:52: 6000000 INFO @ Fri, 10 Dec 2021 18:11:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.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 18:11:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:11:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:11:57: 7000000 INFO @ Fri, 10 Dec 2021 18:11:57: 1000000 INFO @ Fri, 10 Dec 2021 18:12:02: 8000000 INFO @ Fri, 10 Dec 2021 18:12:02: 2000000 INFO @ Fri, 10 Dec 2021 18:12:07: 9000000 INFO @ Fri, 10 Dec 2021 18:12:07: 3000000 INFO @ Fri, 10 Dec 2021 18:12:12: 10000000 INFO @ Fri, 10 Dec 2021 18:12:12: 4000000 INFO @ Fri, 10 Dec 2021 18:12:13: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:12:13: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:12:13: #1 total tags in treatment: 4942148 INFO @ Fri, 10 Dec 2021 18:12:13: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:12:13: #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 18:12:13: #1 tags after filtering in treatment: 4580094 INFO @ Fri, 10 Dec 2021 18:12:13: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 18:12:13: #1 finished! INFO @ Fri, 10 Dec 2021 18:12:13: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:12:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:12:13: #2 number of paired peaks: 617 WARNING @ Fri, 10 Dec 2021 18:12:13: Fewer paired peaks (617) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 617 pairs to build model! INFO @ Fri, 10 Dec 2021 18:12:13: start model_add_line... INFO @ Fri, 10 Dec 2021 18:12:13: start X-correlation... INFO @ Fri, 10 Dec 2021 18:12:13: end of X-cor INFO @ Fri, 10 Dec 2021 18:12:13: #2 finished! INFO @ Fri, 10 Dec 2021 18:12:13: #2 predicted fragment length is 110 bps INFO @ Fri, 10 Dec 2021 18:12:13: #2 alternative fragment length(s) may be 4,110 bps INFO @ Fri, 10 Dec 2021 18:12:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.10_model.r INFO @ Fri, 10 Dec 2021 18:12:13: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:12:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:12:17: 5000000 INFO @ Fri, 10 Dec 2021 18:12:22: 6000000 INFO @ Fri, 10 Dec 2021 18:12:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:12:26: 7000000 INFO @ Fri, 10 Dec 2021 18:12:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:12:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:12:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.10_summits.bed INFO @ Fri, 10 Dec 2021 18:12:28: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (232 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:12:31: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:12:36: 9000000 INFO @ Fri, 10 Dec 2021 18:12:41: 10000000 INFO @ Fri, 10 Dec 2021 18:12:42: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:12:42: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:12:42: #1 total tags in treatment: 4942148 INFO @ Fri, 10 Dec 2021 18:12:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:12:42: #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 18:12:43: #1 tags after filtering in treatment: 4580094 INFO @ Fri, 10 Dec 2021 18:12:43: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 18:12:43: #1 finished! INFO @ Fri, 10 Dec 2021 18:12:43: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:12:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:12:43: #2 number of paired peaks: 617 WARNING @ Fri, 10 Dec 2021 18:12:43: Fewer paired peaks (617) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 617 pairs to build model! INFO @ Fri, 10 Dec 2021 18:12:43: start model_add_line... INFO @ Fri, 10 Dec 2021 18:12:43: start X-correlation... INFO @ Fri, 10 Dec 2021 18:12:43: end of X-cor INFO @ Fri, 10 Dec 2021 18:12:43: #2 finished! INFO @ Fri, 10 Dec 2021 18:12:43: #2 predicted fragment length is 110 bps INFO @ Fri, 10 Dec 2021 18:12:43: #2 alternative fragment length(s) may be 4,110 bps INFO @ Fri, 10 Dec 2021 18:12:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.20_model.r INFO @ Fri, 10 Dec 2021 18:12:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:12:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:12:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:12:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:12:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:12:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078121/SRX11078121.20_summits.bed INFO @ Fri, 10 Dec 2021 18:12:57: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (113 records, 4 fields): 1 millis CompletedMACS2peakCalling