Job ID = 14168281 SRX = SRX11078116 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-10T07:48:10 prefetch.2.10.7: 1) Downloading 'SRR14743544'... 2021-12-10T07:48:10 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T07:49:02 prefetch.2.10.7: HTTPS download succeed 2021-12-10T07:49:02 prefetch.2.10.7: 1) 'SRR14743544' was downloaded successfully 2021-12-10T07:49:02 prefetch.2.10.7: 'SRR14743544' has 0 unresolved dependencies Read 28969672 spots for SRR14743544/SRR14743544.sra Written 28969672 spots for SRR14743544/SRR14743544.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169156 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:06:31 28969672 reads; of these: 28969672 (100.00%) were paired; of these: 26488620 (91.44%) aligned concordantly 0 times 1850792 (6.39%) aligned concordantly exactly 1 time 630260 (2.18%) aligned concordantly >1 times ---- 26488620 pairs aligned concordantly 0 times; of these: 3255 (0.01%) aligned discordantly 1 time ---- 26485365 pairs aligned 0 times concordantly or discordantly; of these: 52970730 mates make up the pairs; of these: 52680585 (99.45%) aligned 0 times 105914 (0.20%) aligned exactly 1 time 184231 (0.35%) aligned >1 times 9.08% overall alignment rate Time searching: 00:06:32 Overall time: 00:06:32 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] 110252 / 2482794 = 0.0444 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 16:59:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.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 16:59:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:59:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:59:27: 1000000 INFO @ Fri, 10 Dec 2021 16:59:31: 2000000 INFO @ Fri, 10 Dec 2021 16:59:35: 3000000 INFO @ Fri, 10 Dec 2021 16:59:39: 4000000 INFO @ Fri, 10 Dec 2021 16:59:43: 5000000 INFO @ Fri, 10 Dec 2021 16:59:43: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 16:59:43: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 16:59:43: #1 total tags in treatment: 2370874 INFO @ Fri, 10 Dec 2021 16:59:43: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:59:43: #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 16:59:43: #1 tags after filtering in treatment: 2273521 INFO @ Fri, 10 Dec 2021 16:59:43: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 16:59:43: #1 finished! INFO @ Fri, 10 Dec 2021 16:59:43: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:59:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:59:43: #2 number of paired peaks: 729 WARNING @ Fri, 10 Dec 2021 16:59:43: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Fri, 10 Dec 2021 16:59:43: start model_add_line... INFO @ Fri, 10 Dec 2021 16:59:43: start X-correlation... INFO @ Fri, 10 Dec 2021 16:59:44: end of X-cor INFO @ Fri, 10 Dec 2021 16:59:44: #2 finished! INFO @ Fri, 10 Dec 2021 16:59:44: #2 predicted fragment length is 104 bps INFO @ Fri, 10 Dec 2021 16:59:44: #2 alternative fragment length(s) may be 104 bps INFO @ Fri, 10 Dec 2021 16:59:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.05_model.r INFO @ Fri, 10 Dec 2021 16:59:44: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:59:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:59:49: #3 Call peaks for each chromosome... 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 16:59:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:59:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:59:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.05_summits.bed INFO @ Fri, 10 Dec 2021 16:59:51: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (308 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:59:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.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 16:59:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:59:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:59:57: 1000000 INFO @ Fri, 10 Dec 2021 17:00:00: 2000000 INFO @ Fri, 10 Dec 2021 17:00:04: 3000000 INFO @ Fri, 10 Dec 2021 17:00:08: 4000000 INFO @ Fri, 10 Dec 2021 17:00:12: 5000000 INFO @ Fri, 10 Dec 2021 17:00:12: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 17:00:12: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 17:00:12: #1 total tags in treatment: 2370874 INFO @ Fri, 10 Dec 2021 17:00:12: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:00:12: #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 17:00:12: #1 tags after filtering in treatment: 2273521 INFO @ Fri, 10 Dec 2021 17:00:12: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 17:00:12: #1 finished! INFO @ Fri, 10 Dec 2021 17:00:12: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:00:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:00:13: #2 number of paired peaks: 729 WARNING @ Fri, 10 Dec 2021 17:00:13: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Fri, 10 Dec 2021 17:00:13: start model_add_line... INFO @ Fri, 10 Dec 2021 17:00:13: start X-correlation... INFO @ Fri, 10 Dec 2021 17:00:13: end of X-cor INFO @ Fri, 10 Dec 2021 17:00:13: #2 finished! INFO @ Fri, 10 Dec 2021 17:00:13: #2 predicted fragment length is 104 bps INFO @ Fri, 10 Dec 2021 17:00:13: #2 alternative fragment length(s) may be 104 bps INFO @ Fri, 10 Dec 2021 17:00:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.10_model.r INFO @ Fri, 10 Dec 2021 17:00:13: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:00:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:00:17: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:00:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:00:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:00:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.10_summits.bed INFO @ Fri, 10 Dec 2021 17:00:20: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (158 records, 4 fields): 11 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 17:00:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.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 17:00:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:00:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:00:27: 1000000 INFO @ Fri, 10 Dec 2021 17:00:31: 2000000 INFO @ Fri, 10 Dec 2021 17:00:35: 3000000 INFO @ Fri, 10 Dec 2021 17:00:39: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:00:42: 5000000 INFO @ Fri, 10 Dec 2021 17:00:43: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 17:00:43: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 17:00:43: #1 total tags in treatment: 2370874 INFO @ Fri, 10 Dec 2021 17:00:43: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:00:43: #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 17:00:43: #1 tags after filtering in treatment: 2273521 INFO @ Fri, 10 Dec 2021 17:00:43: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 17:00:43: #1 finished! INFO @ Fri, 10 Dec 2021 17:00:43: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:00:43: #2 number of paired peaks: 729 WARNING @ Fri, 10 Dec 2021 17:00:43: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Fri, 10 Dec 2021 17:00:43: start model_add_line... INFO @ Fri, 10 Dec 2021 17:00:43: start X-correlation... INFO @ Fri, 10 Dec 2021 17:00:43: end of X-cor INFO @ Fri, 10 Dec 2021 17:00:43: #2 finished! INFO @ Fri, 10 Dec 2021 17:00:43: #2 predicted fragment length is 104 bps INFO @ Fri, 10 Dec 2021 17:00:43: #2 alternative fragment length(s) may be 104 bps INFO @ Fri, 10 Dec 2021 17:00:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.20_model.r INFO @ Fri, 10 Dec 2021 17:00:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:00:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:00:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:00:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:00:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:00:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078116/SRX11078116.20_summits.bed INFO @ Fri, 10 Dec 2021 17:00:51: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (70 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。