Job ID = 14167226 SRX = SRX8973509 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8831722 spots for SRR12479624/SRR12479624.sra Written 8831722 spots for SRR12479624/SRR12479624.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167774 ("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: 00:04:33 8831722 reads; of these: 8831722 (100.00%) were paired; of these: 5645255 (63.92%) aligned concordantly 0 times 2689081 (30.45%) aligned concordantly exactly 1 time 497386 (5.63%) aligned concordantly >1 times ---- 5645255 pairs aligned concordantly 0 times; of these: 91553 (1.62%) aligned discordantly 1 time ---- 5553702 pairs aligned 0 times concordantly or discordantly; of these: 11107404 mates make up the pairs; of these: 10579214 (95.24%) aligned 0 times 447022 (4.02%) aligned exactly 1 time 81168 (0.73%) aligned >1 times 40.11% overall alignment rate Time searching: 00:04:33 Overall time: 00:04:33 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] 105545 / 3276880 = 0.0322 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 11:13:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.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 11:13:55: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:13:55: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:14:00: 1000000 INFO @ Fri, 10 Dec 2021 11:14:06: 2000000 INFO @ Fri, 10 Dec 2021 11:14:11: 3000000 INFO @ Fri, 10 Dec 2021 11:14:16: 4000000 INFO @ Fri, 10 Dec 2021 11:14:21: 5000000 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 11:14:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.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 11:14:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:14:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:14:27: 6000000 INFO @ Fri, 10 Dec 2021 11:14:31: 1000000 INFO @ Fri, 10 Dec 2021 11:14:31: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:14:31: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:14:31: #1 total tags in treatment: 3082316 INFO @ Fri, 10 Dec 2021 11:14:31: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:14:31: #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 11:14:32: #1 tags after filtering in treatment: 3011569 INFO @ Fri, 10 Dec 2021 11:14:32: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:14:32: #1 finished! INFO @ Fri, 10 Dec 2021 11:14:32: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:14:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:14:32: #2 number of paired peaks: 4681 INFO @ Fri, 10 Dec 2021 11:14:32: start model_add_line... INFO @ Fri, 10 Dec 2021 11:14:32: start X-correlation... INFO @ Fri, 10 Dec 2021 11:14:32: end of X-cor INFO @ Fri, 10 Dec 2021 11:14:32: #2 finished! INFO @ Fri, 10 Dec 2021 11:14:32: #2 predicted fragment length is 283 bps INFO @ Fri, 10 Dec 2021 11:14:32: #2 alternative fragment length(s) may be 4,283 bps INFO @ Fri, 10 Dec 2021 11:14:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.05_model.r INFO @ Fri, 10 Dec 2021 11:14:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:14:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:14:36: 2000000 INFO @ Fri, 10 Dec 2021 11:14:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:14:42: 3000000 INFO @ Fri, 10 Dec 2021 11:14:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:14:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:14:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.05_summits.bed INFO @ Fri, 10 Dec 2021 11:14:42: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (636 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:14:47: 4000000 INFO @ Fri, 10 Dec 2021 11:14:53: 5000000 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 11:14:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.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 11:14:55: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:14:55: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:14:58: 6000000 INFO @ Fri, 10 Dec 2021 11:15:01: 1000000 INFO @ Fri, 10 Dec 2021 11:15:03: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:15:03: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:15:03: #1 total tags in treatment: 3082316 INFO @ Fri, 10 Dec 2021 11:15:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:15:03: #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 11:15:03: #1 tags after filtering in treatment: 3011569 INFO @ Fri, 10 Dec 2021 11:15:03: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:15:03: #1 finished! INFO @ Fri, 10 Dec 2021 11:15:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:15:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:15:03: #2 number of paired peaks: 4681 INFO @ Fri, 10 Dec 2021 11:15:03: start model_add_line... INFO @ Fri, 10 Dec 2021 11:15:03: start X-correlation... INFO @ Fri, 10 Dec 2021 11:15:03: end of X-cor INFO @ Fri, 10 Dec 2021 11:15:03: #2 finished! INFO @ Fri, 10 Dec 2021 11:15:03: #2 predicted fragment length is 283 bps INFO @ Fri, 10 Dec 2021 11:15:03: #2 alternative fragment length(s) may be 4,283 bps INFO @ Fri, 10 Dec 2021 11:15:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.10_model.r INFO @ Fri, 10 Dec 2021 11:15:03: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:15:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:15:06: 2000000 INFO @ Fri, 10 Dec 2021 11:15:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:15:11: 3000000 INFO @ Fri, 10 Dec 2021 11:15:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:15:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:15:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.10_summits.bed INFO @ Fri, 10 Dec 2021 11:15:14: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (341 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:15:17: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:15:22: 5000000 INFO @ Fri, 10 Dec 2021 11:15:27: 6000000 INFO @ Fri, 10 Dec 2021 11:15:32: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:15:32: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:15:32: #1 total tags in treatment: 3082316 INFO @ Fri, 10 Dec 2021 11:15:32: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:15:32: #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 11:15:32: #1 tags after filtering in treatment: 3011569 INFO @ Fri, 10 Dec 2021 11:15:32: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:15:32: #1 finished! INFO @ Fri, 10 Dec 2021 11:15:32: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:15:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:15:32: #2 number of paired peaks: 4681 INFO @ Fri, 10 Dec 2021 11:15:32: start model_add_line... INFO @ Fri, 10 Dec 2021 11:15:32: start X-correlation... INFO @ Fri, 10 Dec 2021 11:15:32: end of X-cor INFO @ Fri, 10 Dec 2021 11:15:32: #2 finished! INFO @ Fri, 10 Dec 2021 11:15:32: #2 predicted fragment length is 283 bps INFO @ Fri, 10 Dec 2021 11:15:32: #2 alternative fragment length(s) may be 4,283 bps INFO @ Fri, 10 Dec 2021 11:15:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.20_model.r INFO @ Fri, 10 Dec 2021 11:15:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:15:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:15:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:15:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:15:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:15:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973509/SRX8973509.20_summits.bed INFO @ Fri, 10 Dec 2021 11:15:43: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (133 records, 4 fields): 1 millis CompletedMACS2peakCalling