Job ID = 14167223 SRX = SRX8973506 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15186991 spots for SRR12479621/SRR12479621.sra Written 15186991 spots for SRR12479621/SRR12479621.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167806 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:49 15186991 reads; of these: 15186991 (100.00%) were paired; of these: 8982550 (59.15%) aligned concordantly 0 times 5702758 (37.55%) aligned concordantly exactly 1 time 501683 (3.30%) aligned concordantly >1 times ---- 8982550 pairs aligned concordantly 0 times; of these: 191573 (2.13%) aligned discordantly 1 time ---- 8790977 pairs aligned 0 times concordantly or discordantly; of these: 17581954 mates make up the pairs; of these: 17009503 (96.74%) aligned 0 times 424520 (2.41%) aligned exactly 1 time 147931 (0.84%) aligned >1 times 44.00% overall alignment rate Time searching: 00:08:50 Overall time: 00:08:50 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] 176101 / 6394766 = 0.0275 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 11:21:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.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 11:21:17: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:21:17: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:21:27: 1000000 INFO @ Fri, 10 Dec 2021 11:21:38: 2000000 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 11:21:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.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 11:21:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:21:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:21:48: 3000000 INFO @ Fri, 10 Dec 2021 11:21:58: 1000000 INFO @ Fri, 10 Dec 2021 11:21:58: 4000000 INFO @ Fri, 10 Dec 2021 11:22:09: 2000000 INFO @ Fri, 10 Dec 2021 11:22:10: 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 11:22:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.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 11:22:17: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:22:17: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:22:21: 3000000 INFO @ Fri, 10 Dec 2021 11:22:22: 6000000 INFO @ Fri, 10 Dec 2021 11:22:29: 1000000 INFO @ Fri, 10 Dec 2021 11:22:35: 4000000 INFO @ Fri, 10 Dec 2021 11:22:35: 7000000 INFO @ Fri, 10 Dec 2021 11:22:41: 2000000 INFO @ Fri, 10 Dec 2021 11:22:48: 8000000 INFO @ Fri, 10 Dec 2021 11:22:48: 5000000 INFO @ Fri, 10 Dec 2021 11:22:53: 3000000 INFO @ Fri, 10 Dec 2021 11:23:01: 6000000 INFO @ Fri, 10 Dec 2021 11:23:01: 9000000 INFO @ Fri, 10 Dec 2021 11:23:06: 4000000 INFO @ Fri, 10 Dec 2021 11:23:13: 7000000 INFO @ Fri, 10 Dec 2021 11:23:15: 10000000 INFO @ Fri, 10 Dec 2021 11:23:20: 5000000 INFO @ Fri, 10 Dec 2021 11:23:25: 8000000 INFO @ Fri, 10 Dec 2021 11:23:26: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:23:33: 6000000 INFO @ Fri, 10 Dec 2021 11:23:37: 9000000 INFO @ Fri, 10 Dec 2021 11:23:40: 12000000 INFO @ Fri, 10 Dec 2021 11:23:46: 7000000 INFO @ Fri, 10 Dec 2021 11:23:49: 10000000 INFO @ Fri, 10 Dec 2021 11:23:53: 13000000 INFO @ Fri, 10 Dec 2021 11:23:53: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:23:53: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:23:53: #1 total tags in treatment: 6030730 INFO @ Fri, 10 Dec 2021 11:23:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:23:53: #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 11:23:53: #1 tags after filtering in treatment: 5707248 INFO @ Fri, 10 Dec 2021 11:23:53: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 11:23:53: #1 finished! INFO @ Fri, 10 Dec 2021 11:23:53: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:23:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:23:54: #2 number of paired peaks: 8651 INFO @ Fri, 10 Dec 2021 11:23:54: start model_add_line... INFO @ Fri, 10 Dec 2021 11:23:54: start X-correlation... INFO @ Fri, 10 Dec 2021 11:23:54: end of X-cor INFO @ Fri, 10 Dec 2021 11:23:54: #2 finished! INFO @ Fri, 10 Dec 2021 11:23:54: #2 predicted fragment length is 259 bps INFO @ Fri, 10 Dec 2021 11:23:54: #2 alternative fragment length(s) may be 4,259 bps INFO @ Fri, 10 Dec 2021 11:23:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.05_model.r INFO @ Fri, 10 Dec 2021 11:23:54: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:23:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:23:57: 8000000 INFO @ Fri, 10 Dec 2021 11:23:59: 11000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:24:09: 9000000 INFO @ Fri, 10 Dec 2021 11:24:11: 12000000 INFO @ Fri, 10 Dec 2021 11:24:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:24:20: 10000000 INFO @ Fri, 10 Dec 2021 11:24:22: 13000000 INFO @ Fri, 10 Dec 2021 11:24:22: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:24:22: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:24:22: #1 total tags in treatment: 6030730 INFO @ Fri, 10 Dec 2021 11:24:22: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:24:22: #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 11:24:22: #1 tags after filtering in treatment: 5707248 INFO @ Fri, 10 Dec 2021 11:24:22: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 11:24:22: #1 finished! INFO @ Fri, 10 Dec 2021 11:24:22: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:24:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:24:23: #2 number of paired peaks: 8651 INFO @ Fri, 10 Dec 2021 11:24:23: start model_add_line... INFO @ Fri, 10 Dec 2021 11:24:23: start X-correlation... INFO @ Fri, 10 Dec 2021 11:24:23: end of X-cor INFO @ Fri, 10 Dec 2021 11:24:23: #2 finished! INFO @ Fri, 10 Dec 2021 11:24:23: #2 predicted fragment length is 259 bps INFO @ Fri, 10 Dec 2021 11:24:23: #2 alternative fragment length(s) may be 4,259 bps INFO @ Fri, 10 Dec 2021 11:24:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.10_model.r INFO @ Fri, 10 Dec 2021 11:24:23: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:24:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:24:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:24:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:24:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.05_summits.bed INFO @ Fri, 10 Dec 2021 11:24:26: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6321 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:24:30: 11000000 INFO @ Fri, 10 Dec 2021 11:24:39: 12000000 INFO @ Fri, 10 Dec 2021 11:24:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:24:49: 13000000 INFO @ Fri, 10 Dec 2021 11:24:49: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:24:49: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:24:49: #1 total tags in treatment: 6030730 INFO @ Fri, 10 Dec 2021 11:24:49: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:24:49: #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 11:24:49: #1 tags after filtering in treatment: 5707248 INFO @ Fri, 10 Dec 2021 11:24:49: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 11:24:49: #1 finished! INFO @ Fri, 10 Dec 2021 11:24:49: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:24:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:24:50: #2 number of paired peaks: 8651 INFO @ Fri, 10 Dec 2021 11:24:50: start model_add_line... INFO @ Fri, 10 Dec 2021 11:24:50: start X-correlation... INFO @ Fri, 10 Dec 2021 11:24:50: end of X-cor INFO @ Fri, 10 Dec 2021 11:24:51: #2 finished! INFO @ Fri, 10 Dec 2021 11:24:51: #2 predicted fragment length is 259 bps INFO @ Fri, 10 Dec 2021 11:24:51: #2 alternative fragment length(s) may be 4,259 bps INFO @ Fri, 10 Dec 2021 11:24:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.20_model.r INFO @ Fri, 10 Dec 2021 11:24:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:24:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:24:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:24:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:24:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.10_summits.bed INFO @ Fri, 10 Dec 2021 11:24:53: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2850 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:25:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:25:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:25:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:25:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973506/SRX8973506.20_summits.bed INFO @ Fri, 10 Dec 2021 11:25:21: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (540 records, 4 fields): 3 millis CompletedMACS2peakCalling