Job ID = 16439484 SRX = SRX9518326 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7469960 spots for SRR13070809/SRR13070809.sra Written 7469960 spots for SRR13070809/SRR13070809.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439656 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:26:11 7469960 reads; of these: 7469960 (100.00%) were paired; of these: 1019518 (13.65%) aligned concordantly 0 times 5248604 (70.26%) aligned concordantly exactly 1 time 1201838 (16.09%) aligned concordantly >1 times ---- 1019518 pairs aligned concordantly 0 times; of these: 477871 (46.87%) aligned discordantly 1 time ---- 541647 pairs aligned 0 times concordantly or discordantly; of these: 1083294 mates make up the pairs; of these: 694808 (64.14%) aligned 0 times 154568 (14.27%) aligned exactly 1 time 233918 (21.59%) aligned >1 times 95.35% overall alignment rate Time searching: 00:26:12 Overall time: 00:26:12 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_sort_core] merging from 8 files... [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] 300804 / 6921229 = 0.0435 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:52:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.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 @ Tue, 02 Aug 2022 15:52:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:52:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:52:58: 1000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:53:13: 2000000 INFO @ Tue, 02 Aug 2022 15:53:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.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 @ Tue, 02 Aug 2022 15:53:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:53:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:53:28: 1000000 INFO @ Tue, 02 Aug 2022 15:53:29: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:53:42: 2000000 INFO @ Tue, 02 Aug 2022 15:53:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.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 @ Tue, 02 Aug 2022 15:53:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:53:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:53:45: 4000000 INFO @ Tue, 02 Aug 2022 15:53:56: 3000000 INFO @ Tue, 02 Aug 2022 15:53:59: 1000000 INFO @ Tue, 02 Aug 2022 15:54:01: 5000000 INFO @ Tue, 02 Aug 2022 15:54:11: 4000000 INFO @ Tue, 02 Aug 2022 15:54:16: 2000000 INFO @ Tue, 02 Aug 2022 15:54:17: 6000000 INFO @ Tue, 02 Aug 2022 15:54:25: 5000000 INFO @ Tue, 02 Aug 2022 15:54:31: 3000000 INFO @ Tue, 02 Aug 2022 15:54:32: 7000000 INFO @ Tue, 02 Aug 2022 15:54:39: 6000000 INFO @ Tue, 02 Aug 2022 15:54:47: 4000000 INFO @ Tue, 02 Aug 2022 15:54:48: 8000000 INFO @ Tue, 02 Aug 2022 15:54:53: 7000000 INFO @ Tue, 02 Aug 2022 15:55:03: 5000000 INFO @ Tue, 02 Aug 2022 15:55:03: 9000000 INFO @ Tue, 02 Aug 2022 15:55:07: 8000000 INFO @ Tue, 02 Aug 2022 15:55:19: 10000000 INFO @ Tue, 02 Aug 2022 15:55:19: 6000000 INFO @ Tue, 02 Aug 2022 15:55:20: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:55:35: 10000000 INFO @ Tue, 02 Aug 2022 15:55:35: 11000000 INFO @ Tue, 02 Aug 2022 15:55:36: 7000000 INFO @ Tue, 02 Aug 2022 15:55:49: 11000000 INFO @ Tue, 02 Aug 2022 15:55:50: 12000000 INFO @ Tue, 02 Aug 2022 15:55:52: 8000000 INFO @ Tue, 02 Aug 2022 15:56:02: 12000000 INFO @ Tue, 02 Aug 2022 15:56:03: 13000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:56:07: 9000000 INFO @ Tue, 02 Aug 2022 15:56:12: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:56:12: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:56:12: #1 total tags in treatment: 6171728 INFO @ Tue, 02 Aug 2022 15:56:12: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:56:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:56:13: #1 tags after filtering in treatment: 5607787 INFO @ Tue, 02 Aug 2022 15:56:13: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 15:56:13: #1 finished! INFO @ Tue, 02 Aug 2022 15:56:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:56:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:56:13: #2 number of paired peaks: 4859 INFO @ Tue, 02 Aug 2022 15:56:13: start model_add_line... INFO @ Tue, 02 Aug 2022 15:56:14: start X-correlation... INFO @ Tue, 02 Aug 2022 15:56:14: end of X-cor INFO @ Tue, 02 Aug 2022 15:56:14: #2 finished! INFO @ Tue, 02 Aug 2022 15:56:14: #2 predicted fragment length is 242 bps INFO @ Tue, 02 Aug 2022 15:56:14: #2 alternative fragment length(s) may be 242 bps INFO @ Tue, 02 Aug 2022 15:56:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.05_model.r INFO @ Tue, 02 Aug 2022 15:56:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:56:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:56:16: 13000000 INFO @ Tue, 02 Aug 2022 15:56:22: 10000000 INFO @ Tue, 02 Aug 2022 15:56:24: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:56:24: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:56:24: #1 total tags in treatment: 6171728 INFO @ Tue, 02 Aug 2022 15:56:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:56:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:56:25: #1 tags after filtering in treatment: 5607787 INFO @ Tue, 02 Aug 2022 15:56:25: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 15:56:25: #1 finished! INFO @ Tue, 02 Aug 2022 15:56:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:56:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:56:26: #2 number of paired peaks: 4859 INFO @ Tue, 02 Aug 2022 15:56:26: start model_add_line... INFO @ Tue, 02 Aug 2022 15:56:26: start X-correlation... INFO @ Tue, 02 Aug 2022 15:56:26: end of X-cor INFO @ Tue, 02 Aug 2022 15:56:26: #2 finished! INFO @ Tue, 02 Aug 2022 15:56:26: #2 predicted fragment length is 242 bps INFO @ Tue, 02 Aug 2022 15:56:26: #2 alternative fragment length(s) may be 242 bps INFO @ Tue, 02 Aug 2022 15:56:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.10_model.r INFO @ Tue, 02 Aug 2022 15:56:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:56:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:56:38: 11000000 INFO @ Tue, 02 Aug 2022 15:56:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:56:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:56:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:56:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.05_summits.bed INFO @ Tue, 02 Aug 2022 15:56:51: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3500 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:56:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:56:53: 12000000 INFO @ Tue, 02 Aug 2022 15:57:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:57:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:57:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.10_summits.bed INFO @ Tue, 02 Aug 2022 15:57:05: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2428 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:57:08: 13000000 INFO @ Tue, 02 Aug 2022 15:57:17: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:57:17: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:57:17: #1 total tags in treatment: 6171728 INFO @ Tue, 02 Aug 2022 15:57:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:57:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:57:18: #1 tags after filtering in treatment: 5607787 INFO @ Tue, 02 Aug 2022 15:57:18: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 15:57:18: #1 finished! INFO @ Tue, 02 Aug 2022 15:57:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:57:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:57:18: #2 number of paired peaks: 4859 INFO @ Tue, 02 Aug 2022 15:57:18: start model_add_line... INFO @ Tue, 02 Aug 2022 15:57:19: start X-correlation... INFO @ Tue, 02 Aug 2022 15:57:19: end of X-cor INFO @ Tue, 02 Aug 2022 15:57:19: #2 finished! INFO @ Tue, 02 Aug 2022 15:57:19: #2 predicted fragment length is 242 bps INFO @ Tue, 02 Aug 2022 15:57:19: #2 alternative fragment length(s) may be 242 bps INFO @ Tue, 02 Aug 2022 15:57:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.20_model.r INFO @ Tue, 02 Aug 2022 15:57:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:57:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:57:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:57:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:57:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:57:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518326/SRX9518326.20_summits.bed INFO @ Tue, 02 Aug 2022 15:57:55: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1641 records, 4 fields): 12 millis CompletedMACS2peakCalling