Job ID = 14168221 SRX = SRX7175251 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19272316 spots for SRR10485691/SRR10485691.sra Written 19272316 spots for SRR10485691/SRR10485691.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169433 ("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: 01:19:43 19272316 reads; of these: 19272316 (100.00%) were paired; of these: 4170496 (21.64%) aligned concordantly 0 times 7728125 (40.10%) aligned concordantly exactly 1 time 7373695 (38.26%) aligned concordantly >1 times ---- 4170496 pairs aligned concordantly 0 times; of these: 191198 (4.58%) aligned discordantly 1 time ---- 3979298 pairs aligned 0 times concordantly or discordantly; of these: 7958596 mates make up the pairs; of these: 6832688 (85.85%) aligned 0 times 375506 (4.72%) aligned exactly 1 time 750402 (9.43%) aligned >1 times 82.27% overall alignment rate Time searching: 01:19:43 Overall time: 01:19:43 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 16 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] 8965263 / 15266691 = 0.5872 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 17:42:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.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 17:42:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:42:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:42:41: 1000000 INFO @ Fri, 10 Dec 2021 17:42:51: 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 17:43:01: 3000000 INFO @ Fri, 10 Dec 2021 17:43:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.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 17:43:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:43:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:43:11: 4000000 INFO @ Fri, 10 Dec 2021 17:43:12: 1000000 INFO @ Fri, 10 Dec 2021 17:43:21: 5000000 INFO @ Fri, 10 Dec 2021 17:43:23: 2000000 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 17:43:30: 6000000 INFO @ Fri, 10 Dec 2021 17:43:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.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 17:43:32: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:43:32: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:43:34: 3000000 INFO @ Fri, 10 Dec 2021 17:43:40: 7000000 INFO @ Fri, 10 Dec 2021 17:43:40: 1000000 INFO @ Fri, 10 Dec 2021 17:43:46: 4000000 INFO @ Fri, 10 Dec 2021 17:43:49: 2000000 INFO @ Fri, 10 Dec 2021 17:43:51: 8000000 INFO @ Fri, 10 Dec 2021 17:43:58: 5000000 INFO @ Fri, 10 Dec 2021 17:43:58: 3000000 INFO @ Fri, 10 Dec 2021 17:44:01: 9000000 INFO @ Fri, 10 Dec 2021 17:44:07: 4000000 INFO @ Fri, 10 Dec 2021 17:44:09: 6000000 INFO @ Fri, 10 Dec 2021 17:44:11: 10000000 INFO @ Fri, 10 Dec 2021 17:44:16: 5000000 INFO @ Fri, 10 Dec 2021 17:44:20: 7000000 INFO @ Fri, 10 Dec 2021 17:44:22: 11000000 INFO @ Fri, 10 Dec 2021 17:44:25: 6000000 INFO @ Fri, 10 Dec 2021 17:44:32: 8000000 INFO @ Fri, 10 Dec 2021 17:44:32: 12000000 INFO @ Fri, 10 Dec 2021 17:44:34: 7000000 INFO @ Fri, 10 Dec 2021 17:44:43: 13000000 INFO @ Fri, 10 Dec 2021 17:44:43: 8000000 INFO @ Fri, 10 Dec 2021 17:44:44: 9000000 INFO @ Fri, 10 Dec 2021 17:44:51: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 17:44:51: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 17:44:51: #1 total tags in treatment: 6230334 INFO @ Fri, 10 Dec 2021 17:44:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:44:51: #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 17:44:51: #1 tags after filtering in treatment: 5339847 INFO @ Fri, 10 Dec 2021 17:44:51: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 10 Dec 2021 17:44:51: #1 finished! INFO @ Fri, 10 Dec 2021 17:44:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:44:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:44:52: #2 number of paired peaks: 3282 INFO @ Fri, 10 Dec 2021 17:44:52: start model_add_line... INFO @ Fri, 10 Dec 2021 17:44:52: start X-correlation... INFO @ Fri, 10 Dec 2021 17:44:52: end of X-cor INFO @ Fri, 10 Dec 2021 17:44:52: #2 finished! INFO @ Fri, 10 Dec 2021 17:44:52: #2 predicted fragment length is 189 bps INFO @ Fri, 10 Dec 2021 17:44:52: #2 alternative fragment length(s) may be 189 bps INFO @ Fri, 10 Dec 2021 17:44:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.05_model.r INFO @ Fri, 10 Dec 2021 17:44:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:44:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:44:52: 9000000 INFO @ Fri, 10 Dec 2021 17:44:56: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:45:01: 10000000 INFO @ Fri, 10 Dec 2021 17:45:08: 11000000 INFO @ Fri, 10 Dec 2021 17:45:08: 11000000 INFO @ Fri, 10 Dec 2021 17:45:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:45:16: 12000000 INFO @ Fri, 10 Dec 2021 17:45:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:45:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:45:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.05_summits.bed INFO @ Fri, 10 Dec 2021 17:45:20: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (8672 records, 4 fields): 14 millis INFO @ Fri, 10 Dec 2021 17:45:20: 12000000 CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:45:24: 13000000 INFO @ Fri, 10 Dec 2021 17:45:30: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 17:45:30: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 17:45:30: #1 total tags in treatment: 6230334 INFO @ Fri, 10 Dec 2021 17:45:30: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:45:30: #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 17:45:30: #1 tags after filtering in treatment: 5339847 INFO @ Fri, 10 Dec 2021 17:45:30: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 10 Dec 2021 17:45:30: #1 finished! INFO @ Fri, 10 Dec 2021 17:45:30: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:45:30: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:45:31: #2 number of paired peaks: 3282 INFO @ Fri, 10 Dec 2021 17:45:31: start model_add_line... INFO @ Fri, 10 Dec 2021 17:45:31: start X-correlation... INFO @ Fri, 10 Dec 2021 17:45:31: end of X-cor INFO @ Fri, 10 Dec 2021 17:45:31: #2 finished! INFO @ Fri, 10 Dec 2021 17:45:31: #2 predicted fragment length is 189 bps INFO @ Fri, 10 Dec 2021 17:45:31: #2 alternative fragment length(s) may be 189 bps INFO @ Fri, 10 Dec 2021 17:45:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.20_model.r INFO @ Fri, 10 Dec 2021 17:45:31: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:45:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:45:33: 13000000 INFO @ Fri, 10 Dec 2021 17:45:42: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 17:45:42: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 17:45:42: #1 total tags in treatment: 6230334 INFO @ Fri, 10 Dec 2021 17:45:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:45:42: #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 17:45:42: #1 tags after filtering in treatment: 5339847 INFO @ Fri, 10 Dec 2021 17:45:42: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 10 Dec 2021 17:45:42: #1 finished! INFO @ Fri, 10 Dec 2021 17:45:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:45:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:45:43: #2 number of paired peaks: 3282 INFO @ Fri, 10 Dec 2021 17:45:43: start model_add_line... INFO @ Fri, 10 Dec 2021 17:45:43: start X-correlation... INFO @ Fri, 10 Dec 2021 17:45:43: end of X-cor INFO @ Fri, 10 Dec 2021 17:45:43: #2 finished! INFO @ Fri, 10 Dec 2021 17:45:43: #2 predicted fragment length is 189 bps INFO @ Fri, 10 Dec 2021 17:45:43: #2 alternative fragment length(s) may be 189 bps INFO @ Fri, 10 Dec 2021 17:45:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.10_model.r INFO @ Fri, 10 Dec 2021 17:45:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:45:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:45:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:45:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:45:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:45:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.20_summits.bed INFO @ Fri, 10 Dec 2021 17:45:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1963 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:46:03: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:46:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:46:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:46:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175251/SRX7175251.10_summits.bed INFO @ Fri, 10 Dec 2021 17:46:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4674 records, 4 fields): 8 millis CompletedMACS2peakCalling