Job ID = 16439441 SRX = SRX5101710 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6636172 spots for SRR8287003/SRR8287003.sra Written 6636172 spots for SRR8287003/SRR8287003.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439530 ("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: 00:14:34 6636172 reads; of these: 6636172 (100.00%) were paired; of these: 434161 (6.54%) aligned concordantly 0 times 2713612 (40.89%) aligned concordantly exactly 1 time 3488399 (52.57%) aligned concordantly >1 times ---- 434161 pairs aligned concordantly 0 times; of these: 172562 (39.75%) aligned discordantly 1 time ---- 261599 pairs aligned 0 times concordantly or discordantly; of these: 523198 mates make up the pairs; of these: 167501 (32.01%) aligned 0 times 135026 (25.81%) aligned exactly 1 time 220671 (42.18%) aligned >1 times 98.74% overall alignment rate Time searching: 00:14:35 Overall time: 00:14:35 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] 1923256 / 6193364 = 0.3105 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 15:32:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.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 15:32:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:32:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:33:11: 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 15:33:24: 2000000 INFO @ Tue, 02 Aug 2022 15:33:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.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 15:33:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:33:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:33:36: 3000000 INFO @ Tue, 02 Aug 2022 15:33:37: 1000000 INFO @ Tue, 02 Aug 2022 15:33:48: 2000000 INFO @ Tue, 02 Aug 2022 15:33:49: 4000000 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 15:33:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.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 15:33:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:33:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:34:00: 3000000 INFO @ Tue, 02 Aug 2022 15:34:02: 5000000 INFO @ Tue, 02 Aug 2022 15:34:09: 1000000 INFO @ Tue, 02 Aug 2022 15:34:12: 4000000 INFO @ Tue, 02 Aug 2022 15:34:15: 6000000 INFO @ Tue, 02 Aug 2022 15:34:20: 2000000 INFO @ Tue, 02 Aug 2022 15:34:24: 5000000 INFO @ Tue, 02 Aug 2022 15:34:29: 7000000 INFO @ Tue, 02 Aug 2022 15:34:32: 3000000 INFO @ Tue, 02 Aug 2022 15:34:36: 6000000 INFO @ Tue, 02 Aug 2022 15:34:42: 8000000 INFO @ Tue, 02 Aug 2022 15:34:44: 4000000 INFO @ Tue, 02 Aug 2022 15:34:47: 7000000 INFO @ Tue, 02 Aug 2022 15:34:56: 9000000 INFO @ Tue, 02 Aug 2022 15:34:56: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:34:58: 8000000 INFO @ Tue, 02 Aug 2022 15:34:59: #1 tag size is determined as 70 bps INFO @ Tue, 02 Aug 2022 15:34:59: #1 tag size = 70 INFO @ Tue, 02 Aug 2022 15:34:59: #1 total tags in treatment: 4280191 INFO @ Tue, 02 Aug 2022 15:34:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:34:59: #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 15:34:59: #1 tags after filtering in treatment: 2759024 INFO @ Tue, 02 Aug 2022 15:34:59: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 02 Aug 2022 15:34:59: #1 finished! INFO @ Tue, 02 Aug 2022 15:34:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:34:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:35:00: #2 number of paired peaks: 6348 INFO @ Tue, 02 Aug 2022 15:35:00: start model_add_line... INFO @ Tue, 02 Aug 2022 15:35:00: start X-correlation... INFO @ Tue, 02 Aug 2022 15:35:00: end of X-cor INFO @ Tue, 02 Aug 2022 15:35:00: #2 finished! INFO @ Tue, 02 Aug 2022 15:35:00: #2 predicted fragment length is 192 bps INFO @ Tue, 02 Aug 2022 15:35:00: #2 alternative fragment length(s) may be 192 bps INFO @ Tue, 02 Aug 2022 15:35:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.05_model.r INFO @ Tue, 02 Aug 2022 15:35:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:35:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:35:07: 6000000 INFO @ Tue, 02 Aug 2022 15:35:09: 9000000 INFO @ Tue, 02 Aug 2022 15:35:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:35:12: #1 tag size is determined as 70 bps INFO @ Tue, 02 Aug 2022 15:35:12: #1 tag size = 70 INFO @ Tue, 02 Aug 2022 15:35:12: #1 total tags in treatment: 4280191 INFO @ Tue, 02 Aug 2022 15:35:12: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:35:12: #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 15:35:12: #1 tags after filtering in treatment: 2759024 INFO @ Tue, 02 Aug 2022 15:35:12: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 02 Aug 2022 15:35:12: #1 finished! INFO @ Tue, 02 Aug 2022 15:35:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:35:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:35:13: #2 number of paired peaks: 6348 INFO @ Tue, 02 Aug 2022 15:35:13: start model_add_line... INFO @ Tue, 02 Aug 2022 15:35:13: start X-correlation... INFO @ Tue, 02 Aug 2022 15:35:13: end of X-cor INFO @ Tue, 02 Aug 2022 15:35:13: #2 finished! INFO @ Tue, 02 Aug 2022 15:35:13: #2 predicted fragment length is 192 bps INFO @ Tue, 02 Aug 2022 15:35:13: #2 alternative fragment length(s) may be 192 bps INFO @ Tue, 02 Aug 2022 15:35:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.10_model.r INFO @ Tue, 02 Aug 2022 15:35:13: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:35:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:35:17: 7000000 INFO @ Tue, 02 Aug 2022 15:35:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:35:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:35:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.05_summits.bed INFO @ Tue, 02 Aug 2022 15:35:18: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (7185 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:35:24: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:35:27: 8000000 INFO @ Tue, 02 Aug 2022 15:35:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:35:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:35:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.10_summits.bed INFO @ Tue, 02 Aug 2022 15:35:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4187 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:35:38: 9000000 INFO @ Tue, 02 Aug 2022 15:35:40: #1 tag size is determined as 70 bps INFO @ Tue, 02 Aug 2022 15:35:40: #1 tag size = 70 INFO @ Tue, 02 Aug 2022 15:35:40: #1 total tags in treatment: 4280191 INFO @ Tue, 02 Aug 2022 15:35:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:35:40: #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 15:35:40: #1 tags after filtering in treatment: 2759024 INFO @ Tue, 02 Aug 2022 15:35:40: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 02 Aug 2022 15:35:40: #1 finished! INFO @ Tue, 02 Aug 2022 15:35:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:35:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:35:41: #2 number of paired peaks: 6348 INFO @ Tue, 02 Aug 2022 15:35:41: start model_add_line... INFO @ Tue, 02 Aug 2022 15:35:41: start X-correlation... INFO @ Tue, 02 Aug 2022 15:35:41: end of X-cor INFO @ Tue, 02 Aug 2022 15:35:41: #2 finished! INFO @ Tue, 02 Aug 2022 15:35:41: #2 predicted fragment length is 192 bps INFO @ Tue, 02 Aug 2022 15:35:41: #2 alternative fragment length(s) may be 192 bps INFO @ Tue, 02 Aug 2022 15:35:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.20_model.r INFO @ Tue, 02 Aug 2022 15:35:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:35:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:35:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:35:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:35:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:35:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5101710/SRX5101710.20_summits.bed INFO @ Tue, 02 Aug 2022 15:35:57: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1388 records, 4 fields): 25 millis CompletedMACS2peakCalling