Job ID = 14172262 SRX = SRX9281759 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4879962 spots for SRR12813515/SRR12813515.sra Written 4879962 spots for SRR12813515/SRR12813515.sra Read 4890239 spots for SRR12813516/SRR12813516.sra Written 4890239 spots for SRR12813516/SRR12813516.sra Read 5028226 spots for SRR12813517/SRR12813517.sra Written 5028226 spots for SRR12813517/SRR12813517.sra Read 4611699 spots for SRR12813518/SRR12813518.sra Written 4611699 spots for SRR12813518/SRR12813518.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172721 ("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: 00:04:00 19410126 reads; of these: 19410126 (100.00%) were paired; of these: 17229194 (88.76%) aligned concordantly 0 times 2015984 (10.39%) aligned concordantly exactly 1 time 164948 (0.85%) aligned concordantly >1 times ---- 17229194 pairs aligned concordantly 0 times; of these: 15566 (0.09%) aligned discordantly 1 time ---- 17213628 pairs aligned 0 times concordantly or discordantly; of these: 34427256 mates make up the pairs; of these: 34021180 (98.82%) aligned 0 times 261345 (0.76%) aligned exactly 1 time 144731 (0.42%) aligned >1 times 12.36% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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] 418089 / 2185915 = 0.1913 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 @ Sat, 11 Dec 2021 15:02:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.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 @ Sat, 11 Dec 2021 15:02:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:02:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:02:40: 1000000 INFO @ Sat, 11 Dec 2021 15:02:44: 2000000 INFO @ Sat, 11 Dec 2021 15:02:48: 3000000 INFO @ Sat, 11 Dec 2021 15:02:52: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:02:52: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:02:52: #1 total tags in treatment: 1762995 INFO @ Sat, 11 Dec 2021 15:02:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:02:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:02:52: #1 tags after filtering in treatment: 1115988 INFO @ Sat, 11 Dec 2021 15:02:52: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 11 Dec 2021 15:02:52: #1 finished! INFO @ Sat, 11 Dec 2021 15:02:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:02:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:02:52: #2 number of paired peaks: 9918 INFO @ Sat, 11 Dec 2021 15:02:52: start model_add_line... INFO @ Sat, 11 Dec 2021 15:02:52: start X-correlation... INFO @ Sat, 11 Dec 2021 15:02:52: end of X-cor INFO @ Sat, 11 Dec 2021 15:02:52: #2 finished! INFO @ Sat, 11 Dec 2021 15:02:52: #2 predicted fragment length is 153 bps INFO @ Sat, 11 Dec 2021 15:02:52: #2 alternative fragment length(s) may be 153,311 bps INFO @ Sat, 11 Dec 2021 15:02:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.05_model.r INFO @ Sat, 11 Dec 2021 15:02:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:02:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:02:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:02:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:02:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:02:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.05_summits.bed INFO @ Sat, 11 Dec 2021 15:02:56: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7240 records, 4 fields): 8 millis CompletedMACS2peakCalling 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 @ Sat, 11 Dec 2021 15:03:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.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 @ Sat, 11 Dec 2021 15:03:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:03:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:03:10: 1000000 INFO @ Sat, 11 Dec 2021 15:03:14: 2000000 INFO @ Sat, 11 Dec 2021 15:03:18: 3000000 INFO @ Sat, 11 Dec 2021 15:03:22: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:03:22: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:03:22: #1 total tags in treatment: 1762995 INFO @ Sat, 11 Dec 2021 15:03:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:03:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:03:22: #1 tags after filtering in treatment: 1115988 INFO @ Sat, 11 Dec 2021 15:03:22: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 11 Dec 2021 15:03:22: #1 finished! INFO @ Sat, 11 Dec 2021 15:03:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:03:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:03:22: #2 number of paired peaks: 9918 INFO @ Sat, 11 Dec 2021 15:03:22: start model_add_line... INFO @ Sat, 11 Dec 2021 15:03:22: start X-correlation... INFO @ Sat, 11 Dec 2021 15:03:22: end of X-cor INFO @ Sat, 11 Dec 2021 15:03:22: #2 finished! INFO @ Sat, 11 Dec 2021 15:03:22: #2 predicted fragment length is 153 bps INFO @ Sat, 11 Dec 2021 15:03:22: #2 alternative fragment length(s) may be 153,311 bps INFO @ Sat, 11 Dec 2021 15:03:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.10_model.r INFO @ Sat, 11 Dec 2021 15:03:22: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:03:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:03:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:03:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:03:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:03:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.10_summits.bed INFO @ Sat, 11 Dec 2021 15:03:26: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5357 records, 4 fields): 6 millis CompletedMACS2peakCalling 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 @ Sat, 11 Dec 2021 15:03:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.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 @ Sat, 11 Dec 2021 15:03:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:03:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:03:41: 1000000 INFO @ Sat, 11 Dec 2021 15:03:45: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:03:49: 3000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:03:53: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:03:53: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:03:53: #1 total tags in treatment: 1762995 INFO @ Sat, 11 Dec 2021 15:03:53: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:03:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:03:53: #1 tags after filtering in treatment: 1115988 INFO @ Sat, 11 Dec 2021 15:03:53: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 11 Dec 2021 15:03:53: #1 finished! INFO @ Sat, 11 Dec 2021 15:03:53: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:03:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:03:53: #2 number of paired peaks: 9918 INFO @ Sat, 11 Dec 2021 15:03:53: start model_add_line... INFO @ Sat, 11 Dec 2021 15:03:53: start X-correlation... INFO @ Sat, 11 Dec 2021 15:03:53: end of X-cor INFO @ Sat, 11 Dec 2021 15:03:53: #2 finished! INFO @ Sat, 11 Dec 2021 15:03:53: #2 predicted fragment length is 153 bps INFO @ Sat, 11 Dec 2021 15:03:53: #2 alternative fragment length(s) may be 153,311 bps INFO @ Sat, 11 Dec 2021 15:03:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.20_model.r INFO @ Sat, 11 Dec 2021 15:03:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:03:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:03:56: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:03:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:03:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:03:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281759/SRX9281759.20_summits.bed INFO @ Sat, 11 Dec 2021 15:03:57: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2352 records, 4 fields): 4 millis CompletedMACS2peakCalling