Job ID = 14172257 SRX = SRX9281756 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5195528 spots for SRR12813503/SRR12813503.sra Written 5195528 spots for SRR12813503/SRR12813503.sra Read 5218688 spots for SRR12813504/SRR12813504.sra Written 5218688 spots for SRR12813504/SRR12813504.sra Read 5368418 spots for SRR12813505/SRR12813505.sra Written 5368418 spots for SRR12813505/SRR12813505.sra Read 4821104 spots for SRR12813506/SRR12813506.sra Written 4821104 spots for SRR12813506/SRR12813506.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172720 ("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: 00:04:12 20603738 reads; of these: 20603738 (100.00%) were paired; of these: 18374624 (89.18%) aligned concordantly 0 times 2050910 (9.95%) aligned concordantly exactly 1 time 178204 (0.86%) aligned concordantly >1 times ---- 18374624 pairs aligned concordantly 0 times; of these: 37939 (0.21%) aligned discordantly 1 time ---- 18336685 pairs aligned 0 times concordantly or discordantly; of these: 36673370 mates make up the pairs; of these: 35967529 (98.08%) aligned 0 times 513712 (1.40%) aligned exactly 1 time 192129 (0.52%) aligned >1 times 12.72% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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] 321362 / 2240369 = 0.1434 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 15:02:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.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 15:02:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:02:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:02:21: 1000000 INFO @ Sat, 11 Dec 2021 15:02:25: 2000000 INFO @ Sat, 11 Dec 2021 15:02:29: 3000000 INFO @ Sat, 11 Dec 2021 15:02:33: 4000000 INFO @ Sat, 11 Dec 2021 15:02:36: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:02:36: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:02:36: #1 total tags in treatment: 1908027 INFO @ Sat, 11 Dec 2021 15:02:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:02:36: #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 15:02:36: #1 tags after filtering in treatment: 1205226 INFO @ Sat, 11 Dec 2021 15:02:36: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 11 Dec 2021 15:02:36: #1 finished! INFO @ Sat, 11 Dec 2021 15:02:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:02:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:02:36: #2 number of paired peaks: 10357 INFO @ Sat, 11 Dec 2021 15:02:36: start model_add_line... INFO @ Sat, 11 Dec 2021 15:02:36: start X-correlation... INFO @ Sat, 11 Dec 2021 15:02:36: end of X-cor INFO @ Sat, 11 Dec 2021 15:02:36: #2 finished! INFO @ Sat, 11 Dec 2021 15:02:36: #2 predicted fragment length is 154 bps INFO @ Sat, 11 Dec 2021 15:02:36: #2 alternative fragment length(s) may be 154,223 bps INFO @ Sat, 11 Dec 2021 15:02:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.05_model.r INFO @ Sat, 11 Dec 2021 15:02:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:02:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:02:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:02:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:02:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:02:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.05_summits.bed INFO @ Sat, 11 Dec 2021 15:02:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7250 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 15:02:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.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 15:02:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:02:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:02:52: 1000000 INFO @ Sat, 11 Dec 2021 15:02:57: 2000000 INFO @ Sat, 11 Dec 2021 15:03:02: 3000000 INFO @ Sat, 11 Dec 2021 15:03:06: 4000000 INFO @ Sat, 11 Dec 2021 15:03:09: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:03:09: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:03:09: #1 total tags in treatment: 1908027 INFO @ Sat, 11 Dec 2021 15:03:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:03:09: #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 15:03:09: #1 tags after filtering in treatment: 1205226 INFO @ Sat, 11 Dec 2021 15:03:09: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 11 Dec 2021 15:03:09: #1 finished! INFO @ Sat, 11 Dec 2021 15:03:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:03:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:03:10: #2 number of paired peaks: 10357 INFO @ Sat, 11 Dec 2021 15:03:10: start model_add_line... INFO @ Sat, 11 Dec 2021 15:03:10: start X-correlation... INFO @ Sat, 11 Dec 2021 15:03:10: end of X-cor INFO @ Sat, 11 Dec 2021 15:03:10: #2 finished! INFO @ Sat, 11 Dec 2021 15:03:10: #2 predicted fragment length is 154 bps INFO @ Sat, 11 Dec 2021 15:03:10: #2 alternative fragment length(s) may be 154,223 bps INFO @ Sat, 11 Dec 2021 15:03:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.10_model.r INFO @ Sat, 11 Dec 2021 15:03:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:03:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:03:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:03:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:03:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:03:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.10_summits.bed INFO @ Sat, 11 Dec 2021 15:03:14: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5595 records, 4 fields): 7 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 15:03:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.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 15:03:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:03:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:03:21: 1000000 INFO @ Sat, 11 Dec 2021 15:03:25: 2000000 INFO @ Sat, 11 Dec 2021 15:03:29: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:03:33: 4000000 INFO @ Sat, 11 Dec 2021 15:03:35: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:03:35: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:03:35: #1 total tags in treatment: 1908027 INFO @ Sat, 11 Dec 2021 15:03:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:03:35: #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 15:03:36: #1 tags after filtering in treatment: 1205226 INFO @ Sat, 11 Dec 2021 15:03:36: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 11 Dec 2021 15:03:36: #1 finished! INFO @ Sat, 11 Dec 2021 15:03:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:03:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:03:36: #2 number of paired peaks: 10357 INFO @ Sat, 11 Dec 2021 15:03:36: start model_add_line... INFO @ Sat, 11 Dec 2021 15:03:36: start X-correlation... INFO @ Sat, 11 Dec 2021 15:03:36: end of X-cor INFO @ Sat, 11 Dec 2021 15:03:36: #2 finished! INFO @ Sat, 11 Dec 2021 15:03:36: #2 predicted fragment length is 154 bps INFO @ Sat, 11 Dec 2021 15:03:36: #2 alternative fragment length(s) may be 154,223 bps INFO @ Sat, 11 Dec 2021 15:03:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.20_model.r INFO @ Sat, 11 Dec 2021 15:03:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:03:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:03:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:03:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:03:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:03:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281756/SRX9281756.20_summits.bed INFO @ Sat, 11 Dec 2021 15:03:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2700 records, 4 fields): 4 millis CompletedMACS2peakCalling