Job ID = 16439445 SRX = SRX5101714 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5897098 spots for SRR8287007/SRR8287007.sra Written 5897098 spots for SRR8287007/SRR8287007.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439526 ("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: 00:12:43 5897098 reads; of these: 5897098 (100.00%) were paired; of these: 325629 (5.52%) aligned concordantly 0 times 2320744 (39.35%) aligned concordantly exactly 1 time 3250725 (55.12%) aligned concordantly >1 times ---- 325629 pairs aligned concordantly 0 times; of these: 117851 (36.19%) aligned discordantly 1 time ---- 207778 pairs aligned 0 times concordantly or discordantly; of these: 415556 mates make up the pairs; of these: 148646 (35.77%) aligned 0 times 111029 (26.72%) aligned exactly 1 time 155881 (37.51%) aligned >1 times 98.74% overall alignment rate Time searching: 00:12:44 Overall time: 00:12:44 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] 1811135 / 5501767 = 0.3292 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 15:30:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.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 15:30:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:30:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:30:43: 1000000 INFO @ Tue, 02 Aug 2022 15:30:52: 2000000 INFO @ Tue, 02 Aug 2022 15:31:00: 3000000 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 15:31:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.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 15:31:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:31:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:31:09: 4000000 INFO @ Tue, 02 Aug 2022 15:31:13: 1000000 INFO @ Tue, 02 Aug 2022 15:31:19: 5000000 INFO @ Tue, 02 Aug 2022 15:31:21: 2000000 INFO @ Tue, 02 Aug 2022 15:31:27: 6000000 INFO @ Tue, 02 Aug 2022 15:31:30: 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 15:31:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.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 15:31:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:31:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:31:36: 7000000 INFO @ Tue, 02 Aug 2022 15:31:39: 4000000 INFO @ Tue, 02 Aug 2022 15:31:44: 1000000 INFO @ Tue, 02 Aug 2022 15:31:46: 8000000 INFO @ Tue, 02 Aug 2022 15:31:46: #1 tag size is determined as 72 bps INFO @ Tue, 02 Aug 2022 15:31:46: #1 tag size = 72 INFO @ Tue, 02 Aug 2022 15:31:46: #1 total tags in treatment: 3761299 INFO @ Tue, 02 Aug 2022 15:31:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:31:46: #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 15:31:46: #1 tags after filtering in treatment: 2483471 INFO @ Tue, 02 Aug 2022 15:31:46: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 02 Aug 2022 15:31:46: #1 finished! INFO @ Tue, 02 Aug 2022 15:31:46: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:31:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:31:46: #2 number of paired peaks: 5251 INFO @ Tue, 02 Aug 2022 15:31:46: start model_add_line... INFO @ Tue, 02 Aug 2022 15:31:46: start X-correlation... INFO @ Tue, 02 Aug 2022 15:31:47: end of X-cor INFO @ Tue, 02 Aug 2022 15:31:47: #2 finished! INFO @ Tue, 02 Aug 2022 15:31:47: #2 predicted fragment length is 172 bps INFO @ Tue, 02 Aug 2022 15:31:47: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 02 Aug 2022 15:31:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.05_model.r INFO @ Tue, 02 Aug 2022 15:31:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:31:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:31:48: 5000000 INFO @ Tue, 02 Aug 2022 15:31:53: 2000000 INFO @ Tue, 02 Aug 2022 15:31:56: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:31:57: 6000000 INFO @ Tue, 02 Aug 2022 15:32:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:32:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:32:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.05_summits.bed INFO @ Tue, 02 Aug 2022 15:32:01: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6506 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:32:02: 3000000 INFO @ Tue, 02 Aug 2022 15:32:06: 7000000 INFO @ Tue, 02 Aug 2022 15:32:11: 4000000 INFO @ Tue, 02 Aug 2022 15:32:17: 8000000 INFO @ Tue, 02 Aug 2022 15:32:17: #1 tag size is determined as 72 bps INFO @ Tue, 02 Aug 2022 15:32:17: #1 tag size = 72 INFO @ Tue, 02 Aug 2022 15:32:17: #1 total tags in treatment: 3761299 INFO @ Tue, 02 Aug 2022 15:32:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:32:17: #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 15:32:17: #1 tags after filtering in treatment: 2483471 INFO @ Tue, 02 Aug 2022 15:32:17: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 02 Aug 2022 15:32:17: #1 finished! INFO @ Tue, 02 Aug 2022 15:32:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:32:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:32:18: #2 number of paired peaks: 5251 INFO @ Tue, 02 Aug 2022 15:32:18: start model_add_line... INFO @ Tue, 02 Aug 2022 15:32:18: start X-correlation... INFO @ Tue, 02 Aug 2022 15:32:18: end of X-cor INFO @ Tue, 02 Aug 2022 15:32:18: #2 finished! INFO @ Tue, 02 Aug 2022 15:32:18: #2 predicted fragment length is 172 bps INFO @ Tue, 02 Aug 2022 15:32:18: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 02 Aug 2022 15:32:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.10_model.r INFO @ Tue, 02 Aug 2022 15:32:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:32:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:32:21: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:32:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:32:29: 6000000 INFO @ Tue, 02 Aug 2022 15:32:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:32:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:32:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.10_summits.bed INFO @ Tue, 02 Aug 2022 15:32:32: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3058 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:32:37: 7000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:32:46: 8000000 INFO @ Tue, 02 Aug 2022 15:32:46: #1 tag size is determined as 72 bps INFO @ Tue, 02 Aug 2022 15:32:46: #1 tag size = 72 INFO @ Tue, 02 Aug 2022 15:32:46: #1 total tags in treatment: 3761299 INFO @ Tue, 02 Aug 2022 15:32:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:32:46: #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 15:32:46: #1 tags after filtering in treatment: 2483471 INFO @ Tue, 02 Aug 2022 15:32:46: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 02 Aug 2022 15:32:46: #1 finished! INFO @ Tue, 02 Aug 2022 15:32:46: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:32:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:32:47: #2 number of paired peaks: 5251 INFO @ Tue, 02 Aug 2022 15:32:47: start model_add_line... INFO @ Tue, 02 Aug 2022 15:32:47: start X-correlation... INFO @ Tue, 02 Aug 2022 15:32:47: end of X-cor INFO @ Tue, 02 Aug 2022 15:32:47: #2 finished! INFO @ Tue, 02 Aug 2022 15:32:47: #2 predicted fragment length is 172 bps INFO @ Tue, 02 Aug 2022 15:32:47: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 02 Aug 2022 15:32:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.20_model.r INFO @ Tue, 02 Aug 2022 15:32:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:32:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:32:56: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:33:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:33:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:33:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5101714/SRX5101714.20_summits.bed INFO @ Tue, 02 Aug 2022 15:33:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (771 records, 4 fields): 15 millis CompletedMACS2peakCalling