Job ID = 14172279 SRX = SRX5681709 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3223383 spots for SRR8895579/SRR8895579.sra Written 3223383 spots for SRR8895579/SRR8895579.sra Read 2968948 spots for SRR8895580/SRR8895580.sra Written 2968948 spots for SRR8895580/SRR8895580.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172775 ("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: 00:08:00 6192331 reads; of these: 6192331 (100.00%) were paired; of these: 1453493 (23.47%) aligned concordantly 0 times 4351251 (70.27%) aligned concordantly exactly 1 time 387587 (6.26%) aligned concordantly >1 times ---- 1453493 pairs aligned concordantly 0 times; of these: 492259 (33.87%) aligned discordantly 1 time ---- 961234 pairs aligned 0 times concordantly or discordantly; of these: 1922468 mates make up the pairs; of these: 1448135 (75.33%) aligned 0 times 346783 (18.04%) aligned exactly 1 time 127550 (6.63%) aligned >1 times 88.31% overall alignment rate Time searching: 00:08:00 Overall time: 00:08:00 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_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] 242781 / 5218872 = 0.0465 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 15:13:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.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 15:13:05: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:13:05: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:13:12: 1000000 INFO @ Sat, 11 Dec 2021 15:13:19: 2000000 INFO @ Sat, 11 Dec 2021 15:13:26: 3000000 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 15:13:34: 4000000 INFO @ Sat, 11 Dec 2021 15:13:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.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 15:13:35: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:13:35: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:13:42: 5000000 INFO @ Sat, 11 Dec 2021 15:13:43: 1000000 INFO @ Sat, 11 Dec 2021 15:13:51: 6000000 INFO @ Sat, 11 Dec 2021 15:13:52: 2000000 INFO @ Sat, 11 Dec 2021 15:13:58: 7000000 INFO @ Sat, 11 Dec 2021 15:14:00: 3000000 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 15:14:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.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 15:14:05: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:14:05: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:14:06: 8000000 INFO @ Sat, 11 Dec 2021 15:14:09: 4000000 INFO @ Sat, 11 Dec 2021 15:14:13: 9000000 INFO @ Sat, 11 Dec 2021 15:14:14: 1000000 INFO @ Sat, 11 Dec 2021 15:14:18: 5000000 INFO @ Sat, 11 Dec 2021 15:14:22: 10000000 INFO @ Sat, 11 Dec 2021 15:14:22: 2000000 INFO @ Sat, 11 Dec 2021 15:14:25: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 15:14:25: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 15:14:25: #1 total tags in treatment: 4517550 INFO @ Sat, 11 Dec 2021 15:14:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:14:25: #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 15:14:26: #1 tags after filtering in treatment: 3834139 INFO @ Sat, 11 Dec 2021 15:14:26: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 15:14:26: #1 finished! INFO @ Sat, 11 Dec 2021 15:14:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:14:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:14:26: #2 number of paired peaks: 5511 INFO @ Sat, 11 Dec 2021 15:14:26: start model_add_line... INFO @ Sat, 11 Dec 2021 15:14:26: start X-correlation... INFO @ Sat, 11 Dec 2021 15:14:26: end of X-cor INFO @ Sat, 11 Dec 2021 15:14:26: #2 finished! INFO @ Sat, 11 Dec 2021 15:14:26: #2 predicted fragment length is 257 bps INFO @ Sat, 11 Dec 2021 15:14:26: #2 alternative fragment length(s) may be 257 bps INFO @ Sat, 11 Dec 2021 15:14:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.05_model.r INFO @ Sat, 11 Dec 2021 15:14:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:14:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:14:27: 6000000 INFO @ Sat, 11 Dec 2021 15:14:31: 3000000 INFO @ Sat, 11 Dec 2021 15:14:35: 7000000 INFO @ Sat, 11 Dec 2021 15:14:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:14:40: 4000000 INFO @ Sat, 11 Dec 2021 15:14:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:14:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:14:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.05_summits.bed INFO @ Sat, 11 Dec 2021 15:14:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7948 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:14:42: 8000000 INFO @ Sat, 11 Dec 2021 15:14:49: 5000000 INFO @ Sat, 11 Dec 2021 15:14:50: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:14:57: 6000000 INFO @ Sat, 11 Dec 2021 15:14:59: 10000000 INFO @ Sat, 11 Dec 2021 15:15:02: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 15:15:02: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 15:15:02: #1 total tags in treatment: 4517550 INFO @ Sat, 11 Dec 2021 15:15:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:15:02: #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 15:15:02: #1 tags after filtering in treatment: 3834139 INFO @ Sat, 11 Dec 2021 15:15:02: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 15:15:02: #1 finished! INFO @ Sat, 11 Dec 2021 15:15:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:15:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:15:03: #2 number of paired peaks: 5511 INFO @ Sat, 11 Dec 2021 15:15:03: start model_add_line... INFO @ Sat, 11 Dec 2021 15:15:03: start X-correlation... INFO @ Sat, 11 Dec 2021 15:15:03: end of X-cor INFO @ Sat, 11 Dec 2021 15:15:03: #2 finished! INFO @ Sat, 11 Dec 2021 15:15:03: #2 predicted fragment length is 257 bps INFO @ Sat, 11 Dec 2021 15:15:03: #2 alternative fragment length(s) may be 257 bps INFO @ Sat, 11 Dec 2021 15:15:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.10_model.r INFO @ Sat, 11 Dec 2021 15:15:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:15:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:15:05: 7000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:15:12: 8000000 INFO @ Sat, 11 Dec 2021 15:15:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:15:19: 9000000 INFO @ Sat, 11 Dec 2021 15:15:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:15:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:15:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.10_summits.bed INFO @ Sat, 11 Dec 2021 15:15:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3355 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:15:26: 10000000 INFO @ Sat, 11 Dec 2021 15:15:29: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 15:15:29: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 15:15:29: #1 total tags in treatment: 4517550 INFO @ Sat, 11 Dec 2021 15:15:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:15:29: #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 15:15:29: #1 tags after filtering in treatment: 3834139 INFO @ Sat, 11 Dec 2021 15:15:29: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 15:15:29: #1 finished! INFO @ Sat, 11 Dec 2021 15:15:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:15:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:15:29: #2 number of paired peaks: 5511 INFO @ Sat, 11 Dec 2021 15:15:29: start model_add_line... INFO @ Sat, 11 Dec 2021 15:15:29: start X-correlation... INFO @ Sat, 11 Dec 2021 15:15:29: end of X-cor INFO @ Sat, 11 Dec 2021 15:15:29: #2 finished! INFO @ Sat, 11 Dec 2021 15:15:29: #2 predicted fragment length is 257 bps INFO @ Sat, 11 Dec 2021 15:15:29: #2 alternative fragment length(s) may be 257 bps INFO @ Sat, 11 Dec 2021 15:15:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.20_model.r INFO @ Sat, 11 Dec 2021 15:15:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:15:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:15:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:15:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:15:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:15:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.20_summits.bed INFO @ Sat, 11 Dec 2021 15:15:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1148 records, 4 fields): 3 millis CompletedMACS2peakCalling