Job ID = 10165816 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 10166157 ("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: 00:07:58 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: 00:07:58 Overall time: 00:07:58 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:08:49: # 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 @ Thu, 08 Oct 2020 20:08:49: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:08:49: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:08:56: 1000000 INFO @ Thu, 08 Oct 2020 20:09:02: 2000000 INFO @ Thu, 08 Oct 2020 20:09:09: 3000000 INFO @ Thu, 08 Oct 2020 20:09:15: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:09:19: # 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 @ Thu, 08 Oct 2020 20:09:19: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:09:19: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:09:21: 5000000 INFO @ Thu, 08 Oct 2020 20:09:27: 1000000 INFO @ Thu, 08 Oct 2020 20:09:29: 6000000 INFO @ Thu, 08 Oct 2020 20:09:34: 2000000 INFO @ Thu, 08 Oct 2020 20:09:36: 7000000 INFO @ Thu, 08 Oct 2020 20:09:42: 3000000 INFO @ Thu, 08 Oct 2020 20:09:43: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:09:49: 4000000 INFO @ Thu, 08 Oct 2020 20:09:49: # 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 @ Thu, 08 Oct 2020 20:09:49: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:09:49: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:09:50: 9000000 INFO @ Thu, 08 Oct 2020 20:09:56: 5000000 INFO @ Thu, 08 Oct 2020 20:09:57: 1000000 INFO @ Thu, 08 Oct 2020 20:09:57: 10000000 INFO @ Thu, 08 Oct 2020 20:10:00: #1 tag size is determined as 100 bps INFO @ Thu, 08 Oct 2020 20:10:00: #1 tag size = 100 INFO @ Thu, 08 Oct 2020 20:10:00: #1 total tags in treatment: 4517550 INFO @ Thu, 08 Oct 2020 20:10:00: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:10:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:10:00: #1 tags after filtering in treatment: 3834139 INFO @ Thu, 08 Oct 2020 20:10:00: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 08 Oct 2020 20:10:00: #1 finished! INFO @ Thu, 08 Oct 2020 20:10:00: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:10:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:10:01: #2 number of paired peaks: 5511 INFO @ Thu, 08 Oct 2020 20:10:01: start model_add_line... INFO @ Thu, 08 Oct 2020 20:10:01: start X-correlation... INFO @ Thu, 08 Oct 2020 20:10:01: end of X-cor INFO @ Thu, 08 Oct 2020 20:10:01: #2 finished! INFO @ Thu, 08 Oct 2020 20:10:01: #2 predicted fragment length is 257 bps INFO @ Thu, 08 Oct 2020 20:10:01: #2 alternative fragment length(s) may be 257 bps INFO @ Thu, 08 Oct 2020 20:10:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.05_model.r INFO @ Thu, 08 Oct 2020 20:10:01: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:10:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:10:04: 6000000 INFO @ Thu, 08 Oct 2020 20:10:04: 2000000 INFO @ Thu, 08 Oct 2020 20:10:11: 7000000 INFO @ Thu, 08 Oct 2020 20:10:11: 3000000 INFO @ Thu, 08 Oct 2020 20:10:13: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:10:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:10:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:10:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.05_summits.bed INFO @ Thu, 08 Oct 2020 20:10:18: Done! INFO @ Thu, 08 Oct 2020 20:10:18: 8000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7948 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:10:19: 4000000 INFO @ Thu, 08 Oct 2020 20:10:25: 9000000 INFO @ Thu, 08 Oct 2020 20:10:26: 5000000 INFO @ Thu, 08 Oct 2020 20:10:32: 10000000 INFO @ Thu, 08 Oct 2020 20:10:33: 6000000 INFO @ Thu, 08 Oct 2020 20:10:35: #1 tag size is determined as 100 bps INFO @ Thu, 08 Oct 2020 20:10:35: #1 tag size = 100 INFO @ Thu, 08 Oct 2020 20:10:35: #1 total tags in treatment: 4517550 INFO @ Thu, 08 Oct 2020 20:10:35: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:10:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:10:35: #1 tags after filtering in treatment: 3834139 INFO @ Thu, 08 Oct 2020 20:10:35: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 08 Oct 2020 20:10:35: #1 finished! INFO @ Thu, 08 Oct 2020 20:10:35: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:10:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:10:36: #2 number of paired peaks: 5511 INFO @ Thu, 08 Oct 2020 20:10:36: start model_add_line... INFO @ Thu, 08 Oct 2020 20:10:36: start X-correlation... INFO @ Thu, 08 Oct 2020 20:10:36: end of X-cor INFO @ Thu, 08 Oct 2020 20:10:36: #2 finished! INFO @ Thu, 08 Oct 2020 20:10:36: #2 predicted fragment length is 257 bps INFO @ Thu, 08 Oct 2020 20:10:36: #2 alternative fragment length(s) may be 257 bps INFO @ Thu, 08 Oct 2020 20:10:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.10_model.r INFO @ Thu, 08 Oct 2020 20:10:36: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:10:36: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:10:40: 7000000 INFO @ Thu, 08 Oct 2020 20:10:47: 8000000 INFO @ Thu, 08 Oct 2020 20:10:47: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:10:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:10:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:10:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.10_summits.bed INFO @ Thu, 08 Oct 2020 20:10:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3355 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:10:53: 9000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:11:00: 10000000 INFO @ Thu, 08 Oct 2020 20:11:03: #1 tag size is determined as 100 bps INFO @ Thu, 08 Oct 2020 20:11:03: #1 tag size = 100 INFO @ Thu, 08 Oct 2020 20:11:03: #1 total tags in treatment: 4517550 INFO @ Thu, 08 Oct 2020 20:11:03: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:11:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:11:03: #1 tags after filtering in treatment: 3834139 INFO @ Thu, 08 Oct 2020 20:11:03: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 08 Oct 2020 20:11:03: #1 finished! INFO @ Thu, 08 Oct 2020 20:11:03: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:11:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:11:03: #2 number of paired peaks: 5511 INFO @ Thu, 08 Oct 2020 20:11:03: start model_add_line... INFO @ Thu, 08 Oct 2020 20:11:03: start X-correlation... INFO @ Thu, 08 Oct 2020 20:11:03: end of X-cor INFO @ Thu, 08 Oct 2020 20:11:03: #2 finished! INFO @ Thu, 08 Oct 2020 20:11:03: #2 predicted fragment length is 257 bps INFO @ Thu, 08 Oct 2020 20:11:03: #2 alternative fragment length(s) may be 257 bps INFO @ Thu, 08 Oct 2020 20:11:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.20_model.r INFO @ Thu, 08 Oct 2020 20:11:03: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:11:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:11:14: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:11:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:11:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:11:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5681709/SRX5681709.20_summits.bed INFO @ Thu, 08 Oct 2020 20:11:19: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1148 records, 4 fields): 3 millis CompletedMACS2peakCalling