Job ID = 10165827 SRX = SRX5681715 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5922976 spots for SRR8895591/SRR8895591.sra Written 5922976 spots for SRR8895591/SRR8895591.sra Read 3376611 spots for SRR8895592/SRR8895592.sra Written 3376611 spots for SRR8895592/SRR8895592.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166215 ("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: 00:13:09 9299587 reads; of these: 9299587 (100.00%) were paired; of these: 2393117 (25.73%) aligned concordantly 0 times 6042952 (64.98%) aligned concordantly exactly 1 time 863518 (9.29%) aligned concordantly >1 times ---- 2393117 pairs aligned concordantly 0 times; of these: 488134 (20.40%) aligned discordantly 1 time ---- 1904983 pairs aligned 0 times concordantly or discordantly; of these: 3809966 mates make up the pairs; of these: 3166939 (83.12%) aligned 0 times 432769 (11.36%) aligned exactly 1 time 210258 (5.52%) aligned >1 times 82.97% overall alignment rate Time searching: 00:13:09 Overall time: 00:13:09 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] 383500 / 7363526 = 0.0521 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 20:16:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.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 20:16:33: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:16:33: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:16:47: 1000000 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 20:17:01: 2000000 INFO @ Thu, 08 Oct 2020 20:17:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.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 20:17:03: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:17:03: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:17:14: 3000000 INFO @ Thu, 08 Oct 2020 20:17:16: 1000000 INFO @ Thu, 08 Oct 2020 20:17:25: 4000000 INFO @ Thu, 08 Oct 2020 20:17:26: 2000000 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 20:17:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.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 20:17:33: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:17:33: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:17:34: 5000000 INFO @ Thu, 08 Oct 2020 20:17:35: 3000000 INFO @ Thu, 08 Oct 2020 20:17:40: 1000000 INFO @ Thu, 08 Oct 2020 20:17:43: 6000000 INFO @ Thu, 08 Oct 2020 20:17:44: 4000000 INFO @ Thu, 08 Oct 2020 20:17:47: 2000000 INFO @ Thu, 08 Oct 2020 20:17:52: 7000000 INFO @ Thu, 08 Oct 2020 20:17:53: 5000000 INFO @ Thu, 08 Oct 2020 20:17:54: 3000000 INFO @ Thu, 08 Oct 2020 20:18:01: 4000000 INFO @ Thu, 08 Oct 2020 20:18:01: 8000000 INFO @ Thu, 08 Oct 2020 20:18:02: 6000000 INFO @ Thu, 08 Oct 2020 20:18:07: 5000000 INFO @ Thu, 08 Oct 2020 20:18:10: 9000000 INFO @ Thu, 08 Oct 2020 20:18:11: 7000000 INFO @ Thu, 08 Oct 2020 20:18:14: 6000000 INFO @ Thu, 08 Oct 2020 20:18:18: 10000000 INFO @ Thu, 08 Oct 2020 20:18:19: 8000000 INFO @ Thu, 08 Oct 2020 20:18:21: 7000000 INFO @ Thu, 08 Oct 2020 20:18:26: 11000000 INFO @ Thu, 08 Oct 2020 20:18:27: 9000000 INFO @ Thu, 08 Oct 2020 20:18:28: 8000000 INFO @ Thu, 08 Oct 2020 20:18:35: 9000000 INFO @ Thu, 08 Oct 2020 20:18:35: 12000000 INFO @ Thu, 08 Oct 2020 20:18:36: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:18:42: 10000000 INFO @ Thu, 08 Oct 2020 20:18:44: 13000000 INFO @ Thu, 08 Oct 2020 20:18:45: 11000000 INFO @ Thu, 08 Oct 2020 20:18:49: 11000000 INFO @ Thu, 08 Oct 2020 20:18:53: 14000000 INFO @ Thu, 08 Oct 2020 20:18:54: 12000000 INFO @ Thu, 08 Oct 2020 20:18:56: 12000000 INFO @ Thu, 08 Oct 2020 20:18:59: #1 tag size is determined as 100 bps INFO @ Thu, 08 Oct 2020 20:18:59: #1 tag size = 100 INFO @ Thu, 08 Oct 2020 20:18:59: #1 total tags in treatment: 6542806 INFO @ Thu, 08 Oct 2020 20:18:59: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:18:59: #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 20:18:59: #1 tags after filtering in treatment: 5771567 INFO @ Thu, 08 Oct 2020 20:18:59: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 08 Oct 2020 20:18:59: #1 finished! INFO @ Thu, 08 Oct 2020 20:18:59: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:18:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:18:59: #2 number of paired peaks: 2186 INFO @ Thu, 08 Oct 2020 20:18:59: start model_add_line... INFO @ Thu, 08 Oct 2020 20:18:59: start X-correlation... INFO @ Thu, 08 Oct 2020 20:18:59: end of X-cor INFO @ Thu, 08 Oct 2020 20:18:59: #2 finished! INFO @ Thu, 08 Oct 2020 20:18:59: #2 predicted fragment length is 236 bps INFO @ Thu, 08 Oct 2020 20:18:59: #2 alternative fragment length(s) may be 236 bps INFO @ Thu, 08 Oct 2020 20:18:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.05_model.r INFO @ Thu, 08 Oct 2020 20:18:59: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:18:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:19:02: 13000000 INFO @ Thu, 08 Oct 2020 20:19:03: 13000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:19:10: 14000000 INFO @ Thu, 08 Oct 2020 20:19:11: 14000000 INFO @ Thu, 08 Oct 2020 20:19:15: #1 tag size is determined as 100 bps INFO @ Thu, 08 Oct 2020 20:19:15: #1 tag size = 100 INFO @ Thu, 08 Oct 2020 20:19:15: #1 total tags in treatment: 6542806 INFO @ Thu, 08 Oct 2020 20:19:15: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:19:15: #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 20:19:15: #1 tags after filtering in treatment: 5771567 INFO @ Thu, 08 Oct 2020 20:19:15: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 08 Oct 2020 20:19:15: #1 finished! INFO @ Thu, 08 Oct 2020 20:19:15: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:19:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:19:15: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:19:16: #2 number of paired peaks: 2186 INFO @ Thu, 08 Oct 2020 20:19:16: start model_add_line... INFO @ Thu, 08 Oct 2020 20:19:16: start X-correlation... INFO @ Thu, 08 Oct 2020 20:19:16: end of X-cor INFO @ Thu, 08 Oct 2020 20:19:16: #2 finished! INFO @ Thu, 08 Oct 2020 20:19:16: #2 predicted fragment length is 236 bps INFO @ Thu, 08 Oct 2020 20:19:16: #2 alternative fragment length(s) may be 236 bps INFO @ Thu, 08 Oct 2020 20:19:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.20_model.r INFO @ Thu, 08 Oct 2020 20:19:16: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:19:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:19:16: #1 tag size is determined as 100 bps INFO @ Thu, 08 Oct 2020 20:19:16: #1 tag size = 100 INFO @ Thu, 08 Oct 2020 20:19:16: #1 total tags in treatment: 6542806 INFO @ Thu, 08 Oct 2020 20:19:16: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:19:16: #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 20:19:16: #1 tags after filtering in treatment: 5771567 INFO @ Thu, 08 Oct 2020 20:19:16: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 08 Oct 2020 20:19:16: #1 finished! INFO @ Thu, 08 Oct 2020 20:19:16: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:19:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:19:17: #2 number of paired peaks: 2186 INFO @ Thu, 08 Oct 2020 20:19:17: start model_add_line... INFO @ Thu, 08 Oct 2020 20:19:17: start X-correlation... INFO @ Thu, 08 Oct 2020 20:19:17: end of X-cor INFO @ Thu, 08 Oct 2020 20:19:17: #2 finished! INFO @ Thu, 08 Oct 2020 20:19:17: #2 predicted fragment length is 236 bps INFO @ Thu, 08 Oct 2020 20:19:17: #2 alternative fragment length(s) may be 236 bps INFO @ Thu, 08 Oct 2020 20:19:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.10_model.r INFO @ Thu, 08 Oct 2020 20:19:17: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:19:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:19:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:19:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:19:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.05_summits.bed INFO @ Thu, 08 Oct 2020 20:19:24: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11943 records, 4 fields): 178 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:19:29: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:19:32: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:19:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:19:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:19:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.20_summits.bed INFO @ Thu, 08 Oct 2020 20:19:35: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1178 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:19:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:19:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:19:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5681715/SRX5681715.10_summits.bed INFO @ Thu, 08 Oct 2020 20:19:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5158 records, 4 fields): 6 millis CompletedMACS2peakCalling