Job ID = 6627015 SRX = SRX8325346 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:23:44 prefetch.2.10.7: 1) Downloading 'SRR11772152'... 2020-07-14T00:23:44 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:27:06 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:27:06 prefetch.2.10.7: 1) 'SRR11772152' was downloaded successfully 2020-07-14T00:27:06 prefetch.2.10.7: 'SRR11772152' has 0 unresolved dependencies Read 11412092 spots for SRR11772152/SRR11772152.sra Written 11412092 spots for SRR11772152/SRR11772152.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627324 ("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: 00:40:59 11412092 reads; of these: 11412092 (100.00%) were paired; of these: 3506709 (30.73%) aligned concordantly 0 times 6087551 (53.34%) aligned concordantly exactly 1 time 1817832 (15.93%) aligned concordantly >1 times ---- 3506709 pairs aligned concordantly 0 times; of these: 1511543 (43.10%) aligned discordantly 1 time ---- 1995166 pairs aligned 0 times concordantly or discordantly; of these: 3990332 mates make up the pairs; of these: 1897539 (47.55%) aligned 0 times 1131401 (28.35%) aligned exactly 1 time 961392 (24.09%) aligned >1 times 91.69% overall alignment rate Time searching: 00:40:59 Overall time: 00:40:59 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 16 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] 2997481 / 9113660 = 0.3289 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 @ Tue, 14 Jul 2020 10:20:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.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, 14 Jul 2020 10:20:00: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:20:00: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:20:08: 1000000 INFO @ Tue, 14 Jul 2020 10:20:17: 2000000 INFO @ Tue, 14 Jul 2020 10:20:25: 3000000 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 @ Tue, 14 Jul 2020 10:20:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.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, 14 Jul 2020 10:20:30: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:20:30: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:20:34: 4000000 INFO @ Tue, 14 Jul 2020 10:20:39: 1000000 INFO @ Tue, 14 Jul 2020 10:20:43: 5000000 INFO @ Tue, 14 Jul 2020 10:20:48: 2000000 INFO @ Tue, 14 Jul 2020 10:20:52: 6000000 INFO @ Tue, 14 Jul 2020 10:20:56: 3000000 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 @ Tue, 14 Jul 2020 10:21:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.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, 14 Jul 2020 10:21:00: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:21:00: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:21:01: 7000000 INFO @ Tue, 14 Jul 2020 10:21:05: 4000000 INFO @ Tue, 14 Jul 2020 10:21:09: 1000000 INFO @ Tue, 14 Jul 2020 10:21:10: 8000000 INFO @ Tue, 14 Jul 2020 10:21:14: 5000000 INFO @ Tue, 14 Jul 2020 10:21:19: 2000000 INFO @ Tue, 14 Jul 2020 10:21:19: 9000000 INFO @ Tue, 14 Jul 2020 10:21:23: 6000000 INFO @ Tue, 14 Jul 2020 10:21:28: 3000000 INFO @ Tue, 14 Jul 2020 10:21:29: 10000000 INFO @ Tue, 14 Jul 2020 10:21:32: 7000000 INFO @ Tue, 14 Jul 2020 10:21:38: 4000000 INFO @ Tue, 14 Jul 2020 10:21:38: 11000000 INFO @ Tue, 14 Jul 2020 10:21:41: 8000000 INFO @ Tue, 14 Jul 2020 10:21:47: 5000000 INFO @ Tue, 14 Jul 2020 10:21:47: 12000000 INFO @ Tue, 14 Jul 2020 10:21:50: 9000000 INFO @ Tue, 14 Jul 2020 10:21:56: 6000000 INFO @ Tue, 14 Jul 2020 10:21:57: 13000000 INFO @ Tue, 14 Jul 2020 10:21:59: 10000000 INFO @ Tue, 14 Jul 2020 10:22:05: 7000000 INFO @ Tue, 14 Jul 2020 10:22:05: 14000000 INFO @ Tue, 14 Jul 2020 10:22:08: 11000000 INFO @ Tue, 14 Jul 2020 10:22:14: #1 tag size is determined as 104 bps INFO @ Tue, 14 Jul 2020 10:22:14: #1 tag size = 104 INFO @ Tue, 14 Jul 2020 10:22:14: #1 total tags in treatment: 5281405 INFO @ Tue, 14 Jul 2020 10:22:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:22:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:22:14: #1 tags after filtering in treatment: 4679252 INFO @ Tue, 14 Jul 2020 10:22:14: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 14 Jul 2020 10:22:14: #1 finished! INFO @ Tue, 14 Jul 2020 10:22:14: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:22:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:22:14: 8000000 INFO @ Tue, 14 Jul 2020 10:22:14: #2 number of paired peaks: 2691 INFO @ Tue, 14 Jul 2020 10:22:14: start model_add_line... INFO @ Tue, 14 Jul 2020 10:22:14: start X-correlation... INFO @ Tue, 14 Jul 2020 10:22:15: end of X-cor INFO @ Tue, 14 Jul 2020 10:22:15: #2 finished! INFO @ Tue, 14 Jul 2020 10:22:15: #2 predicted fragment length is 246 bps INFO @ Tue, 14 Jul 2020 10:22:15: #2 alternative fragment length(s) may be 246 bps INFO @ Tue, 14 Jul 2020 10:22:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.05_model.r INFO @ Tue, 14 Jul 2020 10:22:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:22:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:22:17: 12000000 INFO @ Tue, 14 Jul 2020 10:22:23: 9000000 INFO @ Tue, 14 Jul 2020 10:22:26: 13000000 INFO @ Tue, 14 Jul 2020 10:22:29: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:22:32: 10000000 INFO @ Tue, 14 Jul 2020 10:22:35: 14000000 INFO @ Tue, 14 Jul 2020 10:22:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:22:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:22:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.05_summits.bed INFO @ Tue, 14 Jul 2020 10:22:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7700 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:22:41: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:22:43: #1 tag size is determined as 104 bps INFO @ Tue, 14 Jul 2020 10:22:43: #1 tag size = 104 INFO @ Tue, 14 Jul 2020 10:22:43: #1 total tags in treatment: 5281405 INFO @ Tue, 14 Jul 2020 10:22:43: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:22:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:22:43: #1 tags after filtering in treatment: 4679252 INFO @ Tue, 14 Jul 2020 10:22:43: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 14 Jul 2020 10:22:43: #1 finished! INFO @ Tue, 14 Jul 2020 10:22:43: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:22:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:22:44: #2 number of paired peaks: 2691 INFO @ Tue, 14 Jul 2020 10:22:44: start model_add_line... INFO @ Tue, 14 Jul 2020 10:22:44: start X-correlation... INFO @ Tue, 14 Jul 2020 10:22:44: end of X-cor INFO @ Tue, 14 Jul 2020 10:22:44: #2 finished! INFO @ Tue, 14 Jul 2020 10:22:44: #2 predicted fragment length is 246 bps INFO @ Tue, 14 Jul 2020 10:22:44: #2 alternative fragment length(s) may be 246 bps INFO @ Tue, 14 Jul 2020 10:22:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.10_model.r INFO @ Tue, 14 Jul 2020 10:22:44: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:22:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:22:50: 12000000 INFO @ Tue, 14 Jul 2020 10:22:57: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:22:58: 13000000 INFO @ Tue, 14 Jul 2020 10:23:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:23:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:23:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.10_summits.bed INFO @ Tue, 14 Jul 2020 10:23:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4248 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:23:06: 14000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:23:14: #1 tag size is determined as 104 bps INFO @ Tue, 14 Jul 2020 10:23:14: #1 tag size = 104 INFO @ Tue, 14 Jul 2020 10:23:14: #1 total tags in treatment: 5281405 INFO @ Tue, 14 Jul 2020 10:23:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:23:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:23:14: #1 tags after filtering in treatment: 4679252 INFO @ Tue, 14 Jul 2020 10:23:14: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 14 Jul 2020 10:23:14: #1 finished! INFO @ Tue, 14 Jul 2020 10:23:14: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:23:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:23:14: #2 number of paired peaks: 2691 INFO @ Tue, 14 Jul 2020 10:23:14: start model_add_line... INFO @ Tue, 14 Jul 2020 10:23:14: start X-correlation... INFO @ Tue, 14 Jul 2020 10:23:14: end of X-cor INFO @ Tue, 14 Jul 2020 10:23:14: #2 finished! INFO @ Tue, 14 Jul 2020 10:23:14: #2 predicted fragment length is 246 bps INFO @ Tue, 14 Jul 2020 10:23:14: #2 alternative fragment length(s) may be 246 bps INFO @ Tue, 14 Jul 2020 10:23:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.20_model.r INFO @ Tue, 14 Jul 2020 10:23:14: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:23:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:23:28: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:23:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:23:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:23:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325346/SRX8325346.20_summits.bed INFO @ Tue, 14 Jul 2020 10:23:35: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2132 records, 4 fields): 4 millis CompletedMACS2peakCalling