Job ID = 14167133 SRX = SRX11016837 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2021-12-10T01:18:48 prefetch.2.10.7: 1) Downloading 'SRR14678417'... 2021-12-10T01:18:48 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T01:19:43 prefetch.2.10.7: HTTPS download succeed 2021-12-10T01:19:43 prefetch.2.10.7: 1) 'SRR14678417' was downloaded successfully 2021-12-10T01:19:43 prefetch.2.10.7: 'SRR14678417' has 0 unresolved dependencies Read 30119902 spots for SRR14678417/SRR14678417.sra Written 30119902 spots for SRR14678417/SRR14678417.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167610 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:12 30119902 reads; of these: 30119902 (100.00%) were unpaired; of these: 1253261 (4.16%) aligned 0 times 26335402 (87.44%) aligned exactly 1 time 2531239 (8.40%) aligned >1 times 95.84% overall alignment rate Time searching: 00:10:13 Overall time: 00:10:13 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 12 files... [bam_rmdupse_core] 16527319 / 28866641 = 0.5725 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 @ Fri, 10 Dec 2021 10:37:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.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 @ Fri, 10 Dec 2021 10:37:29: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:37:29: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:37:36: 1000000 INFO @ Fri, 10 Dec 2021 10:37:42: 2000000 INFO @ Fri, 10 Dec 2021 10:37:49: 3000000 INFO @ Fri, 10 Dec 2021 10:37:55: 4000000 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 @ Fri, 10 Dec 2021 10:37:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.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 @ Fri, 10 Dec 2021 10:37:59: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:37:59: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:38:01: 5000000 INFO @ Fri, 10 Dec 2021 10:38:06: 1000000 INFO @ Fri, 10 Dec 2021 10:38:08: 6000000 INFO @ Fri, 10 Dec 2021 10:38:13: 2000000 INFO @ Fri, 10 Dec 2021 10:38:14: 7000000 INFO @ Fri, 10 Dec 2021 10:38:20: 3000000 INFO @ Fri, 10 Dec 2021 10:38:20: 8000000 INFO @ Fri, 10 Dec 2021 10:38:26: 4000000 INFO @ Fri, 10 Dec 2021 10:38:27: 9000000 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 @ Fri, 10 Dec 2021 10:38:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.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 @ Fri, 10 Dec 2021 10:38:29: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:38:29: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:38:33: 5000000 INFO @ Fri, 10 Dec 2021 10:38:33: 10000000 INFO @ Fri, 10 Dec 2021 10:38:35: 1000000 INFO @ Fri, 10 Dec 2021 10:38:39: 6000000 INFO @ Fri, 10 Dec 2021 10:38:40: 11000000 INFO @ Fri, 10 Dec 2021 10:38:41: 2000000 INFO @ Fri, 10 Dec 2021 10:38:46: 7000000 INFO @ Fri, 10 Dec 2021 10:38:46: 12000000 INFO @ Fri, 10 Dec 2021 10:38:47: 3000000 INFO @ Fri, 10 Dec 2021 10:38:48: #1 tag size is determined as 76 bps INFO @ Fri, 10 Dec 2021 10:38:48: #1 tag size = 76 INFO @ Fri, 10 Dec 2021 10:38:48: #1 total tags in treatment: 12339322 INFO @ Fri, 10 Dec 2021 10:38:48: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:38:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:38:49: #1 tags after filtering in treatment: 12339322 INFO @ Fri, 10 Dec 2021 10:38:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:38:49: #1 finished! INFO @ Fri, 10 Dec 2021 10:38:49: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:38:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:38:50: #2 number of paired peaks: 3657 INFO @ Fri, 10 Dec 2021 10:38:50: start model_add_line... INFO @ Fri, 10 Dec 2021 10:38:50: start X-correlation... INFO @ Fri, 10 Dec 2021 10:38:50: end of X-cor INFO @ Fri, 10 Dec 2021 10:38:50: #2 finished! INFO @ Fri, 10 Dec 2021 10:38:50: #2 predicted fragment length is 217 bps INFO @ Fri, 10 Dec 2021 10:38:50: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 10 Dec 2021 10:38:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.05_model.r INFO @ Fri, 10 Dec 2021 10:38:50: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:38:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:38:52: 8000000 INFO @ Fri, 10 Dec 2021 10:38:53: 4000000 INFO @ Fri, 10 Dec 2021 10:38:59: 9000000 INFO @ Fri, 10 Dec 2021 10:38:59: 5000000 INFO @ Fri, 10 Dec 2021 10:39:05: 6000000 INFO @ Fri, 10 Dec 2021 10:39:05: 10000000 INFO @ Fri, 10 Dec 2021 10:39:11: 7000000 INFO @ Fri, 10 Dec 2021 10:39:12: 11000000 INFO @ Fri, 10 Dec 2021 10:39:16: 8000000 INFO @ Fri, 10 Dec 2021 10:39:18: 12000000 INFO @ Fri, 10 Dec 2021 10:39:20: #1 tag size is determined as 76 bps INFO @ Fri, 10 Dec 2021 10:39:20: #1 tag size = 76 INFO @ Fri, 10 Dec 2021 10:39:20: #1 total tags in treatment: 12339322 INFO @ Fri, 10 Dec 2021 10:39:20: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:39:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:39:20: #1 tags after filtering in treatment: 12339322 INFO @ Fri, 10 Dec 2021 10:39:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:39:20: #1 finished! INFO @ Fri, 10 Dec 2021 10:39:20: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:39:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:39:21: #2 number of paired peaks: 3657 INFO @ Fri, 10 Dec 2021 10:39:21: start model_add_line... INFO @ Fri, 10 Dec 2021 10:39:22: start X-correlation... INFO @ Fri, 10 Dec 2021 10:39:22: end of X-cor INFO @ Fri, 10 Dec 2021 10:39:22: #2 finished! INFO @ Fri, 10 Dec 2021 10:39:22: #2 predicted fragment length is 217 bps INFO @ Fri, 10 Dec 2021 10:39:22: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 10 Dec 2021 10:39:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.10_model.r INFO @ Fri, 10 Dec 2021 10:39:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:39:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:39:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:39:22: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:39:28: 10000000 INFO @ Fri, 10 Dec 2021 10:39:33: 11000000 INFO @ Fri, 10 Dec 2021 10:39:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:39:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:39:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.05_summits.bed INFO @ Fri, 10 Dec 2021 10:39:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (9184 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:39:39: 12000000 INFO @ Fri, 10 Dec 2021 10:39:40: #1 tag size is determined as 76 bps INFO @ Fri, 10 Dec 2021 10:39:40: #1 tag size = 76 INFO @ Fri, 10 Dec 2021 10:39:40: #1 total tags in treatment: 12339322 INFO @ Fri, 10 Dec 2021 10:39:40: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:39:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:39:41: #1 tags after filtering in treatment: 12339322 INFO @ Fri, 10 Dec 2021 10:39:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:39:41: #1 finished! INFO @ Fri, 10 Dec 2021 10:39:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:39:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:39:42: #2 number of paired peaks: 3657 INFO @ Fri, 10 Dec 2021 10:39:42: start model_add_line... INFO @ Fri, 10 Dec 2021 10:39:42: start X-correlation... INFO @ Fri, 10 Dec 2021 10:39:42: end of X-cor INFO @ Fri, 10 Dec 2021 10:39:42: #2 finished! INFO @ Fri, 10 Dec 2021 10:39:42: #2 predicted fragment length is 217 bps INFO @ Fri, 10 Dec 2021 10:39:42: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 10 Dec 2021 10:39:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.20_model.r INFO @ Fri, 10 Dec 2021 10:39:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:39:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:39:53: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:40:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:40:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:40:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.10_summits.bed INFO @ Fri, 10 Dec 2021 10:40:08: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6442 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:40:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:40:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:40:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:40:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11016837/SRX11016837.20_summits.bed INFO @ Fri, 10 Dec 2021 10:40:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3670 records, 4 fields): 5 millis CompletedMACS2peakCalling