Job ID = 6497693 SRX = SRX1021227 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:50:42 prefetch.2.10.7: 1) Downloading 'SRR2013424'... 2020-06-25T22:50:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:54:28 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:54:28 prefetch.2.10.7: 1) 'SRR2013424' was downloaded successfully Read 20475732 spots for SRR2013424/SRR2013424.sra Written 20475732 spots for SRR2013424/SRR2013424.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:30:54 20475732 reads; of these: 20475732 (100.00%) were paired; of these: 5971900 (29.17%) aligned concordantly 0 times 10647311 (52.00%) aligned concordantly exactly 1 time 3856521 (18.83%) aligned concordantly >1 times ---- 5971900 pairs aligned concordantly 0 times; of these: 27983 (0.47%) aligned discordantly 1 time ---- 5943917 pairs aligned 0 times concordantly or discordantly; of these: 11887834 mates make up the pairs; of these: 11358237 (95.55%) aligned 0 times 373561 (3.14%) aligned exactly 1 time 156036 (1.31%) aligned >1 times 72.26% overall alignment rate Time searching: 00:30:54 Overall time: 00:30:54 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] 9484078 / 14516130 = 0.6533 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 @ Fri, 26 Jun 2020 08:34:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.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, 26 Jun 2020 08:34:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:34:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:34:22: 1000000 INFO @ Fri, 26 Jun 2020 08:34:27: 2000000 INFO @ Fri, 26 Jun 2020 08:34:32: 3000000 INFO @ Fri, 26 Jun 2020 08:34:37: 4000000 INFO @ Fri, 26 Jun 2020 08:34:42: 5000000 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 @ Fri, 26 Jun 2020 08:34:47: 6000000 INFO @ Fri, 26 Jun 2020 08:34:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.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, 26 Jun 2020 08:34:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:34:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:34:52: 7000000 INFO @ Fri, 26 Jun 2020 08:34:52: 1000000 INFO @ Fri, 26 Jun 2020 08:34:57: 8000000 INFO @ Fri, 26 Jun 2020 08:34:57: 2000000 INFO @ Fri, 26 Jun 2020 08:35:02: 9000000 INFO @ Fri, 26 Jun 2020 08:35:02: 3000000 INFO @ Fri, 26 Jun 2020 08:35:07: 10000000 INFO @ Fri, 26 Jun 2020 08:35:07: 4000000 INFO @ Fri, 26 Jun 2020 08:35:10: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:35:10: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:35:10: #1 total tags in treatment: 5029589 INFO @ Fri, 26 Jun 2020 08:35:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:35:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:35:10: #1 tags after filtering in treatment: 4634919 INFO @ Fri, 26 Jun 2020 08:35:10: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 08:35:10: #1 finished! INFO @ Fri, 26 Jun 2020 08:35:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:35:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:35:10: #2 number of paired peaks: 2487 INFO @ Fri, 26 Jun 2020 08:35:10: start model_add_line... INFO @ Fri, 26 Jun 2020 08:35:10: start X-correlation... INFO @ Fri, 26 Jun 2020 08:35:10: end of X-cor INFO @ Fri, 26 Jun 2020 08:35:10: #2 finished! INFO @ Fri, 26 Jun 2020 08:35:10: #2 predicted fragment length is 115 bps INFO @ Fri, 26 Jun 2020 08:35:10: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 26 Jun 2020 08:35:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.05_model.r INFO @ Fri, 26 Jun 2020 08:35:10: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:35:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:35:12: 5000000 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 @ Fri, 26 Jun 2020 08:35:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.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, 26 Jun 2020 08:35:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:35:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:35:17: 6000000 INFO @ Fri, 26 Jun 2020 08:35:22: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:35:22: 1000000 INFO @ Fri, 26 Jun 2020 08:35:22: 7000000 INFO @ Fri, 26 Jun 2020 08:35:27: 8000000 INFO @ Fri, 26 Jun 2020 08:35:27: 2000000 INFO @ Fri, 26 Jun 2020 08:35:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:35:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:35:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.05_summits.bed INFO @ Fri, 26 Jun 2020 08:35:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5648 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:35:32: 3000000 INFO @ Fri, 26 Jun 2020 08:35:32: 9000000 INFO @ Fri, 26 Jun 2020 08:35:37: 4000000 INFO @ Fri, 26 Jun 2020 08:35:37: 10000000 INFO @ Fri, 26 Jun 2020 08:35:40: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:35:40: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:35:40: #1 total tags in treatment: 5029589 INFO @ Fri, 26 Jun 2020 08:35:40: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:35:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:35:40: #1 tags after filtering in treatment: 4634919 INFO @ Fri, 26 Jun 2020 08:35:40: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 08:35:40: #1 finished! INFO @ Fri, 26 Jun 2020 08:35:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:35:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:35:41: #2 number of paired peaks: 2487 INFO @ Fri, 26 Jun 2020 08:35:41: start model_add_line... INFO @ Fri, 26 Jun 2020 08:35:41: start X-correlation... INFO @ Fri, 26 Jun 2020 08:35:41: end of X-cor INFO @ Fri, 26 Jun 2020 08:35:41: #2 finished! INFO @ Fri, 26 Jun 2020 08:35:41: #2 predicted fragment length is 115 bps INFO @ Fri, 26 Jun 2020 08:35:41: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 26 Jun 2020 08:35:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.10_model.r INFO @ Fri, 26 Jun 2020 08:35:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:35:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:35:42: 5000000 INFO @ Fri, 26 Jun 2020 08:35:47: 6000000 INFO @ Fri, 26 Jun 2020 08:35:52: 7000000 INFO @ Fri, 26 Jun 2020 08:35:52: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:35:56: 8000000 INFO @ Fri, 26 Jun 2020 08:35:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:35:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:35:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.10_summits.bed INFO @ Fri, 26 Jun 2020 08:35:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2707 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:36:01: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:36:06: 10000000 INFO @ Fri, 26 Jun 2020 08:36:09: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:36:09: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:36:09: #1 total tags in treatment: 5029589 INFO @ Fri, 26 Jun 2020 08:36:09: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:36:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:36:09: #1 tags after filtering in treatment: 4634919 INFO @ Fri, 26 Jun 2020 08:36:09: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 08:36:09: #1 finished! INFO @ Fri, 26 Jun 2020 08:36:09: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:36:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:36:10: #2 number of paired peaks: 2487 INFO @ Fri, 26 Jun 2020 08:36:10: start model_add_line... INFO @ Fri, 26 Jun 2020 08:36:10: start X-correlation... INFO @ Fri, 26 Jun 2020 08:36:10: end of X-cor INFO @ Fri, 26 Jun 2020 08:36:10: #2 finished! INFO @ Fri, 26 Jun 2020 08:36:10: #2 predicted fragment length is 115 bps INFO @ Fri, 26 Jun 2020 08:36:10: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 26 Jun 2020 08:36:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.20_model.r INFO @ Fri, 26 Jun 2020 08:36:10: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:36:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:36:21: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:36:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:36:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:36:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1021227/SRX1021227.20_summits.bed INFO @ Fri, 26 Jun 2020 08:36:26: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1024 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。