Job ID = 6498447 SRX = SRX511345 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T23:43:52 prefetch.2.10.7: 1) Downloading 'SRR1217607'... 2020-06-25T23:43:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:46:26 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:46:27 prefetch.2.10.7: 'SRR1217607' is valid 2020-06-25T23:46:27 prefetch.2.10.7: 1) 'SRR1217607' was downloaded successfully Read 8709466 spots for SRR1217607/SRR1217607.sra Written 8709466 spots for SRR1217607/SRR1217607.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: 00:17:39 8709466 reads; of these: 8709466 (100.00%) were paired; of these: 1773163 (20.36%) aligned concordantly 0 times 4824953 (55.40%) aligned concordantly exactly 1 time 2111350 (24.24%) aligned concordantly >1 times ---- 1773163 pairs aligned concordantly 0 times; of these: 5308 (0.30%) aligned discordantly 1 time ---- 1767855 pairs aligned 0 times concordantly or discordantly; of these: 3535710 mates make up the pairs; of these: 3321085 (93.93%) aligned 0 times 145977 (4.13%) aligned exactly 1 time 68648 (1.94%) aligned >1 times 80.93% overall alignment rate Time searching: 00:17:39 Overall time: 00:17:39 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] 1031435 / 6934910 = 0.1487 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 09:09:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.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 09:09:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:09:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:09:24: 1000000 INFO @ Fri, 26 Jun 2020 09:09:30: 2000000 INFO @ Fri, 26 Jun 2020 09:09:36: 3000000 INFO @ Fri, 26 Jun 2020 09:09:42: 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 @ Fri, 26 Jun 2020 09:09:47: 5000000 INFO @ Fri, 26 Jun 2020 09:09:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.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 09:09:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:09:48: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:09:53: 6000000 INFO @ Fri, 26 Jun 2020 09:09:55: 1000000 INFO @ Fri, 26 Jun 2020 09:10:00: 7000000 INFO @ Fri, 26 Jun 2020 09:10:01: 2000000 INFO @ Fri, 26 Jun 2020 09:10:06: 8000000 INFO @ Fri, 26 Jun 2020 09:10:08: 3000000 INFO @ Fri, 26 Jun 2020 09:10:12: 9000000 INFO @ Fri, 26 Jun 2020 09:10:14: 4000000 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 09:10:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.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 09:10:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:10:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:10:19: 10000000 INFO @ Fri, 26 Jun 2020 09:10:21: 5000000 INFO @ Fri, 26 Jun 2020 09:10:25: 11000000 INFO @ Fri, 26 Jun 2020 09:10:26: 1000000 INFO @ Fri, 26 Jun 2020 09:10:28: 6000000 INFO @ Fri, 26 Jun 2020 09:10:32: 12000000 INFO @ Fri, 26 Jun 2020 09:10:32: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:10:32: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:10:32: #1 total tags in treatment: 5905437 INFO @ Fri, 26 Jun 2020 09:10:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:10:32: #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 09:10:32: #1 tags after filtering in treatment: 5358708 INFO @ Fri, 26 Jun 2020 09:10:32: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 09:10:32: #1 finished! INFO @ Fri, 26 Jun 2020 09:10:32: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:10:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:10:33: #2 number of paired peaks: 4239 INFO @ Fri, 26 Jun 2020 09:10:33: start model_add_line... INFO @ Fri, 26 Jun 2020 09:10:33: start X-correlation... INFO @ Fri, 26 Jun 2020 09:10:33: end of X-cor INFO @ Fri, 26 Jun 2020 09:10:33: #2 finished! INFO @ Fri, 26 Jun 2020 09:10:33: #2 predicted fragment length is 149 bps INFO @ Fri, 26 Jun 2020 09:10:33: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 26 Jun 2020 09:10:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.05_model.r INFO @ Fri, 26 Jun 2020 09:10:33: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:10:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:10:35: 2000000 INFO @ Fri, 26 Jun 2020 09:10:35: 7000000 INFO @ Fri, 26 Jun 2020 09:10:42: 8000000 INFO @ Fri, 26 Jun 2020 09:10:43: 3000000 INFO @ Fri, 26 Jun 2020 09:10:49: 9000000 INFO @ Fri, 26 Jun 2020 09:10:51: 4000000 INFO @ Fri, 26 Jun 2020 09:10:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:10:56: 10000000 INFO @ Fri, 26 Jun 2020 09:10:59: 5000000 INFO @ Fri, 26 Jun 2020 09:11:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:11:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:11:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.05_summits.bed INFO @ Fri, 26 Jun 2020 09:11:00: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7132 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:11:03: 11000000 INFO @ Fri, 26 Jun 2020 09:11:07: 6000000 INFO @ Fri, 26 Jun 2020 09:11:10: 12000000 INFO @ Fri, 26 Jun 2020 09:11:10: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:11:10: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:11:10: #1 total tags in treatment: 5905437 INFO @ Fri, 26 Jun 2020 09:11:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:11:10: #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 09:11:10: #1 tags after filtering in treatment: 5358708 INFO @ Fri, 26 Jun 2020 09:11:10: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 09:11:10: #1 finished! INFO @ Fri, 26 Jun 2020 09:11:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:11:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:11:11: #2 number of paired peaks: 4239 INFO @ Fri, 26 Jun 2020 09:11:11: start model_add_line... INFO @ Fri, 26 Jun 2020 09:11:11: start X-correlation... INFO @ Fri, 26 Jun 2020 09:11:11: end of X-cor INFO @ Fri, 26 Jun 2020 09:11:11: #2 finished! INFO @ Fri, 26 Jun 2020 09:11:11: #2 predicted fragment length is 149 bps INFO @ Fri, 26 Jun 2020 09:11:11: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 26 Jun 2020 09:11:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.10_model.r INFO @ Fri, 26 Jun 2020 09:11:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:11:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:11:15: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:11:23: 8000000 INFO @ Fri, 26 Jun 2020 09:11:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:11:30: 9000000 INFO @ Fri, 26 Jun 2020 09:11:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:11:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:11:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.10_summits.bed INFO @ Fri, 26 Jun 2020 09:11:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4359 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:11:38: 10000000 INFO @ Fri, 26 Jun 2020 09:11:45: 11000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:11:52: 12000000 INFO @ Fri, 26 Jun 2020 09:11:53: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:11:53: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:11:53: #1 total tags in treatment: 5905437 INFO @ Fri, 26 Jun 2020 09:11:53: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:11:53: #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 09:11:53: #1 tags after filtering in treatment: 5358708 INFO @ Fri, 26 Jun 2020 09:11:53: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 09:11:53: #1 finished! INFO @ Fri, 26 Jun 2020 09:11:53: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:11:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:11:53: #2 number of paired peaks: 4239 INFO @ Fri, 26 Jun 2020 09:11:53: start model_add_line... INFO @ Fri, 26 Jun 2020 09:11:53: start X-correlation... INFO @ Fri, 26 Jun 2020 09:11:53: end of X-cor INFO @ Fri, 26 Jun 2020 09:11:53: #2 finished! INFO @ Fri, 26 Jun 2020 09:11:53: #2 predicted fragment length is 149 bps INFO @ Fri, 26 Jun 2020 09:11:53: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 26 Jun 2020 09:11:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.20_model.r INFO @ Fri, 26 Jun 2020 09:11:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:11:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:12:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:12:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:12:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:12:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511345/SRX511345.20_summits.bed INFO @ Fri, 26 Jun 2020 09:12:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2158 records, 4 fields): 5 millis CompletedMACS2peakCalling