Job ID = 14168353 SRX = SRX11078123 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-10T08:58:03 prefetch.2.10.7: 1) Downloading 'SRR14743551'... 2021-12-10T08:58:03 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T08:58:51 prefetch.2.10.7: HTTPS download succeed 2021-12-10T08:58:51 prefetch.2.10.7: 1) 'SRR14743551' was downloaded successfully 2021-12-10T08:58:51 prefetch.2.10.7: 'SRR14743551' has 0 unresolved dependencies Read 21930820 spots for SRR14743551/SRR14743551.sra Written 21930820 spots for SRR14743551/SRR14743551.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169533 ("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: 00:11:24 21930820 reads; of these: 21930820 (100.00%) were paired; of these: 17078587 (77.87%) aligned concordantly 0 times 3750245 (17.10%) aligned concordantly exactly 1 time 1101988 (5.02%) aligned concordantly >1 times ---- 17078587 pairs aligned concordantly 0 times; of these: 12441 (0.07%) aligned discordantly 1 time ---- 17066146 pairs aligned 0 times concordantly or discordantly; of these: 34132292 mates make up the pairs; of these: 33791291 (99.00%) aligned 0 times 182498 (0.53%) aligned exactly 1 time 158503 (0.46%) aligned >1 times 22.96% overall alignment rate Time searching: 00:11:25 Overall time: 00:11:25 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_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] 304530 / 4860518 = 0.0627 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 18:15:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.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 18:15:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:15:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:15:26: 1000000 INFO @ Fri, 10 Dec 2021 18:15:31: 2000000 INFO @ Fri, 10 Dec 2021 18:15:36: 3000000 INFO @ Fri, 10 Dec 2021 18:15:41: 4000000 INFO @ Fri, 10 Dec 2021 18:15:46: 5000000 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 18:15:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.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 18:15:50: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:15:50: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:15:52: 6000000 INFO @ Fri, 10 Dec 2021 18:15:56: 1000000 INFO @ Fri, 10 Dec 2021 18:15:57: 7000000 INFO @ Fri, 10 Dec 2021 18:16:02: 2000000 INFO @ Fri, 10 Dec 2021 18:16:03: 8000000 INFO @ Fri, 10 Dec 2021 18:16:07: 3000000 INFO @ Fri, 10 Dec 2021 18:16:08: 9000000 INFO @ Fri, 10 Dec 2021 18:16:11: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:16:11: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:16:11: #1 total tags in treatment: 4547913 INFO @ Fri, 10 Dec 2021 18:16:11: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:16:11: #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 18:16:11: #1 tags after filtering in treatment: 4235631 INFO @ Fri, 10 Dec 2021 18:16:11: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 18:16:11: #1 finished! INFO @ Fri, 10 Dec 2021 18:16:11: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:16:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:16:11: #2 number of paired peaks: 604 WARNING @ Fri, 10 Dec 2021 18:16:11: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Fri, 10 Dec 2021 18:16:11: start model_add_line... INFO @ Fri, 10 Dec 2021 18:16:11: start X-correlation... INFO @ Fri, 10 Dec 2021 18:16:11: end of X-cor INFO @ Fri, 10 Dec 2021 18:16:11: #2 finished! INFO @ Fri, 10 Dec 2021 18:16:11: #2 predicted fragment length is 137 bps INFO @ Fri, 10 Dec 2021 18:16:11: #2 alternative fragment length(s) may be 4,137,583 bps INFO @ Fri, 10 Dec 2021 18:16:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.05_model.r INFO @ Fri, 10 Dec 2021 18:16:11: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:16:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:16:13: 4000000 INFO @ Fri, 10 Dec 2021 18:16:18: 5000000 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 18:16:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.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 18:16:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:16:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:16:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:16:23: 6000000 INFO @ Fri, 10 Dec 2021 18:16:26: 1000000 INFO @ Fri, 10 Dec 2021 18:16:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:16:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:16:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.05_summits.bed INFO @ Fri, 10 Dec 2021 18:16:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (449 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:16:28: 7000000 INFO @ Fri, 10 Dec 2021 18:16:31: 2000000 INFO @ Fri, 10 Dec 2021 18:16:34: 8000000 INFO @ Fri, 10 Dec 2021 18:16:36: 3000000 INFO @ Fri, 10 Dec 2021 18:16:39: 9000000 INFO @ Fri, 10 Dec 2021 18:16:41: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:16:41: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:16:41: #1 total tags in treatment: 4547913 INFO @ Fri, 10 Dec 2021 18:16:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:16:41: #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 18:16:42: #1 tags after filtering in treatment: 4235631 INFO @ Fri, 10 Dec 2021 18:16:42: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 18:16:42: #1 finished! INFO @ Fri, 10 Dec 2021 18:16:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:16:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:16:42: 4000000 INFO @ Fri, 10 Dec 2021 18:16:42: #2 number of paired peaks: 604 WARNING @ Fri, 10 Dec 2021 18:16:42: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Fri, 10 Dec 2021 18:16:42: start model_add_line... INFO @ Fri, 10 Dec 2021 18:16:42: start X-correlation... INFO @ Fri, 10 Dec 2021 18:16:42: end of X-cor INFO @ Fri, 10 Dec 2021 18:16:42: #2 finished! INFO @ Fri, 10 Dec 2021 18:16:42: #2 predicted fragment length is 137 bps INFO @ Fri, 10 Dec 2021 18:16:42: #2 alternative fragment length(s) may be 4,137,583 bps INFO @ Fri, 10 Dec 2021 18:16:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.10_model.r INFO @ Fri, 10 Dec 2021 18:16:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:16:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:16:47: 5000000 INFO @ Fri, 10 Dec 2021 18:16:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:16:53: 6000000 INFO @ Fri, 10 Dec 2021 18:16:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:16:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:16:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.10_summits.bed INFO @ Fri, 10 Dec 2021 18:16:56: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (227 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:16:58: 7000000 INFO @ Fri, 10 Dec 2021 18:17:04: 8000000 INFO @ Fri, 10 Dec 2021 18:17:09: 9000000 INFO @ Fri, 10 Dec 2021 18:17:11: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:17:11: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:17:11: #1 total tags in treatment: 4547913 INFO @ Fri, 10 Dec 2021 18:17:11: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:17:11: #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 18:17:11: #1 tags after filtering in treatment: 4235631 INFO @ Fri, 10 Dec 2021 18:17:11: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 18:17:11: #1 finished! INFO @ Fri, 10 Dec 2021 18:17:11: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:17:11: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:17:12: #2 number of paired peaks: 604 WARNING @ Fri, 10 Dec 2021 18:17:12: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Fri, 10 Dec 2021 18:17:12: start model_add_line... INFO @ Fri, 10 Dec 2021 18:17:12: start X-correlation... INFO @ Fri, 10 Dec 2021 18:17:12: end of X-cor INFO @ Fri, 10 Dec 2021 18:17:12: #2 finished! INFO @ Fri, 10 Dec 2021 18:17:12: #2 predicted fragment length is 137 bps INFO @ Fri, 10 Dec 2021 18:17:12: #2 alternative fragment length(s) may be 4,137,583 bps INFO @ Fri, 10 Dec 2021 18:17:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.20_model.r INFO @ Fri, 10 Dec 2021 18:17:12: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:17:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:17:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:17:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:17:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:17:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078123/SRX11078123.20_summits.bed INFO @ Fri, 10 Dec 2021 18:17:26: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (107 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。