Job ID = 6498733 SRX = SRX749058 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T00:01:25 prefetch.2.10.7: 1) Downloading 'SRR1636786'... 2020-06-26T00:01:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:07:31 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:07:31 prefetch.2.10.7: 1) 'SRR1636786' was downloaded successfully Read 26001353 spots for SRR1636786/SRR1636786.sra Written 26001353 spots for SRR1636786/SRR1636786.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: 00:36:03 26001353 reads; of these: 26001353 (100.00%) were paired; of these: 12894350 (49.59%) aligned concordantly 0 times 8433292 (32.43%) aligned concordantly exactly 1 time 4673711 (17.97%) aligned concordantly >1 times ---- 12894350 pairs aligned concordantly 0 times; of these: 17608 (0.14%) aligned discordantly 1 time ---- 12876742 pairs aligned 0 times concordantly or discordantly; of these: 25753484 mates make up the pairs; of these: 25298640 (98.23%) aligned 0 times 275968 (1.07%) aligned exactly 1 time 178876 (0.69%) aligned >1 times 51.35% overall alignment rate Time searching: 00:36:03 Overall time: 00:36:03 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_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] 1966007 / 13105355 = 0.1500 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 09:54:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.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 09:54:21: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:54:21: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:54:27: 1000000 INFO @ Fri, 26 Jun 2020 09:54:32: 2000000 INFO @ Fri, 26 Jun 2020 09:54:38: 3000000 INFO @ Fri, 26 Jun 2020 09:54:43: 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 09:54:49: 5000000 INFO @ Fri, 26 Jun 2020 09:54:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.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 09:54:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:54:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:54:55: 6000000 INFO @ Fri, 26 Jun 2020 09:54:57: 1000000 INFO @ Fri, 26 Jun 2020 09:55:01: 7000000 INFO @ Fri, 26 Jun 2020 09:55:03: 2000000 INFO @ Fri, 26 Jun 2020 09:55:07: 8000000 INFO @ Fri, 26 Jun 2020 09:55:09: 3000000 INFO @ Fri, 26 Jun 2020 09:55:13: 9000000 INFO @ Fri, 26 Jun 2020 09:55:15: 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 09:55:19: 10000000 INFO @ Fri, 26 Jun 2020 09:55:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.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 09:55:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:55:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:55:21: 5000000 INFO @ Fri, 26 Jun 2020 09:55:25: 11000000 INFO @ Fri, 26 Jun 2020 09:55:27: 1000000 INFO @ Fri, 26 Jun 2020 09:55:27: 6000000 INFO @ Fri, 26 Jun 2020 09:55:31: 12000000 INFO @ Fri, 26 Jun 2020 09:55:33: 2000000 INFO @ Fri, 26 Jun 2020 09:55:33: 7000000 INFO @ Fri, 26 Jun 2020 09:55:37: 13000000 INFO @ Fri, 26 Jun 2020 09:55:39: 3000000 INFO @ Fri, 26 Jun 2020 09:55:39: 8000000 INFO @ Fri, 26 Jun 2020 09:55:43: 14000000 INFO @ Fri, 26 Jun 2020 09:55:45: 4000000 INFO @ Fri, 26 Jun 2020 09:55:45: 9000000 INFO @ Fri, 26 Jun 2020 09:55:49: 15000000 INFO @ Fri, 26 Jun 2020 09:55:52: 10000000 INFO @ Fri, 26 Jun 2020 09:55:52: 5000000 INFO @ Fri, 26 Jun 2020 09:55:56: 16000000 INFO @ Fri, 26 Jun 2020 09:55:58: 11000000 INFO @ Fri, 26 Jun 2020 09:55:58: 6000000 INFO @ Fri, 26 Jun 2020 09:56:02: 17000000 INFO @ Fri, 26 Jun 2020 09:56:04: 12000000 INFO @ Fri, 26 Jun 2020 09:56:04: 7000000 INFO @ Fri, 26 Jun 2020 09:56:08: 18000000 INFO @ Fri, 26 Jun 2020 09:56:11: 13000000 INFO @ Fri, 26 Jun 2020 09:56:11: 8000000 INFO @ Fri, 26 Jun 2020 09:56:15: 19000000 INFO @ Fri, 26 Jun 2020 09:56:17: 9000000 INFO @ Fri, 26 Jun 2020 09:56:17: 14000000 INFO @ Fri, 26 Jun 2020 09:56:21: 20000000 INFO @ Fri, 26 Jun 2020 09:56:23: 10000000 INFO @ Fri, 26 Jun 2020 09:56:23: 15000000 INFO @ Fri, 26 Jun 2020 09:56:27: 21000000 INFO @ Fri, 26 Jun 2020 09:56:30: 11000000 INFO @ Fri, 26 Jun 2020 09:56:30: 16000000 INFO @ Fri, 26 Jun 2020 09:56:34: 22000000 INFO @ Fri, 26 Jun 2020 09:56:36: 12000000 INFO @ Fri, 26 Jun 2020 09:56:36: 17000000 INFO @ Fri, 26 Jun 2020 09:56:39: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:56:39: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:56:39: #1 total tags in treatment: 11142055 INFO @ Fri, 26 Jun 2020 09:56:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:56:39: #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 09:56:39: #1 tags after filtering in treatment: 10387700 INFO @ Fri, 26 Jun 2020 09:56:39: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 09:56:39: #1 finished! INFO @ Fri, 26 Jun 2020 09:56:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:56:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:56:40: #2 number of paired peaks: 663 WARNING @ Fri, 26 Jun 2020 09:56:40: Fewer paired peaks (663) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 663 pairs to build model! INFO @ Fri, 26 Jun 2020 09:56:40: start model_add_line... INFO @ Fri, 26 Jun 2020 09:56:40: start X-correlation... INFO @ Fri, 26 Jun 2020 09:56:40: end of X-cor INFO @ Fri, 26 Jun 2020 09:56:40: #2 finished! INFO @ Fri, 26 Jun 2020 09:56:40: #2 predicted fragment length is 111 bps INFO @ Fri, 26 Jun 2020 09:56:40: #2 alternative fragment length(s) may be 111 bps INFO @ Fri, 26 Jun 2020 09:56:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.05_model.r INFO @ Fri, 26 Jun 2020 09:56:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:56:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:56:42: 13000000 INFO @ Fri, 26 Jun 2020 09:56:43: 18000000 INFO @ Fri, 26 Jun 2020 09:56:49: 14000000 INFO @ Fri, 26 Jun 2020 09:56:49: 19000000 INFO @ Fri, 26 Jun 2020 09:56:55: 15000000 INFO @ Fri, 26 Jun 2020 09:56:55: 20000000 INFO @ Fri, 26 Jun 2020 09:57:01: 16000000 INFO @ Fri, 26 Jun 2020 09:57:01: 21000000 INFO @ Fri, 26 Jun 2020 09:57:06: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:57:07: 17000000 INFO @ Fri, 26 Jun 2020 09:57:08: 22000000 INFO @ Fri, 26 Jun 2020 09:57:12: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:57:12: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:57:12: #1 total tags in treatment: 11142055 INFO @ Fri, 26 Jun 2020 09:57:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:57:12: #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 09:57:13: #1 tags after filtering in treatment: 10387700 INFO @ Fri, 26 Jun 2020 09:57:13: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 09:57:13: #1 finished! INFO @ Fri, 26 Jun 2020 09:57:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:57:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:57:14: #2 number of paired peaks: 663 WARNING @ Fri, 26 Jun 2020 09:57:14: Fewer paired peaks (663) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 663 pairs to build model! INFO @ Fri, 26 Jun 2020 09:57:14: start model_add_line... INFO @ Fri, 26 Jun 2020 09:57:14: start X-correlation... INFO @ Fri, 26 Jun 2020 09:57:14: end of X-cor INFO @ Fri, 26 Jun 2020 09:57:14: #2 finished! INFO @ Fri, 26 Jun 2020 09:57:14: #2 predicted fragment length is 111 bps INFO @ Fri, 26 Jun 2020 09:57:14: #2 alternative fragment length(s) may be 111 bps INFO @ Fri, 26 Jun 2020 09:57:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.10_model.r INFO @ Fri, 26 Jun 2020 09:57:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:57:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:57:14: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:57:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:57:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:57:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.05_summits.bed INFO @ Fri, 26 Jun 2020 09:57:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2734 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:57:20: 19000000 INFO @ Fri, 26 Jun 2020 09:57:26: 20000000 INFO @ Fri, 26 Jun 2020 09:57:31: 21000000 INFO @ Fri, 26 Jun 2020 09:57:37: 22000000 INFO @ Fri, 26 Jun 2020 09:57:39: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:57:42: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:57:42: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:57:42: #1 total tags in treatment: 11142055 INFO @ Fri, 26 Jun 2020 09:57:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:57:42: #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 09:57:42: #1 tags after filtering in treatment: 10387700 INFO @ Fri, 26 Jun 2020 09:57:42: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 09:57:42: #1 finished! INFO @ Fri, 26 Jun 2020 09:57:42: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:57:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:57:43: #2 number of paired peaks: 663 WARNING @ Fri, 26 Jun 2020 09:57:43: Fewer paired peaks (663) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 663 pairs to build model! INFO @ Fri, 26 Jun 2020 09:57:43: start model_add_line... INFO @ Fri, 26 Jun 2020 09:57:43: start X-correlation... INFO @ Fri, 26 Jun 2020 09:57:43: end of X-cor INFO @ Fri, 26 Jun 2020 09:57:43: #2 finished! INFO @ Fri, 26 Jun 2020 09:57:43: #2 predicted fragment length is 111 bps INFO @ Fri, 26 Jun 2020 09:57:43: #2 alternative fragment length(s) may be 111 bps INFO @ Fri, 26 Jun 2020 09:57:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.20_model.r INFO @ Fri, 26 Jun 2020 09:57:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:57:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:57:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:57:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:57:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.10_summits.bed INFO @ Fri, 26 Jun 2020 09:57:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1446 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:58:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:58:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:58:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:58:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749058/SRX749058.20_summits.bed INFO @ Fri, 26 Jun 2020 09:58:21: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (790 records, 4 fields): 3 millis CompletedMACS2peakCalling