Job ID = 12265189 SRX = SRX3426791 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20678082 spots for SRR6327142/SRR6327142.sra Written 20678082 spots for SRR6327142/SRR6327142.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265436 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:21:02 20678082 reads; of these: 20678082 (100.00%) were paired; of these: 14070610 (68.05%) aligned concordantly 0 times 4490714 (21.72%) aligned concordantly exactly 1 time 2116758 (10.24%) aligned concordantly >1 times ---- 14070610 pairs aligned concordantly 0 times; of these: 1265382 (8.99%) aligned discordantly 1 time ---- 12805228 pairs aligned 0 times concordantly or discordantly; of these: 25610456 mates make up the pairs; of these: 17684971 (69.05%) aligned 0 times 4708776 (18.39%) aligned exactly 1 time 3216709 (12.56%) aligned >1 times 57.24% overall alignment rate Time searching: 00:21:02 Overall time: 00:21:02 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] 1079824 / 7804339 = 0.1384 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:40:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.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 @ Sat, 03 Apr 2021 06:40:45: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:40:45: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:40:50: 1000000 INFO @ Sat, 03 Apr 2021 06:40:55: 2000000 INFO @ Sat, 03 Apr 2021 06:40:59: 3000000 INFO @ Sat, 03 Apr 2021 06:41:04: 4000000 INFO @ Sat, 03 Apr 2021 06:41:09: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:41:14: 6000000 INFO @ Sat, 03 Apr 2021 06:41:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.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 @ Sat, 03 Apr 2021 06:41:15: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:41:15: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:41:19: 7000000 INFO @ Sat, 03 Apr 2021 06:41:20: 1000000 INFO @ Sat, 03 Apr 2021 06:41:24: 8000000 INFO @ Sat, 03 Apr 2021 06:41:25: 2000000 INFO @ Sat, 03 Apr 2021 06:41:28: 9000000 INFO @ Sat, 03 Apr 2021 06:41:30: 3000000 INFO @ Sat, 03 Apr 2021 06:41:33: 10000000 INFO @ Sat, 03 Apr 2021 06:41:34: 4000000 INFO @ Sat, 03 Apr 2021 06:41:38: 11000000 INFO @ Sat, 03 Apr 2021 06:41:39: 5000000 INFO @ Sat, 03 Apr 2021 06:41:43: 12000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:41:44: 6000000 INFO @ Sat, 03 Apr 2021 06:41:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.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 @ Sat, 03 Apr 2021 06:41:45: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:41:45: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:41:48: 13000000 INFO @ Sat, 03 Apr 2021 06:41:49: 7000000 INFO @ Sat, 03 Apr 2021 06:41:50: 1000000 INFO @ Sat, 03 Apr 2021 06:41:53: 14000000 INFO @ Sat, 03 Apr 2021 06:41:54: 8000000 INFO @ Sat, 03 Apr 2021 06:41:55: 2000000 INFO @ Sat, 03 Apr 2021 06:41:58: 15000000 INFO @ Sat, 03 Apr 2021 06:41:58: 9000000 INFO @ Sat, 03 Apr 2021 06:42:00: 3000000 INFO @ Sat, 03 Apr 2021 06:42:02: 16000000 INFO @ Sat, 03 Apr 2021 06:42:03: 10000000 INFO @ Sat, 03 Apr 2021 06:42:04: 4000000 INFO @ Sat, 03 Apr 2021 06:42:07: 17000000 INFO @ Sat, 03 Apr 2021 06:42:08: 11000000 INFO @ Sat, 03 Apr 2021 06:42:09: 5000000 INFO @ Sat, 03 Apr 2021 06:42:12: 18000000 INFO @ Sat, 03 Apr 2021 06:42:13: 12000000 INFO @ Sat, 03 Apr 2021 06:42:14: 6000000 INFO @ Sat, 03 Apr 2021 06:42:17: 19000000 INFO @ Sat, 03 Apr 2021 06:42:18: 13000000 INFO @ Sat, 03 Apr 2021 06:42:19: 7000000 INFO @ Sat, 03 Apr 2021 06:42:22: 20000000 INFO @ Sat, 03 Apr 2021 06:42:23: 14000000 INFO @ Sat, 03 Apr 2021 06:42:24: 8000000 INFO @ Sat, 03 Apr 2021 06:42:27: 21000000 INFO @ Sat, 03 Apr 2021 06:42:27: 15000000 INFO @ Sat, 03 Apr 2021 06:42:29: 9000000 INFO @ Sat, 03 Apr 2021 06:42:29: #1 tag size is determined as 37 bps INFO @ Sat, 03 Apr 2021 06:42:29: #1 tag size = 37 INFO @ Sat, 03 Apr 2021 06:42:29: #1 total tags in treatment: 5685020 INFO @ Sat, 03 Apr 2021 06:42:29: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:42:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:42:29: #1 tags after filtering in treatment: 4947925 INFO @ Sat, 03 Apr 2021 06:42:29: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 03 Apr 2021 06:42:29: #1 finished! INFO @ Sat, 03 Apr 2021 06:42:29: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:42:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:42:30: #2 number of paired peaks: 732 WARNING @ Sat, 03 Apr 2021 06:42:30: Fewer paired peaks (732) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 732 pairs to build model! INFO @ Sat, 03 Apr 2021 06:42:30: start model_add_line... INFO @ Sat, 03 Apr 2021 06:42:30: start X-correlation... INFO @ Sat, 03 Apr 2021 06:42:30: end of X-cor INFO @ Sat, 03 Apr 2021 06:42:30: #2 finished! INFO @ Sat, 03 Apr 2021 06:42:30: #2 predicted fragment length is 88 bps INFO @ Sat, 03 Apr 2021 06:42:30: #2 alternative fragment length(s) may be 88 bps INFO @ Sat, 03 Apr 2021 06:42:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.05_model.r INFO @ Sat, 03 Apr 2021 06:42:30: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:42:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:42:32: 16000000 INFO @ Sat, 03 Apr 2021 06:42:34: 10000000 INFO @ Sat, 03 Apr 2021 06:42:37: 17000000 INFO @ Sat, 03 Apr 2021 06:42:38: 11000000 INFO @ Sat, 03 Apr 2021 06:42:42: 18000000 INFO @ Sat, 03 Apr 2021 06:42:42: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:42:43: 12000000 INFO @ Sat, 03 Apr 2021 06:42:46: 19000000 INFO @ Sat, 03 Apr 2021 06:42:48: 13000000 INFO @ Sat, 03 Apr 2021 06:42:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:42:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:42:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.05_summits.bed INFO @ Sat, 03 Apr 2021 06:42:48: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4281 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:42:51: 20000000 INFO @ Sat, 03 Apr 2021 06:42:53: 14000000 INFO @ Sat, 03 Apr 2021 06:42:56: 21000000 INFO @ Sat, 03 Apr 2021 06:42:58: 15000000 INFO @ Sat, 03 Apr 2021 06:42:59: #1 tag size is determined as 37 bps INFO @ Sat, 03 Apr 2021 06:42:59: #1 tag size = 37 INFO @ Sat, 03 Apr 2021 06:42:59: #1 total tags in treatment: 5685020 INFO @ Sat, 03 Apr 2021 06:42:59: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:42:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:42:59: #1 tags after filtering in treatment: 4947925 INFO @ Sat, 03 Apr 2021 06:42:59: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 03 Apr 2021 06:42:59: #1 finished! INFO @ Sat, 03 Apr 2021 06:42:59: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:42:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:42:59: #2 number of paired peaks: 732 WARNING @ Sat, 03 Apr 2021 06:42:59: Fewer paired peaks (732) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 732 pairs to build model! INFO @ Sat, 03 Apr 2021 06:42:59: start model_add_line... INFO @ Sat, 03 Apr 2021 06:42:59: start X-correlation... INFO @ Sat, 03 Apr 2021 06:42:59: end of X-cor INFO @ Sat, 03 Apr 2021 06:42:59: #2 finished! INFO @ Sat, 03 Apr 2021 06:42:59: #2 predicted fragment length is 88 bps INFO @ Sat, 03 Apr 2021 06:42:59: #2 alternative fragment length(s) may be 88 bps INFO @ Sat, 03 Apr 2021 06:42:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.10_model.r INFO @ Sat, 03 Apr 2021 06:42:59: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:42:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:43:02: 16000000 INFO @ Sat, 03 Apr 2021 06:43:07: 17000000 INFO @ Sat, 03 Apr 2021 06:43:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:43:12: 18000000 INFO @ Sat, 03 Apr 2021 06:43:16: 19000000 INFO @ Sat, 03 Apr 2021 06:43:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:43:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:43:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.10_summits.bed INFO @ Sat, 03 Apr 2021 06:43:17: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2106 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:43:21: 20000000 INFO @ Sat, 03 Apr 2021 06:43:26: 21000000 INFO @ Sat, 03 Apr 2021 06:43:28: #1 tag size is determined as 37 bps INFO @ Sat, 03 Apr 2021 06:43:28: #1 tag size = 37 INFO @ Sat, 03 Apr 2021 06:43:28: #1 total tags in treatment: 5685020 INFO @ Sat, 03 Apr 2021 06:43:28: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:43:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:43:28: #1 tags after filtering in treatment: 4947925 INFO @ Sat, 03 Apr 2021 06:43:28: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 03 Apr 2021 06:43:28: #1 finished! INFO @ Sat, 03 Apr 2021 06:43:28: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:43:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:43:29: #2 number of paired peaks: 732 WARNING @ Sat, 03 Apr 2021 06:43:29: Fewer paired peaks (732) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 732 pairs to build model! INFO @ Sat, 03 Apr 2021 06:43:29: start model_add_line... INFO @ Sat, 03 Apr 2021 06:43:29: start X-correlation... INFO @ Sat, 03 Apr 2021 06:43:29: end of X-cor INFO @ Sat, 03 Apr 2021 06:43:29: #2 finished! INFO @ Sat, 03 Apr 2021 06:43:29: #2 predicted fragment length is 88 bps INFO @ Sat, 03 Apr 2021 06:43:29: #2 alternative fragment length(s) may be 88 bps INFO @ Sat, 03 Apr 2021 06:43:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.20_model.r INFO @ Sat, 03 Apr 2021 06:43:29: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:43:29: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:43:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:43:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:43:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:43:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3426791/SRX3426791.20_summits.bed INFO @ Sat, 03 Apr 2021 06:43:47: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (561 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。