Job ID = 14170603 SRX = SRX8497057 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15305095 spots for SRR11952656/SRR11952656.sra Written 15305095 spots for SRR11952656/SRR11952656.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171141 ("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: 00:45:14 15305095 reads; of these: 15305095 (100.00%) were paired; of these: 1891173 (12.36%) aligned concordantly 0 times 7457212 (48.72%) aligned concordantly exactly 1 time 5956710 (38.92%) aligned concordantly >1 times ---- 1891173 pairs aligned concordantly 0 times; of these: 308766 (16.33%) aligned discordantly 1 time ---- 1582407 pairs aligned 0 times concordantly or discordantly; of these: 3164814 mates make up the pairs; of these: 2197594 (69.44%) aligned 0 times 367587 (11.61%) aligned exactly 1 time 599633 (18.95%) aligned >1 times 92.82% overall alignment rate Time searching: 00:45:14 Overall time: 00:45:14 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] 1933227 / 13688662 = 0.1412 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 @ Sat, 11 Dec 2021 08:20:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.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, 11 Dec 2021 08:20:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:20:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:20:42: 1000000 INFO @ Sat, 11 Dec 2021 08:20:48: 2000000 INFO @ Sat, 11 Dec 2021 08:20:53: 3000000 INFO @ Sat, 11 Dec 2021 08:20:58: 4000000 INFO @ Sat, 11 Dec 2021 08:21:03: 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 @ Sat, 11 Dec 2021 08:21:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.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, 11 Dec 2021 08:21:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:21:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:21:08: 6000000 INFO @ Sat, 11 Dec 2021 08:21:13: 1000000 INFO @ Sat, 11 Dec 2021 08:21:14: 7000000 INFO @ Sat, 11 Dec 2021 08:21:18: 2000000 INFO @ Sat, 11 Dec 2021 08:21:19: 8000000 INFO @ Sat, 11 Dec 2021 08:21:23: 3000000 INFO @ Sat, 11 Dec 2021 08:21:24: 9000000 INFO @ Sat, 11 Dec 2021 08:21:29: 4000000 INFO @ Sat, 11 Dec 2021 08:21:30: 10000000 INFO @ Sat, 11 Dec 2021 08:21:34: 5000000 INFO @ Sat, 11 Dec 2021 08:21:35: 11000000 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 @ Sat, 11 Dec 2021 08:21:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.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, 11 Dec 2021 08:21:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:21:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:21:40: 6000000 INFO @ Sat, 11 Dec 2021 08:21:41: 12000000 INFO @ Sat, 11 Dec 2021 08:21:43: 1000000 INFO @ Sat, 11 Dec 2021 08:21:45: 7000000 INFO @ Sat, 11 Dec 2021 08:21:46: 13000000 INFO @ Sat, 11 Dec 2021 08:21:48: 2000000 INFO @ Sat, 11 Dec 2021 08:21:51: 8000000 INFO @ Sat, 11 Dec 2021 08:21:51: 14000000 INFO @ Sat, 11 Dec 2021 08:21:54: 3000000 INFO @ Sat, 11 Dec 2021 08:21:56: 9000000 INFO @ Sat, 11 Dec 2021 08:21:57: 15000000 INFO @ Sat, 11 Dec 2021 08:21:59: 4000000 INFO @ Sat, 11 Dec 2021 08:22:01: 10000000 INFO @ Sat, 11 Dec 2021 08:22:02: 16000000 INFO @ Sat, 11 Dec 2021 08:22:04: 5000000 INFO @ Sat, 11 Dec 2021 08:22:07: 11000000 INFO @ Sat, 11 Dec 2021 08:22:07: 17000000 INFO @ Sat, 11 Dec 2021 08:22:10: 6000000 INFO @ Sat, 11 Dec 2021 08:22:12: 12000000 INFO @ Sat, 11 Dec 2021 08:22:13: 18000000 INFO @ Sat, 11 Dec 2021 08:22:15: 7000000 INFO @ Sat, 11 Dec 2021 08:22:18: 13000000 INFO @ Sat, 11 Dec 2021 08:22:18: 19000000 INFO @ Sat, 11 Dec 2021 08:22:21: 8000000 INFO @ Sat, 11 Dec 2021 08:22:23: 14000000 INFO @ Sat, 11 Dec 2021 08:22:24: 20000000 INFO @ Sat, 11 Dec 2021 08:22:26: 9000000 INFO @ Sat, 11 Dec 2021 08:22:28: 15000000 INFO @ Sat, 11 Dec 2021 08:22:29: 21000000 INFO @ Sat, 11 Dec 2021 08:22:32: 10000000 INFO @ Sat, 11 Dec 2021 08:22:34: 16000000 INFO @ Sat, 11 Dec 2021 08:22:35: 22000000 INFO @ Sat, 11 Dec 2021 08:22:37: 11000000 INFO @ Sat, 11 Dec 2021 08:22:39: 17000000 INFO @ Sat, 11 Dec 2021 08:22:40: 23000000 INFO @ Sat, 11 Dec 2021 08:22:42: 12000000 INFO @ Sat, 11 Dec 2021 08:22:44: 18000000 INFO @ Sat, 11 Dec 2021 08:22:45: 24000000 INFO @ Sat, 11 Dec 2021 08:22:48: 13000000 INFO @ Sat, 11 Dec 2021 08:22:49: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:22:49: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:22:49: #1 total tags in treatment: 11507417 INFO @ Sat, 11 Dec 2021 08:22:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:22:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:22:49: #1 tags after filtering in treatment: 10047717 INFO @ Sat, 11 Dec 2021 08:22:49: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 08:22:49: #1 finished! INFO @ Sat, 11 Dec 2021 08:22:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:22:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:22:49: #2 number of paired peaks: 745 WARNING @ Sat, 11 Dec 2021 08:22:49: Fewer paired peaks (745) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 745 pairs to build model! INFO @ Sat, 11 Dec 2021 08:22:49: start model_add_line... INFO @ Sat, 11 Dec 2021 08:22:49: start X-correlation... INFO @ Sat, 11 Dec 2021 08:22:49: end of X-cor INFO @ Sat, 11 Dec 2021 08:22:49: #2 finished! INFO @ Sat, 11 Dec 2021 08:22:49: #2 predicted fragment length is 210 bps INFO @ Sat, 11 Dec 2021 08:22:49: #2 alternative fragment length(s) may be 210 bps INFO @ Sat, 11 Dec 2021 08:22:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.05_model.r INFO @ Sat, 11 Dec 2021 08:22:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:22:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:22:50: 19000000 INFO @ Sat, 11 Dec 2021 08:22:53: 14000000 INFO @ Sat, 11 Dec 2021 08:22:55: 20000000 INFO @ Sat, 11 Dec 2021 08:22:58: 15000000 INFO @ Sat, 11 Dec 2021 08:23:01: 21000000 INFO @ Sat, 11 Dec 2021 08:23:04: 16000000 INFO @ Sat, 11 Dec 2021 08:23:06: 22000000 INFO @ Sat, 11 Dec 2021 08:23:09: 17000000 INFO @ Sat, 11 Dec 2021 08:23:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:23:12: 23000000 INFO @ Sat, 11 Dec 2021 08:23:14: 18000000 INFO @ Sat, 11 Dec 2021 08:23:17: 24000000 INFO @ Sat, 11 Dec 2021 08:23:20: 19000000 INFO @ Sat, 11 Dec 2021 08:23:20: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:23:20: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:23:20: #1 total tags in treatment: 11507417 INFO @ Sat, 11 Dec 2021 08:23:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:23:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:23:20: #1 tags after filtering in treatment: 10047717 INFO @ Sat, 11 Dec 2021 08:23:20: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 08:23:20: #1 finished! INFO @ Sat, 11 Dec 2021 08:23:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:23:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:23:21: #2 number of paired peaks: 745 WARNING @ Sat, 11 Dec 2021 08:23:21: Fewer paired peaks (745) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 745 pairs to build model! INFO @ Sat, 11 Dec 2021 08:23:21: start model_add_line... INFO @ Sat, 11 Dec 2021 08:23:21: start X-correlation... INFO @ Sat, 11 Dec 2021 08:23:21: end of X-cor INFO @ Sat, 11 Dec 2021 08:23:21: #2 finished! INFO @ Sat, 11 Dec 2021 08:23:21: #2 predicted fragment length is 210 bps INFO @ Sat, 11 Dec 2021 08:23:21: #2 alternative fragment length(s) may be 210 bps INFO @ Sat, 11 Dec 2021 08:23:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.10_model.r INFO @ Sat, 11 Dec 2021 08:23:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:23:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:23:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:23:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:23:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.05_summits.bed INFO @ Sat, 11 Dec 2021 08:23:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5803 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:23:25: 20000000 INFO @ Sat, 11 Dec 2021 08:23:30: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:23:36: 22000000 INFO @ Sat, 11 Dec 2021 08:23:41: 23000000 INFO @ Sat, 11 Dec 2021 08:23:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:23:46: 24000000 INFO @ Sat, 11 Dec 2021 08:23:49: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:23:49: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:23:49: #1 total tags in treatment: 11507417 INFO @ Sat, 11 Dec 2021 08:23:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:23:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:23:50: #1 tags after filtering in treatment: 10047717 INFO @ Sat, 11 Dec 2021 08:23:50: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 08:23:50: #1 finished! INFO @ Sat, 11 Dec 2021 08:23:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:23:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:23:50: #2 number of paired peaks: 745 WARNING @ Sat, 11 Dec 2021 08:23:50: Fewer paired peaks (745) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 745 pairs to build model! INFO @ Sat, 11 Dec 2021 08:23:50: start model_add_line... INFO @ Sat, 11 Dec 2021 08:23:50: start X-correlation... INFO @ Sat, 11 Dec 2021 08:23:50: end of X-cor INFO @ Sat, 11 Dec 2021 08:23:50: #2 finished! INFO @ Sat, 11 Dec 2021 08:23:50: #2 predicted fragment length is 210 bps INFO @ Sat, 11 Dec 2021 08:23:50: #2 alternative fragment length(s) may be 210 bps INFO @ Sat, 11 Dec 2021 08:23:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.20_model.r INFO @ Sat, 11 Dec 2021 08:23:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:23:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:23:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:23:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:23:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.10_summits.bed INFO @ Sat, 11 Dec 2021 08:23:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3269 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:24:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:24:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:24:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:24:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497057/SRX8497057.20_summits.bed INFO @ Sat, 11 Dec 2021 08:24:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1467 records, 4 fields): 19 millis CompletedMACS2peakCalling