Job ID = 14520417 SRX = SRX11781139 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:03:24 prefetch.2.10.7: 1) Downloading 'SRR15481082'... 2022-01-15T10:03:24 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:03:38 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:03:38 prefetch.2.10.7: 'SRR15481082' is valid 2022-01-15T10:03:38 prefetch.2.10.7: 1) 'SRR15481082' was downloaded successfully 2022-01-15T10:03:38 prefetch.2.10.7: 'SRR15481082' has 0 unresolved dependencies Read 5915544 spots for SRR15481082/SRR15481082.sra Written 5915544 spots for SRR15481082/SRR15481082.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: 00:04:03 5915544 reads; of these: 5915544 (100.00%) were paired; of these: 3750548 (63.40%) aligned concordantly 0 times 1944996 (32.88%) aligned concordantly exactly 1 time 220000 (3.72%) aligned concordantly >1 times ---- 3750548 pairs aligned concordantly 0 times; of these: 65514 (1.75%) aligned discordantly 1 time ---- 3685034 pairs aligned 0 times concordantly or discordantly; of these: 7370068 mates make up the pairs; of these: 4167248 (56.54%) aligned 0 times 2825213 (38.33%) aligned exactly 1 time 377607 (5.12%) aligned >1 times 64.78% overall alignment rate Time searching: 00:04:03 Overall time: 00:04:03 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 325873 / 2229654 = 0.1462 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, 15 Jan 2022 19:11:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 15 Jan 2022 19:11:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:11:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:12:01: 1000000 INFO @ Sat, 15 Jan 2022 19:12:14: 2000000 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, 15 Jan 2022 19:12:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 15 Jan 2022 19:12:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:12:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:12:25: 3000000 INFO @ Sat, 15 Jan 2022 19:12:31: 1000000 INFO @ Sat, 15 Jan 2022 19:12:36: 4000000 INFO @ Sat, 15 Jan 2022 19:12:41: 2000000 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, 15 Jan 2022 19:12:48: 5000000 INFO @ Sat, 15 Jan 2022 19:12:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 15 Jan 2022 19:12:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:12:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:12:52: 3000000 INFO @ Sat, 15 Jan 2022 19:12:59: 6000000 INFO @ Sat, 15 Jan 2022 19:12:59: 1000000 INFO @ Sat, 15 Jan 2022 19:13:03: 4000000 INFO @ Sat, 15 Jan 2022 19:13:09: 2000000 INFO @ Sat, 15 Jan 2022 19:13:09: 7000000 INFO @ Sat, 15 Jan 2022 19:13:09: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:13:09: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:13:09: #1 total tags in treatment: 1844582 INFO @ Sat, 15 Jan 2022 19:13:09: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:13:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:13:09: #1 tags after filtering in treatment: 1447778 INFO @ Sat, 15 Jan 2022 19:13:09: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 19:13:09: #1 finished! INFO @ Sat, 15 Jan 2022 19:13:09: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:13:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:13:09: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 19:13:09: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 15 Jan 2022 19:13:09: start model_add_line... INFO @ Sat, 15 Jan 2022 19:13:09: start X-correlation... INFO @ Sat, 15 Jan 2022 19:13:09: end of X-cor INFO @ Sat, 15 Jan 2022 19:13:09: #2 finished! INFO @ Sat, 15 Jan 2022 19:13:09: #2 predicted fragment length is 270 bps INFO @ Sat, 15 Jan 2022 19:13:09: #2 alternative fragment length(s) may be 0,42,210,253,270,290,305 bps INFO @ Sat, 15 Jan 2022 19:13:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.05_model.r INFO @ Sat, 15 Jan 2022 19:13:09: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:13:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:13:13: 5000000 INFO @ Sat, 15 Jan 2022 19:13:15: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:13:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:13:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:13:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.05_summits.bed INFO @ Sat, 15 Jan 2022 19:13:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (24 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:13:18: 3000000 INFO @ Sat, 15 Jan 2022 19:13:23: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:13:28: 4000000 INFO @ Sat, 15 Jan 2022 19:13:32: 7000000 INFO @ Sat, 15 Jan 2022 19:13:32: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:13:32: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:13:32: #1 total tags in treatment: 1844582 INFO @ Sat, 15 Jan 2022 19:13:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:13:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:13:32: #1 tags after filtering in treatment: 1447778 INFO @ Sat, 15 Jan 2022 19:13:32: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 19:13:32: #1 finished! INFO @ Sat, 15 Jan 2022 19:13:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:13:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:13:33: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 19:13:33: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 15 Jan 2022 19:13:33: start model_add_line... INFO @ Sat, 15 Jan 2022 19:13:33: start X-correlation... INFO @ Sat, 15 Jan 2022 19:13:33: end of X-cor INFO @ Sat, 15 Jan 2022 19:13:33: #2 finished! INFO @ Sat, 15 Jan 2022 19:13:33: #2 predicted fragment length is 270 bps INFO @ Sat, 15 Jan 2022 19:13:33: #2 alternative fragment length(s) may be 0,42,210,253,270,290,305 bps INFO @ Sat, 15 Jan 2022 19:13:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.10_model.r INFO @ Sat, 15 Jan 2022 19:13:33: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:13:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:13:37: 5000000 INFO @ Sat, 15 Jan 2022 19:13:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:13:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:13:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:13:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.10_summits.bed INFO @ Sat, 15 Jan 2022 19:13:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:13:45: 6000000 INFO @ Sat, 15 Jan 2022 19:13:54: 7000000 INFO @ Sat, 15 Jan 2022 19:13:54: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:13:54: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:13:54: #1 total tags in treatment: 1844582 INFO @ Sat, 15 Jan 2022 19:13:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:13:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:13:54: #1 tags after filtering in treatment: 1447778 INFO @ Sat, 15 Jan 2022 19:13:54: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 19:13:54: #1 finished! INFO @ Sat, 15 Jan 2022 19:13:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:13:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:13:55: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 19:13:55: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 15 Jan 2022 19:13:55: start model_add_line... INFO @ Sat, 15 Jan 2022 19:13:55: start X-correlation... INFO @ Sat, 15 Jan 2022 19:13:55: end of X-cor INFO @ Sat, 15 Jan 2022 19:13:55: #2 finished! INFO @ Sat, 15 Jan 2022 19:13:55: #2 predicted fragment length is 270 bps INFO @ Sat, 15 Jan 2022 19:13:55: #2 alternative fragment length(s) may be 0,42,210,253,270,290,305 bps INFO @ Sat, 15 Jan 2022 19:13:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.20_model.r INFO @ Sat, 15 Jan 2022 19:13:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:14:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:14:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:14:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:14:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781139/SRX11781139.20_summits.bed INFO @ Sat, 15 Jan 2022 19:14:03: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 2 millis CompletedMACS2peakCalling