Job ID = 7105382 SRX = SRX6911532 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13397705 spots for SRR10191143/SRR10191143.sra Written 13397705 spots for SRR10191143/SRR10191143.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: 00:12:02 13397705 reads; of these: 13397705 (100.00%) were paired; of these: 4574440 (34.14%) aligned concordantly 0 times 7197524 (53.72%) aligned concordantly exactly 1 time 1625741 (12.13%) aligned concordantly >1 times ---- 4574440 pairs aligned concordantly 0 times; of these: 493983 (10.80%) aligned discordantly 1 time ---- 4080457 pairs aligned 0 times concordantly or discordantly; of these: 8160914 mates make up the pairs; of these: 7502345 (91.93%) aligned 0 times 352679 (4.32%) aligned exactly 1 time 305890 (3.75%) aligned >1 times 72.00% overall alignment rate Time searching: 00:12:02 Overall time: 00:12:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 files... [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] 805767 / 9315410 = 0.0865 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 @ Wed, 22 Jul 2020 12:58:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.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 @ Wed, 22 Jul 2020 12:58:08: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:58:08: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:58:14: 1000000 INFO @ Wed, 22 Jul 2020 12:58:21: 2000000 INFO @ Wed, 22 Jul 2020 12:58:28: 3000000 INFO @ Wed, 22 Jul 2020 12:58:34: 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 @ Wed, 22 Jul 2020 12:58:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.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 @ Wed, 22 Jul 2020 12:58:37: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:58:37: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:58:42: 5000000 INFO @ Wed, 22 Jul 2020 12:58:47: 1000000 INFO @ Wed, 22 Jul 2020 12:58:51: 6000000 INFO @ Wed, 22 Jul 2020 12:58:57: 2000000 INFO @ Wed, 22 Jul 2020 12:59:01: 7000000 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 @ Wed, 22 Jul 2020 12:59:06: 3000000 INFO @ Wed, 22 Jul 2020 12:59:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.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 @ Wed, 22 Jul 2020 12:59:07: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:59:07: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:59:10: 8000000 INFO @ Wed, 22 Jul 2020 12:59:16: 4000000 INFO @ Wed, 22 Jul 2020 12:59:17: 1000000 INFO @ Wed, 22 Jul 2020 12:59:19: 9000000 INFO @ Wed, 22 Jul 2020 12:59:26: 5000000 INFO @ Wed, 22 Jul 2020 12:59:27: 2000000 INFO @ Wed, 22 Jul 2020 12:59:28: 10000000 INFO @ Wed, 22 Jul 2020 12:59:35: 6000000 INFO @ Wed, 22 Jul 2020 12:59:36: 3000000 INFO @ Wed, 22 Jul 2020 12:59:37: 11000000 INFO @ Wed, 22 Jul 2020 12:59:45: 7000000 INFO @ Wed, 22 Jul 2020 12:59:45: 4000000 INFO @ Wed, 22 Jul 2020 12:59:46: 12000000 INFO @ Wed, 22 Jul 2020 12:59:54: 8000000 INFO @ Wed, 22 Jul 2020 12:59:55: 5000000 INFO @ Wed, 22 Jul 2020 12:59:55: 13000000 INFO @ Wed, 22 Jul 2020 13:00:04: 9000000 INFO @ Wed, 22 Jul 2020 13:00:04: 14000000 INFO @ Wed, 22 Jul 2020 13:00:05: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 13:00:13: 15000000 INFO @ Wed, 22 Jul 2020 13:00:14: 10000000 INFO @ Wed, 22 Jul 2020 13:00:15: 7000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 13:00:22: 16000000 INFO @ Wed, 22 Jul 2020 13:00:23: 11000000 INFO @ Wed, 22 Jul 2020 13:00:25: 8000000 INFO @ Wed, 22 Jul 2020 13:00:31: 17000000 INFO @ Wed, 22 Jul 2020 13:00:33: 12000000 INFO @ Wed, 22 Jul 2020 13:00:35: 9000000 INFO @ Wed, 22 Jul 2020 13:00:37: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:00:37: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:00:37: #1 total tags in treatment: 8030674 INFO @ Wed, 22 Jul 2020 13:00:37: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:00:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:00:38: #1 tags after filtering in treatment: 3552751 INFO @ Wed, 22 Jul 2020 13:00:38: #1 Redundant rate of treatment: 0.56 INFO @ Wed, 22 Jul 2020 13:00:38: #1 finished! INFO @ Wed, 22 Jul 2020 13:00:38: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:00:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:00:38: #2 number of paired peaks: 699 WARNING @ Wed, 22 Jul 2020 13:00:38: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Wed, 22 Jul 2020 13:00:38: start model_add_line... INFO @ Wed, 22 Jul 2020 13:00:38: start X-correlation... INFO @ Wed, 22 Jul 2020 13:00:38: end of X-cor INFO @ Wed, 22 Jul 2020 13:00:38: #2 finished! INFO @ Wed, 22 Jul 2020 13:00:38: #2 predicted fragment length is 203 bps INFO @ Wed, 22 Jul 2020 13:00:38: #2 alternative fragment length(s) may be 35,37,39,54,83,102,112,114,128,155,160,179,203,230,591,596 bps INFO @ Wed, 22 Jul 2020 13:00:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.05_model.r INFO @ Wed, 22 Jul 2020 13:00:38: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:00:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:00:42: 13000000 INFO @ Wed, 22 Jul 2020 13:00:45: 10000000 INFO @ Wed, 22 Jul 2020 13:00:51: 14000000 INFO @ Wed, 22 Jul 2020 13:00:54: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:00:54: 11000000 INFO @ Wed, 22 Jul 2020 13:00:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.05_peaks.xls INFO @ Wed, 22 Jul 2020 13:00:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:00:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.05_summits.bed INFO @ Wed, 22 Jul 2020 13:00:56: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (435 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 13:01:01: 15000000 INFO @ Wed, 22 Jul 2020 13:01:03: 12000000 INFO @ Wed, 22 Jul 2020 13:01:10: 16000000 INFO @ Wed, 22 Jul 2020 13:01:13: 13000000 INFO @ Wed, 22 Jul 2020 13:01:20: 17000000 INFO @ Wed, 22 Jul 2020 13:01:22: 14000000 INFO @ Wed, 22 Jul 2020 13:01:26: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:01:26: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:01:26: #1 total tags in treatment: 8030674 INFO @ Wed, 22 Jul 2020 13:01:26: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:01:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:01:27: #1 tags after filtering in treatment: 3552751 INFO @ Wed, 22 Jul 2020 13:01:27: #1 Redundant rate of treatment: 0.56 INFO @ Wed, 22 Jul 2020 13:01:27: #1 finished! INFO @ Wed, 22 Jul 2020 13:01:27: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:01:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:01:27: #2 number of paired peaks: 699 WARNING @ Wed, 22 Jul 2020 13:01:27: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Wed, 22 Jul 2020 13:01:27: start model_add_line... INFO @ Wed, 22 Jul 2020 13:01:27: start X-correlation... INFO @ Wed, 22 Jul 2020 13:01:27: end of X-cor INFO @ Wed, 22 Jul 2020 13:01:27: #2 finished! INFO @ Wed, 22 Jul 2020 13:01:27: #2 predicted fragment length is 203 bps INFO @ Wed, 22 Jul 2020 13:01:27: #2 alternative fragment length(s) may be 35,37,39,54,83,102,112,114,128,155,160,179,203,230,591,596 bps INFO @ Wed, 22 Jul 2020 13:01:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.10_model.r INFO @ Wed, 22 Jul 2020 13:01:27: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:01:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:01:31: 15000000 INFO @ Wed, 22 Jul 2020 13:01:39: 16000000 INFO @ Wed, 22 Jul 2020 13:01:42: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:01:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.10_peaks.xls INFO @ Wed, 22 Jul 2020 13:01:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:01:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.10_summits.bed INFO @ Wed, 22 Jul 2020 13:01:45: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (208 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 13:01:48: 17000000 INFO @ Wed, 22 Jul 2020 13:01:53: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:01:53: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:01:53: #1 total tags in treatment: 8030674 INFO @ Wed, 22 Jul 2020 13:01:53: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:01:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:01:54: #1 tags after filtering in treatment: 3552751 INFO @ Wed, 22 Jul 2020 13:01:54: #1 Redundant rate of treatment: 0.56 INFO @ Wed, 22 Jul 2020 13:01:54: #1 finished! INFO @ Wed, 22 Jul 2020 13:01:54: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:01:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:01:54: #2 number of paired peaks: 699 WARNING @ Wed, 22 Jul 2020 13:01:54: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Wed, 22 Jul 2020 13:01:54: start model_add_line... INFO @ Wed, 22 Jul 2020 13:01:54: start X-correlation... INFO @ Wed, 22 Jul 2020 13:01:54: end of X-cor INFO @ Wed, 22 Jul 2020 13:01:54: #2 finished! INFO @ Wed, 22 Jul 2020 13:01:54: #2 predicted fragment length is 203 bps INFO @ Wed, 22 Jul 2020 13:01:54: #2 alternative fragment length(s) may be 35,37,39,54,83,102,112,114,128,155,160,179,203,230,591,596 bps INFO @ Wed, 22 Jul 2020 13:01:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.20_model.r INFO @ Wed, 22 Jul 2020 13:01:54: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:01:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:02:09: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:02:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.20_peaks.xls INFO @ Wed, 22 Jul 2020 13:02:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:02:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911532/SRX6911532.20_summits.bed INFO @ Wed, 22 Jul 2020 13:02:12: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (66 records, 4 fields): 2 millis CompletedMACS2peakCalling