Job ID = 7106946 SRX = SRX6911541 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12296702 spots for SRR10191152/SRR10191152.sra Written 12296702 spots for SRR10191152/SRR10191152.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: 00:05:13 12296702 reads; of these: 12296702 (100.00%) were paired; of these: 9053501 (73.63%) aligned concordantly 0 times 2064444 (16.79%) aligned concordantly exactly 1 time 1178757 (9.59%) aligned concordantly >1 times ---- 9053501 pairs aligned concordantly 0 times; of these: 149159 (1.65%) aligned discordantly 1 time ---- 8904342 pairs aligned 0 times concordantly or discordantly; of these: 17808684 mates make up the pairs; of these: 17499429 (98.26%) aligned 0 times 84592 (0.48%) aligned exactly 1 time 224663 (1.26%) aligned >1 times 28.85% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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] 1530247 / 3391848 = 0.4512 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 13:01:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.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 13:01:12: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:01:12: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:01:20: 1000000 INFO @ Wed, 22 Jul 2020 13:01:27: 2000000 INFO @ Wed, 22 Jul 2020 13:01:34: 3000000 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 13:01:40: 4000000 INFO @ Wed, 22 Jul 2020 13:01:41: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:01:41: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:01:41: #1 total tags in treatment: 1763459 INFO @ Wed, 22 Jul 2020 13:01:41: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:01:41: #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 13:01:41: #1 tags after filtering in treatment: 1010557 INFO @ Wed, 22 Jul 2020 13:01:41: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Jul 2020 13:01:41: #1 finished! INFO @ Wed, 22 Jul 2020 13:01:41: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:01:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:01:41: #2 number of paired peaks: 760 WARNING @ Wed, 22 Jul 2020 13:01:41: Fewer paired peaks (760) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 760 pairs to build model! INFO @ Wed, 22 Jul 2020 13:01:41: start model_add_line... INFO @ Wed, 22 Jul 2020 13:01:41: start X-correlation... INFO @ Wed, 22 Jul 2020 13:01:41: end of X-cor INFO @ Wed, 22 Jul 2020 13:01:41: #2 finished! INFO @ Wed, 22 Jul 2020 13:01:41: #2 predicted fragment length is 221 bps INFO @ Wed, 22 Jul 2020 13:01:41: #2 alternative fragment length(s) may be 2,179,208,221,246,266 bps INFO @ Wed, 22 Jul 2020 13:01:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.05_model.r INFO @ Wed, 22 Jul 2020 13:01:41: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:01:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:01:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.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 13:01:42: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:01:42: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:01:45: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:01:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.05_peaks.xls INFO @ Wed, 22 Jul 2020 13:01:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:01:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.05_summits.bed INFO @ Wed, 22 Jul 2020 13:01:46: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (346 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 13:01:49: 1000000 INFO @ Wed, 22 Jul 2020 13:01:56: 2000000 INFO @ Wed, 22 Jul 2020 13:02:03: 3000000 INFO @ Wed, 22 Jul 2020 13:02:10: 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 @ Wed, 22 Jul 2020 13:02:10: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:02:10: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:02:10: #1 total tags in treatment: 1763459 INFO @ Wed, 22 Jul 2020 13:02:10: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:02:10: #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 13:02:10: #1 tags after filtering in treatment: 1010557 INFO @ Wed, 22 Jul 2020 13:02:10: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Jul 2020 13:02:10: #1 finished! INFO @ Wed, 22 Jul 2020 13:02:10: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:02:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:02:10: #2 number of paired peaks: 760 WARNING @ Wed, 22 Jul 2020 13:02:10: Fewer paired peaks (760) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 760 pairs to build model! INFO @ Wed, 22 Jul 2020 13:02:10: start model_add_line... INFO @ Wed, 22 Jul 2020 13:02:10: start X-correlation... INFO @ Wed, 22 Jul 2020 13:02:10: end of X-cor INFO @ Wed, 22 Jul 2020 13:02:10: #2 finished! INFO @ Wed, 22 Jul 2020 13:02:10: #2 predicted fragment length is 221 bps INFO @ Wed, 22 Jul 2020 13:02:10: #2 alternative fragment length(s) may be 2,179,208,221,246,266 bps INFO @ Wed, 22 Jul 2020 13:02:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.10_model.r INFO @ Wed, 22 Jul 2020 13:02:10: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:02:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:02:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.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 13:02:12: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:02:12: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:02:14: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:02:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.10_peaks.xls INFO @ Wed, 22 Jul 2020 13:02:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:02:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.10_summits.bed INFO @ Wed, 22 Jul 2020 13:02:15: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (180 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 13:02:19: 1000000 INFO @ Wed, 22 Jul 2020 13:02:26: 2000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 13:02:33: 3000000 INFO @ Wed, 22 Jul 2020 13:02:40: 4000000 INFO @ Wed, 22 Jul 2020 13:02:40: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:02:40: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:02:40: #1 total tags in treatment: 1763459 INFO @ Wed, 22 Jul 2020 13:02:40: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:02:40: #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 13:02:40: #1 tags after filtering in treatment: 1010557 INFO @ Wed, 22 Jul 2020 13:02:40: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Jul 2020 13:02:40: #1 finished! INFO @ Wed, 22 Jul 2020 13:02:40: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:02:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:02:40: #2 number of paired peaks: 760 WARNING @ Wed, 22 Jul 2020 13:02:40: Fewer paired peaks (760) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 760 pairs to build model! INFO @ Wed, 22 Jul 2020 13:02:40: start model_add_line... INFO @ Wed, 22 Jul 2020 13:02:40: start X-correlation... INFO @ Wed, 22 Jul 2020 13:02:40: end of X-cor INFO @ Wed, 22 Jul 2020 13:02:40: #2 finished! INFO @ Wed, 22 Jul 2020 13:02:40: #2 predicted fragment length is 221 bps INFO @ Wed, 22 Jul 2020 13:02:40: #2 alternative fragment length(s) may be 2,179,208,221,246,266 bps INFO @ Wed, 22 Jul 2020 13:02:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.20_model.r INFO @ Wed, 22 Jul 2020 13:02:40: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:02:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:02:44: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:02:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.20_peaks.xls INFO @ Wed, 22 Jul 2020 13:02:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:02:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911541/SRX6911541.20_summits.bed INFO @ Wed, 22 Jul 2020 13:02:45: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (50 records, 4 fields): 2 millis CompletedMACS2peakCalling