Job ID = 10223941 SRX = SRX7496390 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17295947 spots for SRR10823001/SRR10823001.sra Written 17295947 spots for SRR10823001/SRR10823001.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: 00:04:08 17295947 reads; of these: 17295947 (100.00%) were paired; of these: 13682663 (79.11%) aligned concordantly 0 times 2363754 (13.67%) aligned concordantly exactly 1 time 1249530 (7.22%) aligned concordantly >1 times ---- 13682663 pairs aligned concordantly 0 times; of these: 21314 (0.16%) aligned discordantly 1 time ---- 13661349 pairs aligned 0 times concordantly or discordantly; of these: 27322698 mates make up the pairs; of these: 23948972 (87.65%) aligned 0 times 2400631 (8.79%) aligned exactly 1 time 973095 (3.56%) aligned >1 times 30.77% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 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] 848464 / 3634055 = 0.2335 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 @ Fri, 16 Oct 2020 09:01:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.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 @ Fri, 16 Oct 2020 09:01:07: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:01:07: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:01:11: 1000000 INFO @ Fri, 16 Oct 2020 09:01:16: 2000000 INFO @ Fri, 16 Oct 2020 09:01:21: 3000000 INFO @ Fri, 16 Oct 2020 09:01:26: 4000000 INFO @ Fri, 16 Oct 2020 09:01:31: 5000000 INFO @ Fri, 16 Oct 2020 09:01:35: 6000000 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 @ Fri, 16 Oct 2020 09:01:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.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 @ Fri, 16 Oct 2020 09:01:37: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:01:37: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:01:40: 7000000 INFO @ Fri, 16 Oct 2020 09:01:42: 1000000 INFO @ Fri, 16 Oct 2020 09:01:45: 8000000 INFO @ Fri, 16 Oct 2020 09:01:47: 2000000 INFO @ Fri, 16 Oct 2020 09:01:49: #1 tag size is determined as 37 bps INFO @ Fri, 16 Oct 2020 09:01:49: #1 tag size = 37 INFO @ Fri, 16 Oct 2020 09:01:49: #1 total tags in treatment: 2765519 INFO @ Fri, 16 Oct 2020 09:01:49: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:01:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:01:49: #1 tags after filtering in treatment: 1345441 INFO @ Fri, 16 Oct 2020 09:01:49: #1 Redundant rate of treatment: 0.51 INFO @ Fri, 16 Oct 2020 09:01:49: #1 finished! INFO @ Fri, 16 Oct 2020 09:01:49: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:01:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:01:50: #2 number of paired peaks: 281 WARNING @ Fri, 16 Oct 2020 09:01:50: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Fri, 16 Oct 2020 09:01:50: start model_add_line... INFO @ Fri, 16 Oct 2020 09:01:50: start X-correlation... INFO @ Fri, 16 Oct 2020 09:01:50: end of X-cor INFO @ Fri, 16 Oct 2020 09:01:50: #2 finished! INFO @ Fri, 16 Oct 2020 09:01:50: #2 predicted fragment length is 222 bps INFO @ Fri, 16 Oct 2020 09:01:50: #2 alternative fragment length(s) may be 0,200,222,254,274,578,580 bps INFO @ Fri, 16 Oct 2020 09:01:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.05_model.r INFO @ Fri, 16 Oct 2020 09:01:50: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:01:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:01:53: 3000000 INFO @ Fri, 16 Oct 2020 09:01:55: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:01:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:01:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:01:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.05_summits.bed INFO @ Fri, 16 Oct 2020 09:01:56: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (398 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:01:58: 4000000 INFO @ Fri, 16 Oct 2020 09:02:04: 5000000 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 @ Fri, 16 Oct 2020 09:02:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.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 @ Fri, 16 Oct 2020 09:02:07: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:02:07: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:02:08: 6000000 INFO @ Fri, 16 Oct 2020 09:02:12: 1000000 INFO @ Fri, 16 Oct 2020 09:02:13: 7000000 INFO @ Fri, 16 Oct 2020 09:02:18: 2000000 INFO @ Fri, 16 Oct 2020 09:02:19: 8000000 INFO @ Fri, 16 Oct 2020 09:02:23: #1 tag size is determined as 37 bps INFO @ Fri, 16 Oct 2020 09:02:23: #1 tag size = 37 INFO @ Fri, 16 Oct 2020 09:02:23: #1 total tags in treatment: 2765519 INFO @ Fri, 16 Oct 2020 09:02:23: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:02:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:02:23: #1 tags after filtering in treatment: 1345441 INFO @ Fri, 16 Oct 2020 09:02:23: #1 Redundant rate of treatment: 0.51 INFO @ Fri, 16 Oct 2020 09:02:23: #1 finished! INFO @ Fri, 16 Oct 2020 09:02:23: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:02:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:02:24: #2 number of paired peaks: 281 WARNING @ Fri, 16 Oct 2020 09:02:24: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Fri, 16 Oct 2020 09:02:24: start model_add_line... INFO @ Fri, 16 Oct 2020 09:02:24: start X-correlation... INFO @ Fri, 16 Oct 2020 09:02:24: end of X-cor INFO @ Fri, 16 Oct 2020 09:02:24: #2 finished! INFO @ Fri, 16 Oct 2020 09:02:24: #2 predicted fragment length is 222 bps INFO @ Fri, 16 Oct 2020 09:02:24: #2 alternative fragment length(s) may be 0,200,222,254,274,578,580 bps INFO @ Fri, 16 Oct 2020 09:02:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.10_model.r INFO @ Fri, 16 Oct 2020 09:02:24: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:02:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:02:24: 3000000 INFO @ Fri, 16 Oct 2020 09:02:29: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:02:29: 4000000 INFO @ Fri, 16 Oct 2020 09:02:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:02:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:02:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.10_summits.bed INFO @ Fri, 16 Oct 2020 09:02:30: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (156 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:02:34: 5000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:02:39: 6000000 INFO @ Fri, 16 Oct 2020 09:02:44: 7000000 INFO @ Fri, 16 Oct 2020 09:02:49: 8000000 INFO @ Fri, 16 Oct 2020 09:02:53: #1 tag size is determined as 37 bps INFO @ Fri, 16 Oct 2020 09:02:53: #1 tag size = 37 INFO @ Fri, 16 Oct 2020 09:02:53: #1 total tags in treatment: 2765519 INFO @ Fri, 16 Oct 2020 09:02:53: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:02:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:02:53: #1 tags after filtering in treatment: 1345441 INFO @ Fri, 16 Oct 2020 09:02:53: #1 Redundant rate of treatment: 0.51 INFO @ Fri, 16 Oct 2020 09:02:53: #1 finished! INFO @ Fri, 16 Oct 2020 09:02:53: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:02:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:02:53: #2 number of paired peaks: 281 WARNING @ Fri, 16 Oct 2020 09:02:53: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Fri, 16 Oct 2020 09:02:53: start model_add_line... INFO @ Fri, 16 Oct 2020 09:02:53: start X-correlation... INFO @ Fri, 16 Oct 2020 09:02:53: end of X-cor INFO @ Fri, 16 Oct 2020 09:02:53: #2 finished! INFO @ Fri, 16 Oct 2020 09:02:53: #2 predicted fragment length is 222 bps INFO @ Fri, 16 Oct 2020 09:02:53: #2 alternative fragment length(s) may be 0,200,222,254,274,578,580 bps INFO @ Fri, 16 Oct 2020 09:02:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.20_model.r INFO @ Fri, 16 Oct 2020 09:02:53: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:02:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:02:58: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:03:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:03:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:03:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496390/SRX7496390.20_summits.bed INFO @ Fri, 16 Oct 2020 09:03:00: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (41 records, 4 fields): 2 millis CompletedMACS2peakCalling