Job ID = 10224047 SRX = SRX8952604 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10388100 spots for SRR12458282/SRR12458282.sra Written 10388100 spots for SRR12458282/SRR12458282.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: 00:02:40 10388100 reads; of these: 10388100 (100.00%) were paired; of these: 9234392 (88.89%) aligned concordantly 0 times 1015882 (9.78%) aligned concordantly exactly 1 time 137826 (1.33%) aligned concordantly >1 times ---- 9234392 pairs aligned concordantly 0 times; of these: 409484 (4.43%) aligned discordantly 1 time ---- 8824908 pairs aligned 0 times concordantly or discordantly; of these: 17649816 mates make up the pairs; of these: 14593529 (82.68%) aligned 0 times 2701075 (15.30%) aligned exactly 1 time 355212 (2.01%) aligned >1 times 29.76% overall alignment rate Time searching: 00:02:40 Overall time: 00:02:40 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] 791353 / 1554632 = 0.5090 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 09:18:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.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 09:18:36: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:18:36: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:18:42: 1000000 INFO @ Fri, 16 Oct 2020 09:18:47: 2000000 INFO @ Fri, 16 Oct 2020 09:18:53: 3000000 INFO @ Fri, 16 Oct 2020 09:18:59: 4000000 INFO @ Fri, 16 Oct 2020 09:19:02: #1 tag size is determined as 35 bps INFO @ Fri, 16 Oct 2020 09:19:02: #1 tag size = 35 INFO @ Fri, 16 Oct 2020 09:19:02: #1 total tags in treatment: 630724 INFO @ Fri, 16 Oct 2020 09:19:02: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:19:02: #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 09:19:02: #1 tags after filtering in treatment: 589819 INFO @ Fri, 16 Oct 2020 09:19:02: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 16 Oct 2020 09:19:02: #1 finished! INFO @ Fri, 16 Oct 2020 09:19:02: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:19:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:19:02: #2 number of paired peaks: 115 WARNING @ Fri, 16 Oct 2020 09:19:02: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Fri, 16 Oct 2020 09:19:02: start model_add_line... INFO @ Fri, 16 Oct 2020 09:19:02: start X-correlation... INFO @ Fri, 16 Oct 2020 09:19:02: end of X-cor INFO @ Fri, 16 Oct 2020 09:19:02: #2 finished! INFO @ Fri, 16 Oct 2020 09:19:02: #2 predicted fragment length is 274 bps INFO @ Fri, 16 Oct 2020 09:19:02: #2 alternative fragment length(s) may be 246,274 bps INFO @ Fri, 16 Oct 2020 09:19:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.05_model.r INFO @ Fri, 16 Oct 2020 09:19:02: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:19:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:19:04: #3 Call peaks for each chromosome... 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 09:19:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:19:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:19:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.05_summits.bed INFO @ Fri, 16 Oct 2020 09:19:04: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (251 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:19:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.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 09:19:06: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:19:06: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:19:11: 1000000 INFO @ Fri, 16 Oct 2020 09:19:17: 2000000 INFO @ Fri, 16 Oct 2020 09:19:23: 3000000 INFO @ Fri, 16 Oct 2020 09:19:29: 4000000 INFO @ Fri, 16 Oct 2020 09:19:32: #1 tag size is determined as 35 bps INFO @ Fri, 16 Oct 2020 09:19:32: #1 tag size = 35 INFO @ Fri, 16 Oct 2020 09:19:32: #1 total tags in treatment: 630724 INFO @ Fri, 16 Oct 2020 09:19:32: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:19:32: #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 09:19:32: #1 tags after filtering in treatment: 589819 INFO @ Fri, 16 Oct 2020 09:19:32: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 16 Oct 2020 09:19:32: #1 finished! INFO @ Fri, 16 Oct 2020 09:19:32: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:19:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:19:32: #2 number of paired peaks: 115 WARNING @ Fri, 16 Oct 2020 09:19:32: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Fri, 16 Oct 2020 09:19:32: start model_add_line... INFO @ Fri, 16 Oct 2020 09:19:32: start X-correlation... INFO @ Fri, 16 Oct 2020 09:19:32: end of X-cor INFO @ Fri, 16 Oct 2020 09:19:32: #2 finished! INFO @ Fri, 16 Oct 2020 09:19:32: #2 predicted fragment length is 274 bps INFO @ Fri, 16 Oct 2020 09:19:32: #2 alternative fragment length(s) may be 246,274 bps INFO @ Fri, 16 Oct 2020 09:19:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.10_model.r INFO @ Fri, 16 Oct 2020 09:19:32: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:19:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:19:34: #3 Call peaks for each chromosome... 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 09:19:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:19:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:19:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.10_summits.bed INFO @ Fri, 16 Oct 2020 09:19:35: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (146 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:19:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.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 09:19:36: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:19:36: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:19:41: 1000000 INFO @ Fri, 16 Oct 2020 09:19:47: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:19:52: 3000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:19:58: 4000000 INFO @ Fri, 16 Oct 2020 09:20:01: #1 tag size is determined as 35 bps INFO @ Fri, 16 Oct 2020 09:20:01: #1 tag size = 35 INFO @ Fri, 16 Oct 2020 09:20:01: #1 total tags in treatment: 630724 INFO @ Fri, 16 Oct 2020 09:20:01: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:20:01: #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 09:20:01: #1 tags after filtering in treatment: 589819 INFO @ Fri, 16 Oct 2020 09:20:01: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 16 Oct 2020 09:20:01: #1 finished! INFO @ Fri, 16 Oct 2020 09:20:01: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:20:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:20:01: #2 number of paired peaks: 115 WARNING @ Fri, 16 Oct 2020 09:20:01: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Fri, 16 Oct 2020 09:20:01: start model_add_line... INFO @ Fri, 16 Oct 2020 09:20:01: start X-correlation... INFO @ Fri, 16 Oct 2020 09:20:01: end of X-cor INFO @ Fri, 16 Oct 2020 09:20:01: #2 finished! INFO @ Fri, 16 Oct 2020 09:20:01: #2 predicted fragment length is 274 bps INFO @ Fri, 16 Oct 2020 09:20:01: #2 alternative fragment length(s) may be 246,274 bps INFO @ Fri, 16 Oct 2020 09:20:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.20_model.r INFO @ Fri, 16 Oct 2020 09:20:01: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:20:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:20:03: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:20:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:20:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:20:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952604/SRX8952604.20_summits.bed INFO @ Fri, 16 Oct 2020 09:20:04: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (62 records, 4 fields): 1 millis CompletedMACS2peakCalling