Job ID = 10224006 SRX = SRX8754195 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3596779 spots for SRR12246266/SRR12246266.sra Written 3596779 spots for SRR12246266/SRR12246266.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: 00:02:03 3596779 reads; of these: 3596779 (100.00%) were paired; of these: 468660 (13.03%) aligned concordantly 0 times 1778304 (49.44%) aligned concordantly exactly 1 time 1349815 (37.53%) aligned concordantly >1 times ---- 468660 pairs aligned concordantly 0 times; of these: 104693 (22.34%) aligned discordantly 1 time ---- 363967 pairs aligned 0 times concordantly or discordantly; of these: 727934 mates make up the pairs; of these: 378688 (52.02%) aligned 0 times 68713 (9.44%) aligned exactly 1 time 280533 (38.54%) aligned >1 times 94.74% overall alignment rate Time searching: 00:02:03 Overall time: 00:02:03 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] 358010 / 3230619 = 0.1108 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 09:07:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.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 09:07:57: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:07:57: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:08:03: 1000000 INFO @ Fri, 16 Oct 2020 09:08:08: 2000000 INFO @ Fri, 16 Oct 2020 09:08:14: 3000000 INFO @ Fri, 16 Oct 2020 09:08:18: 4000000 INFO @ Fri, 16 Oct 2020 09:08:23: 5000000 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 09:08:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.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 09:08:27: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:08:27: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:08:28: 6000000 INFO @ Fri, 16 Oct 2020 09:08:28: #1 tag size is determined as 38 bps INFO @ Fri, 16 Oct 2020 09:08:28: #1 tag size = 38 INFO @ Fri, 16 Oct 2020 09:08:28: #1 total tags in treatment: 2775723 INFO @ Fri, 16 Oct 2020 09:08:28: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:08:28: #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 09:08:29: #1 tags after filtering in treatment: 1646740 INFO @ Fri, 16 Oct 2020 09:08:29: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 16 Oct 2020 09:08:29: #1 finished! INFO @ Fri, 16 Oct 2020 09:08:29: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:08:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:08:29: #2 number of paired peaks: 196 WARNING @ Fri, 16 Oct 2020 09:08:29: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Fri, 16 Oct 2020 09:08:29: start model_add_line... INFO @ Fri, 16 Oct 2020 09:08:29: start X-correlation... INFO @ Fri, 16 Oct 2020 09:08:29: end of X-cor INFO @ Fri, 16 Oct 2020 09:08:29: #2 finished! INFO @ Fri, 16 Oct 2020 09:08:29: #2 predicted fragment length is 241 bps INFO @ Fri, 16 Oct 2020 09:08:29: #2 alternative fragment length(s) may be 4,226,241 bps INFO @ Fri, 16 Oct 2020 09:08:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.05_model.r INFO @ Fri, 16 Oct 2020 09:08:29: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:08:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:08:32: 1000000 INFO @ Fri, 16 Oct 2020 09:08:34: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:08:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:08:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:08:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.05_summits.bed INFO @ Fri, 16 Oct 2020 09:08:35: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (238 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:08:37: 2000000 INFO @ Fri, 16 Oct 2020 09:08:41: 3000000 INFO @ Fri, 16 Oct 2020 09:08:46: 4000000 INFO @ Fri, 16 Oct 2020 09:08:50: 5000000 INFO @ Fri, 16 Oct 2020 09:08:55: 6000000 INFO @ Fri, 16 Oct 2020 09:08:55: #1 tag size is determined as 38 bps INFO @ Fri, 16 Oct 2020 09:08:55: #1 tag size = 38 INFO @ Fri, 16 Oct 2020 09:08:55: #1 total tags in treatment: 2775723 INFO @ Fri, 16 Oct 2020 09:08:55: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:08:55: #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 09:08:55: #1 tags after filtering in treatment: 1646740 INFO @ Fri, 16 Oct 2020 09:08:55: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 16 Oct 2020 09:08:55: #1 finished! INFO @ Fri, 16 Oct 2020 09:08:55: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:08:55: #2 looking for paired plus/minus strand peaks... 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 09:08:56: #2 number of paired peaks: 196 WARNING @ Fri, 16 Oct 2020 09:08:56: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Fri, 16 Oct 2020 09:08:56: start model_add_line... INFO @ Fri, 16 Oct 2020 09:08:56: start X-correlation... INFO @ Fri, 16 Oct 2020 09:08:56: end of X-cor INFO @ Fri, 16 Oct 2020 09:08:56: #2 finished! INFO @ Fri, 16 Oct 2020 09:08:56: #2 predicted fragment length is 241 bps INFO @ Fri, 16 Oct 2020 09:08:56: #2 alternative fragment length(s) may be 4,226,241 bps INFO @ Fri, 16 Oct 2020 09:08:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.10_model.r INFO @ Fri, 16 Oct 2020 09:08:56: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:08:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:08:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.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 09:08:57: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:08:57: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:09:00: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:09:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:09:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:09:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.10_summits.bed INFO @ Fri, 16 Oct 2020 09:09:02: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (125 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:09:02: 1000000 INFO @ Fri, 16 Oct 2020 09:09:07: 2000000 INFO @ Fri, 16 Oct 2020 09:09:13: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:09:18: 4000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:09:23: 5000000 INFO @ Fri, 16 Oct 2020 09:09:29: 6000000 INFO @ Fri, 16 Oct 2020 09:09:29: #1 tag size is determined as 38 bps INFO @ Fri, 16 Oct 2020 09:09:29: #1 tag size = 38 INFO @ Fri, 16 Oct 2020 09:09:29: #1 total tags in treatment: 2775723 INFO @ Fri, 16 Oct 2020 09:09:29: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:09:29: #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 09:09:29: #1 tags after filtering in treatment: 1646740 INFO @ Fri, 16 Oct 2020 09:09:29: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 16 Oct 2020 09:09:29: #1 finished! INFO @ Fri, 16 Oct 2020 09:09:29: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:09:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:09:29: #2 number of paired peaks: 196 WARNING @ Fri, 16 Oct 2020 09:09:29: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Fri, 16 Oct 2020 09:09:29: start model_add_line... INFO @ Fri, 16 Oct 2020 09:09:29: start X-correlation... INFO @ Fri, 16 Oct 2020 09:09:29: end of X-cor INFO @ Fri, 16 Oct 2020 09:09:29: #2 finished! INFO @ Fri, 16 Oct 2020 09:09:29: #2 predicted fragment length is 241 bps INFO @ Fri, 16 Oct 2020 09:09:29: #2 alternative fragment length(s) may be 4,226,241 bps INFO @ Fri, 16 Oct 2020 09:09:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.20_model.r INFO @ Fri, 16 Oct 2020 09:09:29: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:09:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:09:34: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:09:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:09:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:09:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8754195/SRX8754195.20_summits.bed INFO @ Fri, 16 Oct 2020 09:09:36: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (82 records, 4 fields): 2 millis CompletedMACS2peakCalling