Job ID = 10224005 SRX = SRX8754194 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2325927 spots for SRR12246265/SRR12246265.sra Written 2325927 spots for SRR12246265/SRR12246265.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: 00:01:15 2325927 reads; of these: 2325927 (100.00%) were paired; of these: 261593 (11.25%) aligned concordantly 0 times 1335368 (57.41%) aligned concordantly exactly 1 time 728966 (31.34%) aligned concordantly >1 times ---- 261593 pairs aligned concordantly 0 times; of these: 54069 (20.67%) aligned discordantly 1 time ---- 207524 pairs aligned 0 times concordantly or discordantly; of these: 415048 mates make up the pairs; of these: 274837 (66.22%) aligned 0 times 36837 (8.88%) aligned exactly 1 time 103374 (24.91%) aligned >1 times 94.09% overall alignment rate Time searching: 00:01:15 Overall time: 00:01:15 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] 131803 / 2117307 = 0.0623 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 09:06:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.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 09:06:42: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:06:42: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:06:47: 1000000 INFO @ Fri, 16 Oct 2020 09:06:52: 2000000 INFO @ Fri, 16 Oct 2020 09:06:56: 3000000 INFO @ Fri, 16 Oct 2020 09:07:01: 4000000 INFO @ Fri, 16 Oct 2020 09:07:01: #1 tag size is determined as 38 bps INFO @ Fri, 16 Oct 2020 09:07:01: #1 tag size = 38 INFO @ Fri, 16 Oct 2020 09:07:01: #1 total tags in treatment: 1933961 INFO @ Fri, 16 Oct 2020 09:07:01: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:07:01: #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 09:07:01: #1 tags after filtering in treatment: 1326806 INFO @ Fri, 16 Oct 2020 09:07:01: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 16 Oct 2020 09:07:01: #1 finished! INFO @ Fri, 16 Oct 2020 09:07:01: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:07:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:07:01: #2 number of paired peaks: 174 WARNING @ Fri, 16 Oct 2020 09:07:01: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Fri, 16 Oct 2020 09:07:01: start model_add_line... INFO @ Fri, 16 Oct 2020 09:07:01: start X-correlation... INFO @ Fri, 16 Oct 2020 09:07:01: end of X-cor INFO @ Fri, 16 Oct 2020 09:07:01: #2 finished! INFO @ Fri, 16 Oct 2020 09:07:01: #2 predicted fragment length is 239 bps INFO @ Fri, 16 Oct 2020 09:07:01: #2 alternative fragment length(s) may be 4,239 bps INFO @ Fri, 16 Oct 2020 09:07:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.05_model.r INFO @ Fri, 16 Oct 2020 09:07:01: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:07:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:07:05: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:07:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:07:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:07:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.05_summits.bed INFO @ Fri, 16 Oct 2020 09:07:06: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (143 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 09:07:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.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 09:07:12: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:07:12: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:07:17: 1000000 INFO @ Fri, 16 Oct 2020 09:07:22: 2000000 INFO @ Fri, 16 Oct 2020 09:07:27: 3000000 INFO @ Fri, 16 Oct 2020 09:07:32: 4000000 INFO @ Fri, 16 Oct 2020 09:07:33: #1 tag size is determined as 38 bps INFO @ Fri, 16 Oct 2020 09:07:33: #1 tag size = 38 INFO @ Fri, 16 Oct 2020 09:07:33: #1 total tags in treatment: 1933961 INFO @ Fri, 16 Oct 2020 09:07:33: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:07:33: #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 09:07:33: #1 tags after filtering in treatment: 1326806 INFO @ Fri, 16 Oct 2020 09:07:33: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 16 Oct 2020 09:07:33: #1 finished! INFO @ Fri, 16 Oct 2020 09:07:33: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:07:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:07:33: #2 number of paired peaks: 174 WARNING @ Fri, 16 Oct 2020 09:07:33: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Fri, 16 Oct 2020 09:07:33: start model_add_line... INFO @ Fri, 16 Oct 2020 09:07:33: start X-correlation... INFO @ Fri, 16 Oct 2020 09:07:33: end of X-cor INFO @ Fri, 16 Oct 2020 09:07:33: #2 finished! INFO @ Fri, 16 Oct 2020 09:07:33: #2 predicted fragment length is 239 bps INFO @ Fri, 16 Oct 2020 09:07:33: #2 alternative fragment length(s) may be 4,239 bps INFO @ Fri, 16 Oct 2020 09:07:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.10_model.r INFO @ Fri, 16 Oct 2020 09:07:33: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:07:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:07:36: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:07:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:07:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:07:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.10_summits.bed INFO @ Fri, 16 Oct 2020 09:07:38: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (101 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 09:07:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.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 09:07:42: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:07:42: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:07:48: 1000000 INFO @ Fri, 16 Oct 2020 09:07:53: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:07:58: 3000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:08:03: 4000000 INFO @ Fri, 16 Oct 2020 09:08:03: #1 tag size is determined as 38 bps INFO @ Fri, 16 Oct 2020 09:08:03: #1 tag size = 38 INFO @ Fri, 16 Oct 2020 09:08:03: #1 total tags in treatment: 1933961 INFO @ Fri, 16 Oct 2020 09:08:03: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:08:03: #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 09:08:03: #1 tags after filtering in treatment: 1326806 INFO @ Fri, 16 Oct 2020 09:08:03: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 16 Oct 2020 09:08:03: #1 finished! INFO @ Fri, 16 Oct 2020 09:08:03: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:08:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:08:04: #2 number of paired peaks: 174 WARNING @ Fri, 16 Oct 2020 09:08:04: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Fri, 16 Oct 2020 09:08:04: start model_add_line... INFO @ Fri, 16 Oct 2020 09:08:04: start X-correlation... INFO @ Fri, 16 Oct 2020 09:08:04: end of X-cor INFO @ Fri, 16 Oct 2020 09:08:04: #2 finished! INFO @ Fri, 16 Oct 2020 09:08:04: #2 predicted fragment length is 239 bps INFO @ Fri, 16 Oct 2020 09:08:04: #2 alternative fragment length(s) may be 4,239 bps INFO @ Fri, 16 Oct 2020 09:08:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.20_model.r INFO @ Fri, 16 Oct 2020 09:08:04: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:08:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:08:07: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:08:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:08:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:08:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8754194/SRX8754194.20_summits.bed INFO @ Fri, 16 Oct 2020 09:08:09: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (69 records, 4 fields): 2 millis CompletedMACS2peakCalling