Job ID = 14520900 SRX = SRX8245436 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12695548 spots for SRR11684647/SRR11684647.sra Written 12695548 spots for SRR11684647/SRR11684647.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: 00:00:01 Multiseed full-index search: 00:19:57 12695548 reads; of these: 12695548 (100.00%) were paired; of these: 9072394 (71.46%) aligned concordantly 0 times 1901519 (14.98%) aligned concordantly exactly 1 time 1721635 (13.56%) aligned concordantly >1 times ---- 9072394 pairs aligned concordantly 0 times; of these: 480569 (5.30%) aligned discordantly 1 time ---- 8591825 pairs aligned 0 times concordantly or discordantly; of these: 17183650 mates make up the pairs; of these: 13234261 (77.02%) aligned 0 times 2701534 (15.72%) aligned exactly 1 time 1247855 (7.26%) aligned >1 times 47.88% overall alignment rate Time searching: 00:19:58 Overall time: 00:19:58 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_sort_core] merging from 8 files... [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] 827115 / 4103026 = 0.2016 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:34:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.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 @ Sat, 15 Jan 2022 20:34:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:34:26: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:34:35: 1000000 INFO @ Sat, 15 Jan 2022 20:34:43: 2000000 INFO @ Sat, 15 Jan 2022 20:34:51: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:34:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.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 @ Sat, 15 Jan 2022 20:34:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:34:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:34:59: 4000000 INFO @ Sat, 15 Jan 2022 20:35:06: 1000000 INFO @ Sat, 15 Jan 2022 20:35:07: 5000000 INFO @ Sat, 15 Jan 2022 20:35:16: 6000000 INFO @ Sat, 15 Jan 2022 20:35:17: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:35:24: 7000000 INFO @ Sat, 15 Jan 2022 20:35:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.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 @ Sat, 15 Jan 2022 20:35:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:35:26: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:35:28: 3000000 INFO @ Sat, 15 Jan 2022 20:35:33: 8000000 INFO @ Sat, 15 Jan 2022 20:35:37: 1000000 INFO @ Sat, 15 Jan 2022 20:35:38: 4000000 INFO @ Sat, 15 Jan 2022 20:35:42: 9000000 INFO @ Sat, 15 Jan 2022 20:35:48: 2000000 INFO @ Sat, 15 Jan 2022 20:35:49: 5000000 INFO @ Sat, 15 Jan 2022 20:35:51: 10000000 INFO @ Sat, 15 Jan 2022 20:35:56: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:35:56: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:35:56: #1 total tags in treatment: 3202710 INFO @ Sat, 15 Jan 2022 20:35:56: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:35:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:35:56: #1 tags after filtering in treatment: 1790805 INFO @ Sat, 15 Jan 2022 20:35:56: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 15 Jan 2022 20:35:56: #1 finished! INFO @ Sat, 15 Jan 2022 20:35:56: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:35:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:35:56: #2 number of paired peaks: 136 WARNING @ Sat, 15 Jan 2022 20:35:56: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sat, 15 Jan 2022 20:35:56: start model_add_line... INFO @ Sat, 15 Jan 2022 20:35:56: start X-correlation... INFO @ Sat, 15 Jan 2022 20:35:56: end of X-cor INFO @ Sat, 15 Jan 2022 20:35:56: #2 finished! INFO @ Sat, 15 Jan 2022 20:35:56: #2 predicted fragment length is 204 bps INFO @ Sat, 15 Jan 2022 20:35:56: #2 alternative fragment length(s) may be 1,121,172,204,580,596 bps INFO @ Sat, 15 Jan 2022 20:35:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.05_model.r INFO @ Sat, 15 Jan 2022 20:35:56: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:35:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:35:58: 3000000 INFO @ Sat, 15 Jan 2022 20:36:01: 6000000 INFO @ Sat, 15 Jan 2022 20:36:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:36:07: 4000000 INFO @ Sat, 15 Jan 2022 20:36:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:36:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:36:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.05_summits.bed INFO @ Sat, 15 Jan 2022 20:36:08: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (621 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:36:11: 7000000 INFO @ Sat, 15 Jan 2022 20:36:18: 5000000 INFO @ Sat, 15 Jan 2022 20:36:23: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:36:28: 6000000 INFO @ Sat, 15 Jan 2022 20:36:33: 9000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:36:38: 7000000 INFO @ Sat, 15 Jan 2022 20:36:45: 10000000 INFO @ Sat, 15 Jan 2022 20:36:49: 8000000 INFO @ Sat, 15 Jan 2022 20:36:50: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:36:50: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:36:50: #1 total tags in treatment: 3202710 INFO @ Sat, 15 Jan 2022 20:36:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:36:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:36:50: #1 tags after filtering in treatment: 1790805 INFO @ Sat, 15 Jan 2022 20:36:50: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 15 Jan 2022 20:36:50: #1 finished! INFO @ Sat, 15 Jan 2022 20:36:50: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:36:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:36:50: #2 number of paired peaks: 136 WARNING @ Sat, 15 Jan 2022 20:36:50: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sat, 15 Jan 2022 20:36:50: start model_add_line... INFO @ Sat, 15 Jan 2022 20:36:50: start X-correlation... INFO @ Sat, 15 Jan 2022 20:36:50: end of X-cor INFO @ Sat, 15 Jan 2022 20:36:50: #2 finished! INFO @ Sat, 15 Jan 2022 20:36:50: #2 predicted fragment length is 204 bps INFO @ Sat, 15 Jan 2022 20:36:50: #2 alternative fragment length(s) may be 1,121,172,204,580,596 bps INFO @ Sat, 15 Jan 2022 20:36:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.10_model.r INFO @ Sat, 15 Jan 2022 20:36:50: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:36:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:36:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:36:59: 9000000 INFO @ Sat, 15 Jan 2022 20:37:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:37:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:37:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.10_summits.bed INFO @ Sat, 15 Jan 2022 20:37:01: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (369 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:37:10: 10000000 INFO @ Sat, 15 Jan 2022 20:37:15: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:37:15: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:37:15: #1 total tags in treatment: 3202710 INFO @ Sat, 15 Jan 2022 20:37:15: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:37:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:37:15: #1 tags after filtering in treatment: 1790805 INFO @ Sat, 15 Jan 2022 20:37:15: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 15 Jan 2022 20:37:15: #1 finished! INFO @ Sat, 15 Jan 2022 20:37:15: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:37:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:37:15: #2 number of paired peaks: 136 WARNING @ Sat, 15 Jan 2022 20:37:15: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sat, 15 Jan 2022 20:37:15: start model_add_line... INFO @ Sat, 15 Jan 2022 20:37:15: start X-correlation... INFO @ Sat, 15 Jan 2022 20:37:15: end of X-cor INFO @ Sat, 15 Jan 2022 20:37:15: #2 finished! INFO @ Sat, 15 Jan 2022 20:37:15: #2 predicted fragment length is 204 bps INFO @ Sat, 15 Jan 2022 20:37:15: #2 alternative fragment length(s) may be 1,121,172,204,580,596 bps INFO @ Sat, 15 Jan 2022 20:37:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.20_model.r INFO @ Sat, 15 Jan 2022 20:37:15: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:37:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:37:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:37:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:37:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:37:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245436/SRX8245436.20_summits.bed INFO @ Sat, 15 Jan 2022 20:37:26: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (95 records, 4 fields): 2 millis CompletedMACS2peakCalling