Job ID = 14520438 SRX = SRX11781143 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:06:09 prefetch.2.10.7: 1) Downloading 'SRR15481086'... 2022-01-15T10:06:09 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:06:23 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:06:24 prefetch.2.10.7: 'SRR15481086' is valid 2022-01-15T10:06:24 prefetch.2.10.7: 1) 'SRR15481086' was downloaded successfully 2022-01-15T10:06:24 prefetch.2.10.7: 'SRR15481086' has 0 unresolved dependencies Read 6762631 spots for SRR15481086/SRR15481086.sra Written 6762631 spots for SRR15481086/SRR15481086.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: 00:04:05 6762631 reads; of these: 6762631 (100.00%) were paired; of these: 4532489 (67.02%) aligned concordantly 0 times 1947868 (28.80%) aligned concordantly exactly 1 time 282274 (4.17%) aligned concordantly >1 times ---- 4532489 pairs aligned concordantly 0 times; of these: 39958 (0.88%) aligned discordantly 1 time ---- 4492531 pairs aligned 0 times concordantly or discordantly; of these: 8985062 mates make up the pairs; of these: 4869616 (54.20%) aligned 0 times 3575699 (39.80%) aligned exactly 1 time 539747 (6.01%) aligned >1 times 64.00% overall alignment rate Time searching: 00:04:05 Overall time: 00:04:05 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] 257196 / 2269282 = 0.1133 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 19:14:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.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 19:14:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:14:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:14:12: 1000000 INFO @ Sat, 15 Jan 2022 19:14:18: 2000000 INFO @ Sat, 15 Jan 2022 19:14:24: 3000000 INFO @ Sat, 15 Jan 2022 19:14:30: 4000000 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 19:14:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.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 19:14:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:14:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:14:37: 5000000 INFO @ Sat, 15 Jan 2022 19:14:43: 1000000 INFO @ Sat, 15 Jan 2022 19:14:44: 6000000 INFO @ Sat, 15 Jan 2022 19:14:50: 7000000 INFO @ Sat, 15 Jan 2022 19:14:52: 2000000 INFO @ Sat, 15 Jan 2022 19:14:57: 8000000 INFO @ Sat, 15 Jan 2022 19:14:58: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:14:58: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:14:58: #1 total tags in treatment: 1975347 INFO @ Sat, 15 Jan 2022 19:14:58: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:14:58: #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 19:14:58: #1 tags after filtering in treatment: 1426740 INFO @ Sat, 15 Jan 2022 19:14:58: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 19:14:58: #1 finished! INFO @ Sat, 15 Jan 2022 19:14:58: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:14:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:14:58: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 19:14:58: 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 @ Sat, 15 Jan 2022 19:14:58: start model_add_line... INFO @ Sat, 15 Jan 2022 19:14:58: start X-correlation... INFO @ Sat, 15 Jan 2022 19:14:58: end of X-cor INFO @ Sat, 15 Jan 2022 19:14:58: #2 finished! INFO @ Sat, 15 Jan 2022 19:14:58: #2 predicted fragment length is 283 bps INFO @ Sat, 15 Jan 2022 19:14:58: #2 alternative fragment length(s) may be 1,56,211,257,283,305,593 bps INFO @ Sat, 15 Jan 2022 19:14:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.05_model.r INFO @ Sat, 15 Jan 2022 19:14:58: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:14:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:14:59: 3000000 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 19:15:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:15:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:15:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:15:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.05_summits.bed INFO @ Sat, 15 Jan 2022 19:15:05: Done! INFO @ Sat, 15 Jan 2022 19:15:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.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 19:15:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:15:05: #1 read treatment tags... pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (18 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:15:07: 4000000 INFO @ Sat, 15 Jan 2022 19:15:14: 1000000 INFO @ Sat, 15 Jan 2022 19:15:14: 5000000 INFO @ Sat, 15 Jan 2022 19:15:22: 6000000 INFO @ Sat, 15 Jan 2022 19:15:23: 2000000 INFO @ Sat, 15 Jan 2022 19:15:30: 7000000 INFO @ Sat, 15 Jan 2022 19:15:32: 3000000 INFO @ Sat, 15 Jan 2022 19:15:38: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:15:39: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:15:39: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:15:39: #1 total tags in treatment: 1975347 INFO @ Sat, 15 Jan 2022 19:15:39: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:15:39: #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 19:15:39: #1 tags after filtering in treatment: 1426740 INFO @ Sat, 15 Jan 2022 19:15:39: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 19:15:39: #1 finished! INFO @ Sat, 15 Jan 2022 19:15:39: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:15:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:15:39: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 19:15:39: 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 @ Sat, 15 Jan 2022 19:15:39: start model_add_line... INFO @ Sat, 15 Jan 2022 19:15:39: start X-correlation... INFO @ Sat, 15 Jan 2022 19:15:39: end of X-cor INFO @ Sat, 15 Jan 2022 19:15:39: #2 finished! INFO @ Sat, 15 Jan 2022 19:15:39: #2 predicted fragment length is 283 bps INFO @ Sat, 15 Jan 2022 19:15:39: #2 alternative fragment length(s) may be 1,56,211,257,283,305,593 bps INFO @ Sat, 15 Jan 2022 19:15:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.10_model.r INFO @ Sat, 15 Jan 2022 19:15:39: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:15:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:15:40: 4000000 INFO @ Sat, 15 Jan 2022 19:15:45: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:15:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:15:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:15:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.10_summits.bed INFO @ Sat, 15 Jan 2022 19:15:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:15:49: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:15:58: 6000000 INFO @ Sat, 15 Jan 2022 19:16:07: 7000000 INFO @ Sat, 15 Jan 2022 19:16:16: 8000000 INFO @ Sat, 15 Jan 2022 19:16:17: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:16:17: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:16:17: #1 total tags in treatment: 1975347 INFO @ Sat, 15 Jan 2022 19:16:17: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:16:17: #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 19:16:17: #1 tags after filtering in treatment: 1426740 INFO @ Sat, 15 Jan 2022 19:16:17: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 19:16:17: #1 finished! INFO @ Sat, 15 Jan 2022 19:16:17: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:16:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:16:17: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 19:16:17: 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 @ Sat, 15 Jan 2022 19:16:17: start model_add_line... INFO @ Sat, 15 Jan 2022 19:16:17: start X-correlation... INFO @ Sat, 15 Jan 2022 19:16:17: end of X-cor INFO @ Sat, 15 Jan 2022 19:16:17: #2 finished! INFO @ Sat, 15 Jan 2022 19:16:17: #2 predicted fragment length is 283 bps INFO @ Sat, 15 Jan 2022 19:16:17: #2 alternative fragment length(s) may be 1,56,211,257,283,305,593 bps INFO @ Sat, 15 Jan 2022 19:16:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.20_model.r INFO @ Sat, 15 Jan 2022 19:16:17: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:16:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:16:22: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:16:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:16:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:16:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781143/SRX11781143.20_summits.bed INFO @ Sat, 15 Jan 2022 19:16:24: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 2 millis CompletedMACS2peakCalling