Job ID = 14520467 SRX = SRX11781157 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:10:21 prefetch.2.10.7: 1) Downloading 'SRR15481100'... 2022-01-15T10:10:22 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:10:37 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:10:37 prefetch.2.10.7: 'SRR15481100' is valid 2022-01-15T10:10:37 prefetch.2.10.7: 1) 'SRR15481100' was downloaded successfully 2022-01-15T10:10:37 prefetch.2.10.7: 'SRR15481100' has 0 unresolved dependencies Read 6222372 spots for SRR15481100/SRR15481100.sra Written 6222372 spots for SRR15481100/SRR15481100.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: 00:02:46 6222372 reads; of these: 6222372 (100.00%) were paired; of these: 3851204 (61.89%) aligned concordantly 0 times 2063886 (33.17%) aligned concordantly exactly 1 time 307282 (4.94%) aligned concordantly >1 times ---- 3851204 pairs aligned concordantly 0 times; of these: 48525 (1.26%) aligned discordantly 1 time ---- 3802679 pairs aligned 0 times concordantly or discordantly; of these: 7605358 mates make up the pairs; of these: 4156438 (54.65%) aligned 0 times 2975935 (39.13%) aligned exactly 1 time 472985 (6.22%) aligned >1 times 66.60% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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] 301115 / 2418773 = 0.1245 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 19:16:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.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 19:16:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:16:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:16:11: 1000000 INFO @ Sat, 15 Jan 2022 19:16:16: 2000000 INFO @ Sat, 15 Jan 2022 19:16:22: 3000000 INFO @ Sat, 15 Jan 2022 19:16:27: 4000000 INFO @ Sat, 15 Jan 2022 19:16:33: 5000000 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 19:16:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.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 19:16:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:16:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:16:39: 6000000 INFO @ Sat, 15 Jan 2022 19:16:41: 1000000 INFO @ Sat, 15 Jan 2022 19:16:45: 7000000 INFO @ Sat, 15 Jan 2022 19:16:47: 2000000 INFO @ Sat, 15 Jan 2022 19:16:49: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:16:49: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:16:49: #1 total tags in treatment: 2073111 INFO @ Sat, 15 Jan 2022 19:16:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:16:49: #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 19:16:49: #1 tags after filtering in treatment: 1554543 INFO @ Sat, 15 Jan 2022 19:16:49: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 19:16:49: #1 finished! INFO @ Sat, 15 Jan 2022 19:16:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:16:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:16:49: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 19:16:49: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 19:16:49: start model_add_line... INFO @ Sat, 15 Jan 2022 19:16:49: start X-correlation... INFO @ Sat, 15 Jan 2022 19:16:49: end of X-cor INFO @ Sat, 15 Jan 2022 19:16:49: #2 finished! INFO @ Sat, 15 Jan 2022 19:16:49: #2 predicted fragment length is 280 bps INFO @ Sat, 15 Jan 2022 19:16:49: #2 alternative fragment length(s) may be 1,227,264,268,280 bps INFO @ Sat, 15 Jan 2022 19:16:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.05_model.r INFO @ Sat, 15 Jan 2022 19:16:49: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:16:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:16:53: 3000000 INFO @ Sat, 15 Jan 2022 19:16:53: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:16:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:16:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:16:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.05_summits.bed INFO @ Sat, 15 Jan 2022 19:16:55: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (31 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:16:58: 4000000 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 19:17:04: 5000000 INFO @ Sat, 15 Jan 2022 19:17:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.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 19:17:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:17:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:17:10: 6000000 INFO @ Sat, 15 Jan 2022 19:17:11: 1000000 INFO @ Sat, 15 Jan 2022 19:17:16: 7000000 INFO @ Sat, 15 Jan 2022 19:17:16: 2000000 INFO @ Sat, 15 Jan 2022 19:17:20: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:17:20: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:17:20: #1 total tags in treatment: 2073111 INFO @ Sat, 15 Jan 2022 19:17:20: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:17:20: #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 19:17:20: #1 tags after filtering in treatment: 1554543 INFO @ Sat, 15 Jan 2022 19:17:20: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 19:17:20: #1 finished! INFO @ Sat, 15 Jan 2022 19:17:20: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:17:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:17:20: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 19:17:20: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 19:17:20: start model_add_line... INFO @ Sat, 15 Jan 2022 19:17:20: start X-correlation... INFO @ Sat, 15 Jan 2022 19:17:20: end of X-cor INFO @ Sat, 15 Jan 2022 19:17:20: #2 finished! INFO @ Sat, 15 Jan 2022 19:17:20: #2 predicted fragment length is 280 bps INFO @ Sat, 15 Jan 2022 19:17:20: #2 alternative fragment length(s) may be 1,227,264,268,280 bps INFO @ Sat, 15 Jan 2022 19:17:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.10_model.r INFO @ Sat, 15 Jan 2022 19:17:20: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:17:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:17:22: 3000000 INFO @ Sat, 15 Jan 2022 19:17:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:17:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:17:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:17:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.10_summits.bed INFO @ Sat, 15 Jan 2022 19:17:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (13 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:17:26: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:17:31: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:17:36: 6000000 INFO @ Sat, 15 Jan 2022 19:17:41: 7000000 INFO @ Sat, 15 Jan 2022 19:17:44: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:17:44: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:17:44: #1 total tags in treatment: 2073111 INFO @ Sat, 15 Jan 2022 19:17:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:17:44: #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 19:17:44: #1 tags after filtering in treatment: 1554543 INFO @ Sat, 15 Jan 2022 19:17:44: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 19:17:44: #1 finished! INFO @ Sat, 15 Jan 2022 19:17:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:17:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:17:44: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 19:17:44: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 19:17:44: start model_add_line... INFO @ Sat, 15 Jan 2022 19:17:44: start X-correlation... INFO @ Sat, 15 Jan 2022 19:17:44: end of X-cor INFO @ Sat, 15 Jan 2022 19:17:44: #2 finished! INFO @ Sat, 15 Jan 2022 19:17:44: #2 predicted fragment length is 280 bps INFO @ Sat, 15 Jan 2022 19:17:44: #2 alternative fragment length(s) may be 1,227,264,268,280 bps INFO @ Sat, 15 Jan 2022 19:17:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.20_model.r INFO @ Sat, 15 Jan 2022 19:17:44: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:17:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:17:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:17:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:17:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:17:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781157/SRX11781157.20_summits.bed INFO @ Sat, 15 Jan 2022 19:17:49: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling