Job ID = 14520274 SRX = SRX8926526 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4042303 spots for SRR12430725/SRR12430725.sra Written 4042303 spots for SRR12430725/SRR12430725.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: 00:02:37 4042303 reads; of these: 4042303 (100.00%) were paired; of these: 1325863 (32.80%) aligned concordantly 0 times 2090844 (51.72%) aligned concordantly exactly 1 time 625596 (15.48%) aligned concordantly >1 times ---- 1325863 pairs aligned concordantly 0 times; of these: 2725 (0.21%) aligned discordantly 1 time ---- 1323138 pairs aligned 0 times concordantly or discordantly; of these: 2646276 mates make up the pairs; of these: 2613309 (98.75%) aligned 0 times 21654 (0.82%) aligned exactly 1 time 11313 (0.43%) aligned >1 times 67.68% overall alignment rate Time searching: 00:02:37 Overall time: 00:02:37 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] 594252 / 2718938 = 0.2186 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 18:53:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.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 18:53:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:53:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:54:01: 1000000 INFO @ Sat, 15 Jan 2022 18:54:06: 2000000 INFO @ Sat, 15 Jan 2022 18:54:11: 3000000 INFO @ Sat, 15 Jan 2022 18:54:15: 4000000 INFO @ Sat, 15 Jan 2022 18:54:17: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 18:54:17: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 18:54:17: #1 total tags in treatment: 2122399 INFO @ Sat, 15 Jan 2022 18:54:17: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:54:17: #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 18:54:17: #1 tags after filtering in treatment: 1663770 INFO @ Sat, 15 Jan 2022 18:54:17: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 18:54:17: #1 finished! INFO @ Sat, 15 Jan 2022 18:54:17: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:54:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:54:17: #2 number of paired peaks: 158 WARNING @ Sat, 15 Jan 2022 18:54:17: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 15 Jan 2022 18:54:17: start model_add_line... INFO @ Sat, 15 Jan 2022 18:54:17: start X-correlation... INFO @ Sat, 15 Jan 2022 18:54:17: end of X-cor INFO @ Sat, 15 Jan 2022 18:54:17: #2 finished! INFO @ Sat, 15 Jan 2022 18:54:17: #2 predicted fragment length is 192 bps INFO @ Sat, 15 Jan 2022 18:54:17: #2 alternative fragment length(s) may be 192 bps INFO @ Sat, 15 Jan 2022 18:54:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.05_model.r INFO @ Sat, 15 Jan 2022 18:54:17: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:54:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:54:23: #3 Call peaks for each chromosome... 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 18:54:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.05_peaks.xls INFO @ Sat, 15 Jan 2022 18:54:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:54:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.05_summits.bed INFO @ Sat, 15 Jan 2022 18:54:24: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1506 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 18:54:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.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 18:54:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:54:26: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:54:31: 1000000 INFO @ Sat, 15 Jan 2022 18:54:35: 2000000 INFO @ Sat, 15 Jan 2022 18:54:40: 3000000 INFO @ Sat, 15 Jan 2022 18:54:44: 4000000 INFO @ Sat, 15 Jan 2022 18:54:45: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 18:54:45: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 18:54:45: #1 total tags in treatment: 2122399 INFO @ Sat, 15 Jan 2022 18:54:45: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:54:45: #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 18:54:45: #1 tags after filtering in treatment: 1663770 INFO @ Sat, 15 Jan 2022 18:54:45: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 18:54:45: #1 finished! INFO @ Sat, 15 Jan 2022 18:54:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:54:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:54:46: #2 number of paired peaks: 158 WARNING @ Sat, 15 Jan 2022 18:54:46: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 15 Jan 2022 18:54:46: start model_add_line... INFO @ Sat, 15 Jan 2022 18:54:46: start X-correlation... INFO @ Sat, 15 Jan 2022 18:54:46: end of X-cor INFO @ Sat, 15 Jan 2022 18:54:46: #2 finished! INFO @ Sat, 15 Jan 2022 18:54:46: #2 predicted fragment length is 192 bps INFO @ Sat, 15 Jan 2022 18:54:46: #2 alternative fragment length(s) may be 192 bps INFO @ Sat, 15 Jan 2022 18:54:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.10_model.r INFO @ Sat, 15 Jan 2022 18:54:46: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:54:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:54:51: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:54:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.10_peaks.xls INFO @ Sat, 15 Jan 2022 18:54:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:54:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.10_summits.bed INFO @ Sat, 15 Jan 2022 18:54:53: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (987 records, 4 fields): 20 millis CompletedMACS2peakCalling 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 18:54:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.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 18:54:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:54:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:55:01: 1000000 INFO @ Sat, 15 Jan 2022 18:55:05: 2000000 INFO @ Sat, 15 Jan 2022 18:55:10: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 18:55:15: 4000000 INFO @ Sat, 15 Jan 2022 18:55:16: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 18:55:16: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 18:55:16: #1 total tags in treatment: 2122399 INFO @ Sat, 15 Jan 2022 18:55:16: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:55:16: #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 18:55:16: #1 tags after filtering in treatment: 1663770 INFO @ Sat, 15 Jan 2022 18:55:16: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 18:55:16: #1 finished! INFO @ Sat, 15 Jan 2022 18:55:16: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:55:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:55:16: #2 number of paired peaks: 158 WARNING @ Sat, 15 Jan 2022 18:55:16: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 15 Jan 2022 18:55:16: start model_add_line... INFO @ Sat, 15 Jan 2022 18:55:16: start X-correlation... INFO @ Sat, 15 Jan 2022 18:55:16: end of X-cor INFO @ Sat, 15 Jan 2022 18:55:16: #2 finished! INFO @ Sat, 15 Jan 2022 18:55:16: #2 predicted fragment length is 192 bps INFO @ Sat, 15 Jan 2022 18:55:16: #2 alternative fragment length(s) may be 192 bps INFO @ Sat, 15 Jan 2022 18:55:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.20_model.r INFO @ Sat, 15 Jan 2022 18:55:16: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:55:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:55:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 18:55:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.20_peaks.xls INFO @ Sat, 15 Jan 2022 18:55:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:55:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8926526/SRX8926526.20_summits.bed INFO @ Sat, 15 Jan 2022 18:55:23: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (542 records, 4 fields): 3 millis CompletedMACS2peakCalling