Job ID = 14520413 SRX = SRX11781137 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5848511 spots for SRR15481080/SRR15481080.sra Written 5848511 spots for SRR15481080/SRR15481080.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: 00:03:26 5848511 reads; of these: 5848511 (100.00%) were paired; of these: 3812848 (65.19%) aligned concordantly 0 times 1855889 (31.73%) aligned concordantly exactly 1 time 179774 (3.07%) aligned concordantly >1 times ---- 3812848 pairs aligned concordantly 0 times; of these: 60729 (1.59%) aligned discordantly 1 time ---- 3752119 pairs aligned 0 times concordantly or discordantly; of these: 7504238 mates make up the pairs; of these: 4280482 (57.04%) aligned 0 times 2876868 (38.34%) aligned exactly 1 time 346888 (4.62%) aligned >1 times 63.41% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 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] 304514 / 2095501 = 0.1453 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 19:09:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.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 19:09:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:09:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:09:33: 1000000 INFO @ Sat, 15 Jan 2022 19:09:41: 2000000 INFO @ Sat, 15 Jan 2022 19:09:50: 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 19:09:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.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 19:09:53: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:09:53: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:09:59: 4000000 INFO @ Sat, 15 Jan 2022 19:10:02: 1000000 INFO @ Sat, 15 Jan 2022 19:10:08: 5000000 INFO @ Sat, 15 Jan 2022 19:10:10: 2000000 INFO @ Sat, 15 Jan 2022 19:10:17: 6000000 INFO @ Sat, 15 Jan 2022 19:10:18: 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 19:10:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.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 19:10:23: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:10:23: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:10:24: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:10:24: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:10:24: #1 total tags in treatment: 1736285 INFO @ Sat, 15 Jan 2022 19:10:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:10:24: #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 19:10:24: #1 tags after filtering in treatment: 1328667 INFO @ Sat, 15 Jan 2022 19:10:24: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 19:10:24: #1 finished! INFO @ Sat, 15 Jan 2022 19:10:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:10:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:10:24: #2 number of paired peaks: 183 WARNING @ Sat, 15 Jan 2022 19:10:24: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Sat, 15 Jan 2022 19:10:24: start model_add_line... INFO @ Sat, 15 Jan 2022 19:10:24: start X-correlation... INFO @ Sat, 15 Jan 2022 19:10:25: end of X-cor INFO @ Sat, 15 Jan 2022 19:10:25: #2 finished! INFO @ Sat, 15 Jan 2022 19:10:25: #2 predicted fragment length is 247 bps INFO @ Sat, 15 Jan 2022 19:10:25: #2 alternative fragment length(s) may be 1,212,247 bps INFO @ Sat, 15 Jan 2022 19:10:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.05_model.r INFO @ Sat, 15 Jan 2022 19:10:25: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:10:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:10:27: 4000000 INFO @ Sat, 15 Jan 2022 19:10:29: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:10:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:10:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:10:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.05_summits.bed INFO @ Sat, 15 Jan 2022 19:10:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (28 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:10:32: 1000000 INFO @ Sat, 15 Jan 2022 19:10:35: 5000000 INFO @ Sat, 15 Jan 2022 19:10:41: 2000000 INFO @ Sat, 15 Jan 2022 19:10:44: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:10:49: 3000000 INFO @ Sat, 15 Jan 2022 19:10:50: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:10:50: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:10:50: #1 total tags in treatment: 1736285 INFO @ Sat, 15 Jan 2022 19:10:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:10:50: #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 19:10:50: #1 tags after filtering in treatment: 1328667 INFO @ Sat, 15 Jan 2022 19:10:50: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 19:10:50: #1 finished! INFO @ Sat, 15 Jan 2022 19:10:50: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:10:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:10:50: #2 number of paired peaks: 183 WARNING @ Sat, 15 Jan 2022 19:10:50: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Sat, 15 Jan 2022 19:10:50: start model_add_line... INFO @ Sat, 15 Jan 2022 19:10:50: start X-correlation... INFO @ Sat, 15 Jan 2022 19:10:50: end of X-cor INFO @ Sat, 15 Jan 2022 19:10:50: #2 finished! INFO @ Sat, 15 Jan 2022 19:10:50: #2 predicted fragment length is 247 bps INFO @ Sat, 15 Jan 2022 19:10:50: #2 alternative fragment length(s) may be 1,212,247 bps INFO @ Sat, 15 Jan 2022 19:10:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.10_model.r INFO @ Sat, 15 Jan 2022 19:10:50: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:10:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:10:55: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:10:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:10:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:10:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.10_summits.bed INFO @ Sat, 15 Jan 2022 19:10:56: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (14 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:10:58: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:11:06: 5000000 INFO @ Sat, 15 Jan 2022 19:11:15: 6000000 INFO @ Sat, 15 Jan 2022 19:11:21: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:11:21: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:11:21: #1 total tags in treatment: 1736285 INFO @ Sat, 15 Jan 2022 19:11:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:11:21: #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 19:11:21: #1 tags after filtering in treatment: 1328667 INFO @ Sat, 15 Jan 2022 19:11:21: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 19:11:21: #1 finished! INFO @ Sat, 15 Jan 2022 19:11:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:11:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:11:21: #2 number of paired peaks: 183 WARNING @ Sat, 15 Jan 2022 19:11:21: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Sat, 15 Jan 2022 19:11:21: start model_add_line... INFO @ Sat, 15 Jan 2022 19:11:21: start X-correlation... INFO @ Sat, 15 Jan 2022 19:11:21: end of X-cor INFO @ Sat, 15 Jan 2022 19:11:21: #2 finished! INFO @ Sat, 15 Jan 2022 19:11:21: #2 predicted fragment length is 247 bps INFO @ Sat, 15 Jan 2022 19:11:21: #2 alternative fragment length(s) may be 1,212,247 bps INFO @ Sat, 15 Jan 2022 19:11:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.20_model.r INFO @ Sat, 15 Jan 2022 19:11:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:11:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:11:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:11:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:11:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:11:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781137/SRX11781137.20_summits.bed INFO @ Sat, 15 Jan 2022 19:11:27: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (8 records, 4 fields): 12 millis CompletedMACS2peakCalling