Job ID = 14521978 SRX = SRX7637547 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9652306 spots for SRR10972027/SRR10972027.sra Written 9652306 spots for SRR10972027/SRR10972027.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: 00:08:33 9652306 reads; of these: 9652306 (100.00%) were paired; of these: 2792048 (28.93%) aligned concordantly 0 times 4928014 (51.06%) aligned concordantly exactly 1 time 1932244 (20.02%) aligned concordantly >1 times ---- 2792048 pairs aligned concordantly 0 times; of these: 3641 (0.13%) aligned discordantly 1 time ---- 2788407 pairs aligned 0 times concordantly or discordantly; of these: 5576814 mates make up the pairs; of these: 5526647 (99.10%) aligned 0 times 34957 (0.63%) aligned exactly 1 time 15210 (0.27%) aligned >1 times 71.37% overall alignment rate Time searching: 00:08:33 Overall time: 00:08:33 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] 2463309 / 6861950 = 0.3590 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 22:09:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.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 22:09:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:09:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:09:14: 1000000 INFO @ Sat, 15 Jan 2022 22:09:22: 2000000 INFO @ Sat, 15 Jan 2022 22:09:31: 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 22:09:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.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 22:09:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:09:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:09:39: 4000000 INFO @ Sat, 15 Jan 2022 22:09:44: 1000000 INFO @ Sat, 15 Jan 2022 22:09:48: 5000000 INFO @ Sat, 15 Jan 2022 22:09:53: 2000000 INFO @ Sat, 15 Jan 2022 22:09:57: 6000000 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 22:10:02: 3000000 INFO @ Sat, 15 Jan 2022 22:10:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.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 22:10:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:10:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:10:06: 7000000 INFO @ Sat, 15 Jan 2022 22:10:12: 4000000 INFO @ Sat, 15 Jan 2022 22:10:13: 1000000 INFO @ Sat, 15 Jan 2022 22:10:15: 8000000 INFO @ Sat, 15 Jan 2022 22:10:21: 2000000 INFO @ Sat, 15 Jan 2022 22:10:21: 5000000 INFO @ Sat, 15 Jan 2022 22:10:23: #1 tag size is determined as 41 bps INFO @ Sat, 15 Jan 2022 22:10:23: #1 tag size = 41 INFO @ Sat, 15 Jan 2022 22:10:23: #1 total tags in treatment: 4397830 INFO @ Sat, 15 Jan 2022 22:10:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:10:23: #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 22:10:23: #1 tags after filtering in treatment: 2576801 INFO @ Sat, 15 Jan 2022 22:10:23: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 15 Jan 2022 22:10:23: #1 finished! INFO @ Sat, 15 Jan 2022 22:10:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:10:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:10:23: #2 number of paired peaks: 365 WARNING @ Sat, 15 Jan 2022 22:10:23: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Sat, 15 Jan 2022 22:10:23: start model_add_line... INFO @ Sat, 15 Jan 2022 22:10:23: start X-correlation... INFO @ Sat, 15 Jan 2022 22:10:24: end of X-cor INFO @ Sat, 15 Jan 2022 22:10:24: #2 finished! INFO @ Sat, 15 Jan 2022 22:10:24: #2 predicted fragment length is 281 bps INFO @ Sat, 15 Jan 2022 22:10:24: #2 alternative fragment length(s) may be 47,106,135,281,321,369,393 bps INFO @ Sat, 15 Jan 2022 22:10:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.05_model.r INFO @ Sat, 15 Jan 2022 22:10:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:10:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:10:30: 3000000 INFO @ Sat, 15 Jan 2022 22:10:31: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:10:38: 4000000 INFO @ Sat, 15 Jan 2022 22:10:41: 7000000 INFO @ Sat, 15 Jan 2022 22:10:45: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:10:46: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 22:10:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.05_peaks.xls INFO @ Sat, 15 Jan 2022 22:10:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:10:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.05_summits.bed INFO @ Sat, 15 Jan 2022 22:10:48: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (824 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:10:51: 8000000 INFO @ Sat, 15 Jan 2022 22:10:54: 6000000 INFO @ Sat, 15 Jan 2022 22:10:59: #1 tag size is determined as 41 bps INFO @ Sat, 15 Jan 2022 22:10:59: #1 tag size = 41 INFO @ Sat, 15 Jan 2022 22:10:59: #1 total tags in treatment: 4397830 INFO @ Sat, 15 Jan 2022 22:10:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:10:59: #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 22:10:59: #1 tags after filtering in treatment: 2576801 INFO @ Sat, 15 Jan 2022 22:10:59: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 15 Jan 2022 22:10:59: #1 finished! INFO @ Sat, 15 Jan 2022 22:10:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:10:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:10:59: #2 number of paired peaks: 365 WARNING @ Sat, 15 Jan 2022 22:10:59: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Sat, 15 Jan 2022 22:10:59: start model_add_line... INFO @ Sat, 15 Jan 2022 22:10:59: start X-correlation... INFO @ Sat, 15 Jan 2022 22:10:59: end of X-cor INFO @ Sat, 15 Jan 2022 22:10:59: #2 finished! INFO @ Sat, 15 Jan 2022 22:10:59: #2 predicted fragment length is 281 bps INFO @ Sat, 15 Jan 2022 22:10:59: #2 alternative fragment length(s) may be 47,106,135,281,321,369,393 bps INFO @ Sat, 15 Jan 2022 22:10:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.10_model.r INFO @ Sat, 15 Jan 2022 22:10:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:10:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:11:01: 7000000 INFO @ Sat, 15 Jan 2022 22:11:09: 8000000 INFO @ Sat, 15 Jan 2022 22:11:15: #1 tag size is determined as 41 bps INFO @ Sat, 15 Jan 2022 22:11:15: #1 tag size = 41 INFO @ Sat, 15 Jan 2022 22:11:15: #1 total tags in treatment: 4397830 INFO @ Sat, 15 Jan 2022 22:11:15: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:11:15: #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 22:11:15: #1 tags after filtering in treatment: 2576801 INFO @ Sat, 15 Jan 2022 22:11:15: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 15 Jan 2022 22:11:15: #1 finished! INFO @ Sat, 15 Jan 2022 22:11:15: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:11:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:11:15: #2 number of paired peaks: 365 WARNING @ Sat, 15 Jan 2022 22:11:15: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Sat, 15 Jan 2022 22:11:15: start model_add_line... INFO @ Sat, 15 Jan 2022 22:11:15: start X-correlation... INFO @ Sat, 15 Jan 2022 22:11:16: end of X-cor INFO @ Sat, 15 Jan 2022 22:11:16: #2 finished! INFO @ Sat, 15 Jan 2022 22:11:16: #2 predicted fragment length is 281 bps INFO @ Sat, 15 Jan 2022 22:11:16: #2 alternative fragment length(s) may be 47,106,135,281,321,369,393 bps INFO @ Sat, 15 Jan 2022 22:11:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.20_model.r INFO @ Sat, 15 Jan 2022 22:11:16: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:11:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:11:21: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:11:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.10_peaks.xls INFO @ Sat, 15 Jan 2022 22:11:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:11:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.10_summits.bed INFO @ Sat, 15 Jan 2022 22:11:24: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (694 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:11:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:11:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.20_peaks.xls INFO @ Sat, 15 Jan 2022 22:11:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:11:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7637547/SRX7637547.20_summits.bed INFO @ Sat, 15 Jan 2022 22:11:39: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (469 records, 4 fields): 4 millis CompletedMACS2peakCalling