Job ID = 14522128 SRX = SRX9786303 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15010405 spots for SRR13362135/SRR13362135.sra Written 15010405 spots for SRR13362135/SRR13362135.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: 00:11:16 15010405 reads; of these: 15010405 (100.00%) were paired; of these: 8205833 (54.67%) aligned concordantly 0 times 6190945 (41.24%) aligned concordantly exactly 1 time 613627 (4.09%) aligned concordantly >1 times ---- 8205833 pairs aligned concordantly 0 times; of these: 167255 (2.04%) aligned discordantly 1 time ---- 8038578 pairs aligned 0 times concordantly or discordantly; of these: 16077156 mates make up the pairs; of these: 10968603 (68.22%) aligned 0 times 4526627 (28.16%) aligned exactly 1 time 581926 (3.62%) aligned >1 times 63.46% overall alignment rate Time searching: 00:11:16 Overall time: 00:11:16 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] 563818 / 6970518 = 0.0809 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 22:33:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.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 22:33:36: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:33:36: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:33:45: 1000000 INFO @ Sat, 15 Jan 2022 22:33:55: 2000000 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 22:34:04: 3000000 INFO @ Sat, 15 Jan 2022 22:34:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.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 22:34:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:34:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:34:13: 1000000 INFO @ Sat, 15 Jan 2022 22:34:14: 4000000 INFO @ Sat, 15 Jan 2022 22:34:22: 2000000 INFO @ Sat, 15 Jan 2022 22:34:23: 5000000 INFO @ Sat, 15 Jan 2022 22:34:30: 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 22:34:33: 6000000 INFO @ Sat, 15 Jan 2022 22:34:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.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 22:34:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:34:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:34:39: 4000000 INFO @ Sat, 15 Jan 2022 22:34:43: 7000000 INFO @ Sat, 15 Jan 2022 22:34:45: 1000000 INFO @ Sat, 15 Jan 2022 22:34:48: 5000000 INFO @ Sat, 15 Jan 2022 22:34:53: 8000000 INFO @ Sat, 15 Jan 2022 22:34:54: 2000000 INFO @ Sat, 15 Jan 2022 22:34:58: 6000000 INFO @ Sat, 15 Jan 2022 22:35:04: 9000000 INFO @ Sat, 15 Jan 2022 22:35:04: 3000000 INFO @ Sat, 15 Jan 2022 22:35:08: 7000000 INFO @ Sat, 15 Jan 2022 22:35:14: 4000000 INFO @ Sat, 15 Jan 2022 22:35:14: 10000000 INFO @ Sat, 15 Jan 2022 22:35:17: 8000000 INFO @ Sat, 15 Jan 2022 22:35:22: 5000000 INFO @ Sat, 15 Jan 2022 22:35:24: 11000000 INFO @ Sat, 15 Jan 2022 22:35:26: 9000000 INFO @ Sat, 15 Jan 2022 22:35:31: 6000000 INFO @ Sat, 15 Jan 2022 22:35:34: 12000000 INFO @ Sat, 15 Jan 2022 22:35:35: 10000000 INFO @ Sat, 15 Jan 2022 22:35:40: 7000000 INFO @ Sat, 15 Jan 2022 22:35:44: 13000000 INFO @ Sat, 15 Jan 2022 22:35:44: 11000000 INFO @ Sat, 15 Jan 2022 22:35:49: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:35:54: 14000000 INFO @ Sat, 15 Jan 2022 22:35:55: 12000000 INFO @ Sat, 15 Jan 2022 22:36:00: 9000000 INFO @ Sat, 15 Jan 2022 22:36:04: 13000000 INFO @ Sat, 15 Jan 2022 22:36:04: 15000000 INFO @ Sat, 15 Jan 2022 22:36:09: 10000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 22:36:12: 14000000 INFO @ Sat, 15 Jan 2022 22:36:14: 16000000 INFO @ Sat, 15 Jan 2022 22:36:17: 11000000 INFO @ Sat, 15 Jan 2022 22:36:21: 15000000 INFO @ Sat, 15 Jan 2022 22:36:24: 17000000 INFO @ Sat, 15 Jan 2022 22:36:25: 12000000 INFO @ Sat, 15 Jan 2022 22:36:29: 16000000 INFO @ Sat, 15 Jan 2022 22:36:33: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 22:36:33: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 22:36:33: #1 total tags in treatment: 6245982 INFO @ Sat, 15 Jan 2022 22:36:33: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:36:33: #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 22:36:34: #1 tags after filtering in treatment: 4383258 INFO @ Sat, 15 Jan 2022 22:36:34: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 22:36:34: #1 finished! INFO @ Sat, 15 Jan 2022 22:36:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:36:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:36:34: #2 number of paired peaks: 133 WARNING @ Sat, 15 Jan 2022 22:36:34: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Sat, 15 Jan 2022 22:36:34: start model_add_line... INFO @ Sat, 15 Jan 2022 22:36:34: start X-correlation... INFO @ Sat, 15 Jan 2022 22:36:34: end of X-cor INFO @ Sat, 15 Jan 2022 22:36:34: #2 finished! INFO @ Sat, 15 Jan 2022 22:36:34: #2 predicted fragment length is 129 bps INFO @ Sat, 15 Jan 2022 22:36:34: #2 alternative fragment length(s) may be 17,37,52,69,84,129,172,181,188,259,308,331,343,377,431,457,462,478,512,541,556 bps INFO @ Sat, 15 Jan 2022 22:36:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.05_model.r INFO @ Sat, 15 Jan 2022 22:36:34: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:36:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:36:34: 13000000 INFO @ Sat, 15 Jan 2022 22:36:38: 17000000 INFO @ Sat, 15 Jan 2022 22:36:43: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:36:44: 14000000 INFO @ Sat, 15 Jan 2022 22:36:46: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 22:36:46: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 22:36:46: #1 total tags in treatment: 6245982 INFO @ Sat, 15 Jan 2022 22:36:46: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:36:46: #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 22:36:46: #1 tags after filtering in treatment: 4383258 INFO @ Sat, 15 Jan 2022 22:36:46: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 22:36:46: #1 finished! INFO @ Sat, 15 Jan 2022 22:36:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:36:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:36:47: #2 number of paired peaks: 133 WARNING @ Sat, 15 Jan 2022 22:36:47: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Sat, 15 Jan 2022 22:36:47: start model_add_line... INFO @ Sat, 15 Jan 2022 22:36:47: start X-correlation... INFO @ Sat, 15 Jan 2022 22:36:47: end of X-cor INFO @ Sat, 15 Jan 2022 22:36:47: #2 finished! INFO @ Sat, 15 Jan 2022 22:36:47: #2 predicted fragment length is 129 bps INFO @ Sat, 15 Jan 2022 22:36:47: #2 alternative fragment length(s) may be 17,37,52,69,84,129,172,181,188,259,308,331,343,377,431,457,462,478,512,541,556 bps INFO @ Sat, 15 Jan 2022 22:36:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.10_model.r INFO @ Sat, 15 Jan 2022 22:36:47: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:36:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:36:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.05_peaks.xls INFO @ Sat, 15 Jan 2022 22:36:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:36:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.05_summits.bed INFO @ Sat, 15 Jan 2022 22:36:47: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (104 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:36:52: 15000000 INFO @ Sat, 15 Jan 2022 22:36:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:36:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.10_peaks.xls INFO @ Sat, 15 Jan 2022 22:36:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:36:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.10_summits.bed INFO @ Sat, 15 Jan 2022 22:36:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (30 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:37:00: 16000000 INFO @ Sat, 15 Jan 2022 22:37:08: 17000000 INFO @ Sat, 15 Jan 2022 22:37:16: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 22:37:16: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 22:37:16: #1 total tags in treatment: 6245982 INFO @ Sat, 15 Jan 2022 22:37:16: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:37:16: #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 22:37:16: #1 tags after filtering in treatment: 4383258 INFO @ Sat, 15 Jan 2022 22:37:16: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 22:37:16: #1 finished! INFO @ Sat, 15 Jan 2022 22:37:16: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:37:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:37:16: #2 number of paired peaks: 133 WARNING @ Sat, 15 Jan 2022 22:37:16: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Sat, 15 Jan 2022 22:37:16: start model_add_line... INFO @ Sat, 15 Jan 2022 22:37:16: start X-correlation... INFO @ Sat, 15 Jan 2022 22:37:16: end of X-cor INFO @ Sat, 15 Jan 2022 22:37:16: #2 finished! INFO @ Sat, 15 Jan 2022 22:37:16: #2 predicted fragment length is 129 bps INFO @ Sat, 15 Jan 2022 22:37:16: #2 alternative fragment length(s) may be 17,37,52,69,84,129,172,181,188,259,308,331,343,377,431,457,462,478,512,541,556 bps INFO @ Sat, 15 Jan 2022 22:37:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.20_model.r INFO @ Sat, 15 Jan 2022 22:37:16: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:37:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:37:25: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:37:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.20_peaks.xls INFO @ Sat, 15 Jan 2022 22:37:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:37:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9786303/SRX9786303.20_summits.bed INFO @ Sat, 15 Jan 2022 22:37:29: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling