Job ID = 14520742 SRX = SRX8245504 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11317255 spots for SRR11684715/SRR11684715.sra Written 11317255 spots for SRR11684715/SRR11684715.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: 00:05:54 11317255 reads; of these: 11317255 (100.00%) were paired; of these: 7132083 (63.02%) aligned concordantly 0 times 3579992 (31.63%) aligned concordantly exactly 1 time 605180 (5.35%) aligned concordantly >1 times ---- 7132083 pairs aligned concordantly 0 times; of these: 254892 (3.57%) aligned discordantly 1 time ---- 6877191 pairs aligned 0 times concordantly or discordantly; of these: 13754382 mates make up the pairs; of these: 9814530 (71.36%) aligned 0 times 3281692 (23.86%) aligned exactly 1 time 658160 (4.79%) aligned >1 times 56.64% overall alignment rate Time searching: 00:05:54 Overall time: 00:05:54 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] 576718 / 4438222 = 0.1299 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 19:55:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.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 19:55:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:55:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:55:34: 1000000 INFO @ Sat, 15 Jan 2022 19:55:40: 2000000 INFO @ Sat, 15 Jan 2022 19:55:44: 3000000 INFO @ Sat, 15 Jan 2022 19:55:49: 4000000 INFO @ Sat, 15 Jan 2022 19:55:54: 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 19:55:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.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 19:55:59: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:55:59: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:55:59: 6000000 INFO @ Sat, 15 Jan 2022 19:56:05: 1000000 INFO @ Sat, 15 Jan 2022 19:56:06: 7000000 INFO @ Sat, 15 Jan 2022 19:56:11: 2000000 INFO @ Sat, 15 Jan 2022 19:56:12: 8000000 INFO @ Sat, 15 Jan 2022 19:56:17: 3000000 INFO @ Sat, 15 Jan 2022 19:56:17: 9000000 INFO @ Sat, 15 Jan 2022 19:56:23: 4000000 INFO @ Sat, 15 Jan 2022 19:56:24: 10000000 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 19:56:28: 5000000 INFO @ Sat, 15 Jan 2022 19:56:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.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 19:56:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:56:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:56:30: 11000000 INFO @ Sat, 15 Jan 2022 19:56:34: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:56:34: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:56:34: #1 total tags in treatment: 3627971 INFO @ Sat, 15 Jan 2022 19:56:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:56:34: #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 19:56:35: #1 tags after filtering in treatment: 2718444 INFO @ Sat, 15 Jan 2022 19:56:35: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 19:56:35: #1 finished! INFO @ Sat, 15 Jan 2022 19:56:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:56:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:56:35: 6000000 INFO @ Sat, 15 Jan 2022 19:56:35: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 19:56:35: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 15 Jan 2022 19:56:35: start model_add_line... INFO @ Sat, 15 Jan 2022 19:56:35: start X-correlation... INFO @ Sat, 15 Jan 2022 19:56:35: end of X-cor INFO @ Sat, 15 Jan 2022 19:56:35: #2 finished! INFO @ Sat, 15 Jan 2022 19:56:35: #2 predicted fragment length is 263 bps INFO @ Sat, 15 Jan 2022 19:56:35: #2 alternative fragment length(s) may be 0,53,112,129,141,177,217,235,263,295,345,544,579,597 bps INFO @ Sat, 15 Jan 2022 19:56:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.05_model.r INFO @ Sat, 15 Jan 2022 19:56:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:56:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:56:36: 1000000 INFO @ Sat, 15 Jan 2022 19:56:41: 7000000 INFO @ Sat, 15 Jan 2022 19:56:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:56:42: 2000000 INFO @ Sat, 15 Jan 2022 19:56:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:56:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:56:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.05_summits.bed INFO @ Sat, 15 Jan 2022 19:56:44: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (582 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:56:48: 8000000 INFO @ Sat, 15 Jan 2022 19:56:49: 3000000 INFO @ Sat, 15 Jan 2022 19:56:54: 9000000 INFO @ Sat, 15 Jan 2022 19:56:56: 4000000 INFO @ Sat, 15 Jan 2022 19:57:01: 10000000 INFO @ Sat, 15 Jan 2022 19:57:02: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:57:07: 11000000 INFO @ Sat, 15 Jan 2022 19:57:09: 6000000 INFO @ Sat, 15 Jan 2022 19:57:11: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:57:11: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:57:11: #1 total tags in treatment: 3627971 INFO @ Sat, 15 Jan 2022 19:57:11: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:57:11: #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 19:57:11: #1 tags after filtering in treatment: 2718444 INFO @ Sat, 15 Jan 2022 19:57:11: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 19:57:11: #1 finished! INFO @ Sat, 15 Jan 2022 19:57:11: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:57:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:57:12: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 19:57:12: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 15 Jan 2022 19:57:12: start model_add_line... INFO @ Sat, 15 Jan 2022 19:57:12: start X-correlation... INFO @ Sat, 15 Jan 2022 19:57:12: end of X-cor INFO @ Sat, 15 Jan 2022 19:57:12: #2 finished! INFO @ Sat, 15 Jan 2022 19:57:12: #2 predicted fragment length is 263 bps INFO @ Sat, 15 Jan 2022 19:57:12: #2 alternative fragment length(s) may be 0,53,112,129,141,177,217,235,263,295,345,544,579,597 bps INFO @ Sat, 15 Jan 2022 19:57:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.10_model.r INFO @ Sat, 15 Jan 2022 19:57:12: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:57:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:57:15: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:57:18: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:57:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:57:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:57:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.10_summits.bed INFO @ Sat, 15 Jan 2022 19:57:20: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (254 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:57:22: 8000000 INFO @ Sat, 15 Jan 2022 19:57:29: 9000000 INFO @ Sat, 15 Jan 2022 19:57:35: 10000000 INFO @ Sat, 15 Jan 2022 19:57:41: 11000000 INFO @ Sat, 15 Jan 2022 19:57:45: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:57:45: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:57:45: #1 total tags in treatment: 3627971 INFO @ Sat, 15 Jan 2022 19:57:45: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:57:45: #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 19:57:45: #1 tags after filtering in treatment: 2718444 INFO @ Sat, 15 Jan 2022 19:57:45: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 19:57:45: #1 finished! INFO @ Sat, 15 Jan 2022 19:57:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:57:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:57:45: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 19:57:45: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 15 Jan 2022 19:57:45: start model_add_line... INFO @ Sat, 15 Jan 2022 19:57:45: start X-correlation... INFO @ Sat, 15 Jan 2022 19:57:45: end of X-cor INFO @ Sat, 15 Jan 2022 19:57:45: #2 finished! INFO @ Sat, 15 Jan 2022 19:57:45: #2 predicted fragment length is 263 bps INFO @ Sat, 15 Jan 2022 19:57:45: #2 alternative fragment length(s) may be 0,53,112,129,141,177,217,235,263,295,345,544,579,597 bps INFO @ Sat, 15 Jan 2022 19:57:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.20_model.r INFO @ Sat, 15 Jan 2022 19:57:45: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:57:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:57:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:57:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:57:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:57:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245504/SRX8245504.20_summits.bed INFO @ Sat, 15 Jan 2022 19:57:54: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (69 records, 4 fields): 2 millis CompletedMACS2peakCalling