Job ID = 14522036 SRX = SRX10602365 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T13:01:08 prefetch.2.10.7: 1) Downloading 'SRR14239533'... 2022-01-15T13:01:08 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T13:01:25 prefetch.2.10.7: HTTPS download succeed 2022-01-15T13:01:26 prefetch.2.10.7: 'SRR14239533' is valid 2022-01-15T13:01:26 prefetch.2.10.7: 1) 'SRR14239533' was downloaded successfully 2022-01-15T13:01:26 prefetch.2.10.7: 'SRR14239533' has 0 unresolved dependencies Read 6237957 spots for SRR14239533/SRR14239533.sra Written 6237957 spots for SRR14239533/SRR14239533.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: 00:05:07 6237957 reads; of these: 6237957 (100.00%) were paired; of these: 3126269 (50.12%) aligned concordantly 0 times 2289251 (36.70%) aligned concordantly exactly 1 time 822437 (13.18%) aligned concordantly >1 times ---- 3126269 pairs aligned concordantly 0 times; of these: 22256 (0.71%) aligned discordantly 1 time ---- 3104013 pairs aligned 0 times concordantly or discordantly; of these: 6208026 mates make up the pairs; of these: 3775314 (60.81%) aligned 0 times 1809471 (29.15%) aligned exactly 1 time 623241 (10.04%) aligned >1 times 69.74% overall alignment rate Time searching: 00:05:07 Overall time: 00:05:07 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] 205179 / 3132667 = 0.0655 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 22:11:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.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 22:11:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:11:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:11:13: 1000000 INFO @ Sat, 15 Jan 2022 22:11:22: 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 22:11:32: 3000000 INFO @ Sat, 15 Jan 2022 22:11:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.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 22:11:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:11:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:11:42: 4000000 INFO @ Sat, 15 Jan 2022 22:11:43: 1000000 INFO @ Sat, 15 Jan 2022 22:11:52: 5000000 INFO @ Sat, 15 Jan 2022 22:11:54: 2000000 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 22:12:02: 6000000 INFO @ Sat, 15 Jan 2022 22:12:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.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 22:12:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:12:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:12:05: 3000000 INFO @ Sat, 15 Jan 2022 22:12:14: 7000000 INFO @ Sat, 15 Jan 2022 22:12:15: 1000000 INFO @ Sat, 15 Jan 2022 22:12:16: 4000000 INFO @ Sat, 15 Jan 2022 22:12:26: 8000000 INFO @ Sat, 15 Jan 2022 22:12:27: 2000000 INFO @ Sat, 15 Jan 2022 22:12:28: 5000000 INFO @ Sat, 15 Jan 2022 22:12:29: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 22:12:29: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 22:12:29: #1 total tags in treatment: 2906630 INFO @ Sat, 15 Jan 2022 22:12:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:12:29: #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 22:12:29: #1 tags after filtering in treatment: 2027854 INFO @ Sat, 15 Jan 2022 22:12:29: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 22:12:29: #1 finished! INFO @ Sat, 15 Jan 2022 22:12:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:12:30: #2 number of paired peaks: 151 WARNING @ Sat, 15 Jan 2022 22:12:30: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Sat, 15 Jan 2022 22:12:30: start model_add_line... INFO @ Sat, 15 Jan 2022 22:12:30: start X-correlation... INFO @ Sat, 15 Jan 2022 22:12:30: end of X-cor INFO @ Sat, 15 Jan 2022 22:12:30: #2 finished! INFO @ Sat, 15 Jan 2022 22:12:30: #2 predicted fragment length is 283 bps INFO @ Sat, 15 Jan 2022 22:12:30: #2 alternative fragment length(s) may be 3,173,219,247,283,318,350 bps INFO @ Sat, 15 Jan 2022 22:12:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.05_model.r INFO @ Sat, 15 Jan 2022 22:12:30: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:12:30: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:12:38: 3000000 INFO @ Sat, 15 Jan 2022 22:12:39: 6000000 INFO @ Sat, 15 Jan 2022 22:12:41: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:12:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.05_peaks.xls INFO @ Sat, 15 Jan 2022 22:12:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:12:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.05_summits.bed INFO @ Sat, 15 Jan 2022 22:12:45: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (696 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 22:12:49: 7000000 INFO @ Sat, 15 Jan 2022 22:12:50: 4000000 INFO @ Sat, 15 Jan 2022 22:13:00: 8000000 INFO @ Sat, 15 Jan 2022 22:13:01: 5000000 INFO @ Sat, 15 Jan 2022 22:13:03: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 22:13:03: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 22:13:03: #1 total tags in treatment: 2906630 INFO @ Sat, 15 Jan 2022 22:13:03: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:13:03: #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 22:13:03: #1 tags after filtering in treatment: 2027854 INFO @ Sat, 15 Jan 2022 22:13:03: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 22:13:03: #1 finished! INFO @ Sat, 15 Jan 2022 22:13:03: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:13:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:13:03: #2 number of paired peaks: 151 WARNING @ Sat, 15 Jan 2022 22:13:03: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Sat, 15 Jan 2022 22:13:03: start model_add_line... INFO @ Sat, 15 Jan 2022 22:13:03: start X-correlation... INFO @ Sat, 15 Jan 2022 22:13:03: end of X-cor INFO @ Sat, 15 Jan 2022 22:13:03: #2 finished! INFO @ Sat, 15 Jan 2022 22:13:03: #2 predicted fragment length is 283 bps INFO @ Sat, 15 Jan 2022 22:13:03: #2 alternative fragment length(s) may be 3,173,219,247,283,318,350 bps INFO @ Sat, 15 Jan 2022 22:13:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.10_model.r INFO @ Sat, 15 Jan 2022 22:13:03: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:13:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:13:12: 6000000 INFO @ Sat, 15 Jan 2022 22:13:15: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:13:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.10_peaks.xls INFO @ Sat, 15 Jan 2022 22:13:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:13:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.10_summits.bed INFO @ Sat, 15 Jan 2022 22:13:17: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (530 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:13:23: 7000000 INFO @ Sat, 15 Jan 2022 22:13:34: 8000000 INFO @ Sat, 15 Jan 2022 22:13:37: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 22:13:37: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 22:13:37: #1 total tags in treatment: 2906630 INFO @ Sat, 15 Jan 2022 22:13:37: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:13:37: #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 22:13:37: #1 tags after filtering in treatment: 2027854 INFO @ Sat, 15 Jan 2022 22:13:37: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 22:13:37: #1 finished! INFO @ Sat, 15 Jan 2022 22:13:37: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:13:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:13:37: #2 number of paired peaks: 151 WARNING @ Sat, 15 Jan 2022 22:13:37: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Sat, 15 Jan 2022 22:13:37: start model_add_line... INFO @ Sat, 15 Jan 2022 22:13:37: start X-correlation... INFO @ Sat, 15 Jan 2022 22:13:37: end of X-cor INFO @ Sat, 15 Jan 2022 22:13:37: #2 finished! INFO @ Sat, 15 Jan 2022 22:13:37: #2 predicted fragment length is 283 bps INFO @ Sat, 15 Jan 2022 22:13:37: #2 alternative fragment length(s) may be 3,173,219,247,283,318,350 bps INFO @ Sat, 15 Jan 2022 22:13:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.20_model.r INFO @ Sat, 15 Jan 2022 22:13:37: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:13:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:13:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:13:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.20_peaks.xls INFO @ Sat, 15 Jan 2022 22:13:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:13:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10602365/SRX10602365.20_summits.bed INFO @ Sat, 15 Jan 2022 22:13:51: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (339 records, 4 fields): 14 millis CompletedMACS2peakCalling