Job ID = 14520964 SRX = SRX8245450 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15488816 spots for SRR11684661/SRR11684661.sra Written 15488816 spots for SRR11684661/SRR11684661.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: 00:30:45 15488816 reads; of these: 15488816 (100.00%) were paired; of these: 7065204 (45.61%) aligned concordantly 0 times 6048811 (39.05%) aligned concordantly exactly 1 time 2374801 (15.33%) aligned concordantly >1 times ---- 7065204 pairs aligned concordantly 0 times; of these: 94583 (1.34%) aligned discordantly 1 time ---- 6970621 pairs aligned 0 times concordantly or discordantly; of these: 13941242 mates make up the pairs; of these: 8516891 (61.09%) aligned 0 times 3836470 (27.52%) aligned exactly 1 time 1587881 (11.39%) aligned >1 times 72.51% overall alignment rate Time searching: 00:30:45 Overall time: 00:30:45 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 12 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] 568962 / 8512020 = 0.0668 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 20:56:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.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 20:56:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:56:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:56:13: 1000000 INFO @ Sat, 15 Jan 2022 20:56:21: 2000000 INFO @ Sat, 15 Jan 2022 20:56:29: 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 20:56:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.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 20:56:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:56:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:56:37: 4000000 INFO @ Sat, 15 Jan 2022 20:56:44: 1000000 INFO @ Sat, 15 Jan 2022 20:56:46: 5000000 INFO @ Sat, 15 Jan 2022 20:56:53: 2000000 INFO @ Sat, 15 Jan 2022 20:56:54: 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 20:57:03: 3000000 INFO @ Sat, 15 Jan 2022 20:57:03: 7000000 INFO @ Sat, 15 Jan 2022 20:57:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.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 20:57:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:57:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:57:12: 8000000 INFO @ Sat, 15 Jan 2022 20:57:13: 4000000 INFO @ Sat, 15 Jan 2022 20:57:15: 1000000 INFO @ Sat, 15 Jan 2022 20:57:21: 9000000 INFO @ Sat, 15 Jan 2022 20:57:23: 5000000 INFO @ Sat, 15 Jan 2022 20:57:24: 2000000 INFO @ Sat, 15 Jan 2022 20:57:30: 10000000 INFO @ Sat, 15 Jan 2022 20:57:33: 6000000 INFO @ Sat, 15 Jan 2022 20:57:33: 3000000 INFO @ Sat, 15 Jan 2022 20:57:39: 11000000 INFO @ Sat, 15 Jan 2022 20:57:42: 4000000 INFO @ Sat, 15 Jan 2022 20:57:43: 7000000 INFO @ Sat, 15 Jan 2022 20:57:48: 12000000 INFO @ Sat, 15 Jan 2022 20:57:51: 5000000 INFO @ Sat, 15 Jan 2022 20:57:53: 8000000 INFO @ Sat, 15 Jan 2022 20:57:57: 13000000 INFO @ Sat, 15 Jan 2022 20:57:59: 6000000 INFO @ Sat, 15 Jan 2022 20:58:02: 9000000 INFO @ Sat, 15 Jan 2022 20:58:05: 14000000 INFO @ Sat, 15 Jan 2022 20:58:07: 7000000 INFO @ Sat, 15 Jan 2022 20:58:11: 10000000 INFO @ Sat, 15 Jan 2022 20:58:14: 15000000 INFO @ Sat, 15 Jan 2022 20:58:15: 8000000 INFO @ Sat, 15 Jan 2022 20:58:20: 11000000 INFO @ Sat, 15 Jan 2022 20:58:22: 16000000 INFO @ Sat, 15 Jan 2022 20:58:24: 9000000 INFO @ Sat, 15 Jan 2022 20:58:29: 12000000 INFO @ Sat, 15 Jan 2022 20:58:30: 17000000 INFO @ Sat, 15 Jan 2022 20:58:33: 10000000 INFO @ Sat, 15 Jan 2022 20:58:38: 13000000 INFO @ Sat, 15 Jan 2022 20:58:38: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:58:41: 11000000 INFO @ Sat, 15 Jan 2022 20:58:47: 14000000 INFO @ Sat, 15 Jan 2022 20:58:47: 19000000 INFO @ Sat, 15 Jan 2022 20:58:50: 12000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:58:55: 20000000 INFO @ Sat, 15 Jan 2022 20:58:56: 15000000 INFO @ Sat, 15 Jan 2022 20:58:59: 13000000 INFO @ Sat, 15 Jan 2022 20:59:04: 21000000 INFO @ Sat, 15 Jan 2022 20:59:05: 16000000 INFO @ Sat, 15 Jan 2022 20:59:07: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:59:07: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:59:07: #1 total tags in treatment: 7856079 INFO @ Sat, 15 Jan 2022 20:59:07: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:59:07: #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 20:59:07: 14000000 INFO @ Sat, 15 Jan 2022 20:59:07: #1 tags after filtering in treatment: 2602419 INFO @ Sat, 15 Jan 2022 20:59:07: #1 Redundant rate of treatment: 0.67 INFO @ Sat, 15 Jan 2022 20:59:07: #1 finished! INFO @ Sat, 15 Jan 2022 20:59:07: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:59:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:59:08: #2 number of paired peaks: 139 WARNING @ Sat, 15 Jan 2022 20:59:08: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 15 Jan 2022 20:59:08: start model_add_line... INFO @ Sat, 15 Jan 2022 20:59:08: start X-correlation... INFO @ Sat, 15 Jan 2022 20:59:08: end of X-cor INFO @ Sat, 15 Jan 2022 20:59:08: #2 finished! INFO @ Sat, 15 Jan 2022 20:59:08: #2 predicted fragment length is 290 bps INFO @ Sat, 15 Jan 2022 20:59:08: #2 alternative fragment length(s) may be 2,224,245,273,290,324 bps INFO @ Sat, 15 Jan 2022 20:59:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.05_model.r INFO @ Sat, 15 Jan 2022 20:59:08: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:59:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:59:13: 17000000 INFO @ Sat, 15 Jan 2022 20:59:15: 15000000 INFO @ Sat, 15 Jan 2022 20:59:22: 18000000 INFO @ Sat, 15 Jan 2022 20:59:23: 16000000 INFO @ Sat, 15 Jan 2022 20:59:25: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:59:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:59:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:59:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.05_summits.bed INFO @ Sat, 15 Jan 2022 20:59:28: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (188 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:59:31: 17000000 INFO @ Sat, 15 Jan 2022 20:59:31: 19000000 INFO @ Sat, 15 Jan 2022 20:59:39: 18000000 INFO @ Sat, 15 Jan 2022 20:59:40: 20000000 INFO @ Sat, 15 Jan 2022 20:59:46: 19000000 INFO @ Sat, 15 Jan 2022 20:59:49: 21000000 INFO @ Sat, 15 Jan 2022 20:59:52: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:59:52: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:59:52: #1 total tags in treatment: 7856079 INFO @ Sat, 15 Jan 2022 20:59:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:59:52: #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 20:59:52: #1 tags after filtering in treatment: 2602419 INFO @ Sat, 15 Jan 2022 20:59:52: #1 Redundant rate of treatment: 0.67 INFO @ Sat, 15 Jan 2022 20:59:52: #1 finished! INFO @ Sat, 15 Jan 2022 20:59:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:59:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:59:52: #2 number of paired peaks: 139 WARNING @ Sat, 15 Jan 2022 20:59:52: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 15 Jan 2022 20:59:52: start model_add_line... INFO @ Sat, 15 Jan 2022 20:59:52: start X-correlation... INFO @ Sat, 15 Jan 2022 20:59:52: end of X-cor INFO @ Sat, 15 Jan 2022 20:59:52: #2 finished! INFO @ Sat, 15 Jan 2022 20:59:52: #2 predicted fragment length is 290 bps INFO @ Sat, 15 Jan 2022 20:59:52: #2 alternative fragment length(s) may be 2,224,245,273,290,324 bps INFO @ Sat, 15 Jan 2022 20:59:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.10_model.r INFO @ Sat, 15 Jan 2022 20:59:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:59:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:59:55: 20000000 INFO @ Sat, 15 Jan 2022 21:00:03: 21000000 INFO @ Sat, 15 Jan 2022 21:00:06: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:00:06: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:00:06: #1 total tags in treatment: 7856079 INFO @ Sat, 15 Jan 2022 21:00:06: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:00:06: #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 21:00:06: #1 tags after filtering in treatment: 2602419 INFO @ Sat, 15 Jan 2022 21:00:06: #1 Redundant rate of treatment: 0.67 INFO @ Sat, 15 Jan 2022 21:00:06: #1 finished! INFO @ Sat, 15 Jan 2022 21:00:06: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:00:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:00:06: #2 number of paired peaks: 139 WARNING @ Sat, 15 Jan 2022 21:00:06: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 15 Jan 2022 21:00:06: start model_add_line... INFO @ Sat, 15 Jan 2022 21:00:06: start X-correlation... INFO @ Sat, 15 Jan 2022 21:00:06: end of X-cor INFO @ Sat, 15 Jan 2022 21:00:06: #2 finished! INFO @ Sat, 15 Jan 2022 21:00:06: #2 predicted fragment length is 290 bps INFO @ Sat, 15 Jan 2022 21:00:06: #2 alternative fragment length(s) may be 2,224,245,273,290,324 bps INFO @ Sat, 15 Jan 2022 21:00:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.20_model.r INFO @ Sat, 15 Jan 2022 21:00:06: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:00:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:00:09: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:00:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:00:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:00:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.10_summits.bed INFO @ Sat, 15 Jan 2022 21:00:12: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (157 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:00:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:00:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:00:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:00:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245450/SRX8245450.20_summits.bed INFO @ Sat, 15 Jan 2022 21:00:27: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (101 records, 4 fields): 3 millis CompletedMACS2peakCalling