Job ID = 14520784 SRX = SRX8245402 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7860026 spots for SRR11684613/SRR11684613.sra Written 7860026 spots for SRR11684613/SRR11684613.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: 00:04:14 7860026 reads; of these: 7860026 (100.00%) were paired; of these: 4239496 (53.94%) aligned concordantly 0 times 3203954 (40.76%) aligned concordantly exactly 1 time 416576 (5.30%) aligned concordantly >1 times ---- 4239496 pairs aligned concordantly 0 times; of these: 11552 (0.27%) aligned discordantly 1 time ---- 4227944 pairs aligned 0 times concordantly or discordantly; of these: 8455888 mates make up the pairs; of these: 5072204 (59.98%) aligned 0 times 2954480 (34.94%) aligned exactly 1 time 429204 (5.08%) aligned >1 times 67.73% overall alignment rate Time searching: 00:04:14 Overall time: 00:04:14 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] 160978 / 3631495 = 0.0443 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 20:00:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.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 20:00:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:00:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:00:24: 1000000 INFO @ Sat, 15 Jan 2022 20:00:30: 2000000 INFO @ Sat, 15 Jan 2022 20:00:35: 3000000 INFO @ Sat, 15 Jan 2022 20:00:41: 4000000 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 20:00:47: 5000000 INFO @ Sat, 15 Jan 2022 20:00:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.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 20:00:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:00:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:00:53: 6000000 INFO @ Sat, 15 Jan 2022 20:00:54: 1000000 INFO @ Sat, 15 Jan 2022 20:00:59: 7000000 INFO @ Sat, 15 Jan 2022 20:01:00: 2000000 INFO @ Sat, 15 Jan 2022 20:01:05: 3000000 INFO @ Sat, 15 Jan 2022 20:01:05: 8000000 INFO @ Sat, 15 Jan 2022 20:01:10: 4000000 INFO @ Sat, 15 Jan 2022 20:01:12: 9000000 INFO @ Sat, 15 Jan 2022 20:01:15: 5000000 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 20:01:18: 10000000 INFO @ Sat, 15 Jan 2022 20:01:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.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 20:01:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:01:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:01:20: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:01:20: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:01:20: #1 total tags in treatment: 3459994 INFO @ Sat, 15 Jan 2022 20:01:20: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:01:20: #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 20:01:20: #1 tags after filtering in treatment: 2206891 INFO @ Sat, 15 Jan 2022 20:01:20: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Jan 2022 20:01:20: #1 finished! INFO @ Sat, 15 Jan 2022 20:01:20: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:01:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:01:20: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:01:20: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 20:01:20: start model_add_line... INFO @ Sat, 15 Jan 2022 20:01:20: start X-correlation... INFO @ Sat, 15 Jan 2022 20:01:20: end of X-cor INFO @ Sat, 15 Jan 2022 20:01:20: #2 finished! INFO @ Sat, 15 Jan 2022 20:01:20: #2 predicted fragment length is 61 bps INFO @ Sat, 15 Jan 2022 20:01:20: #2 alternative fragment length(s) may be 61,114,127,188,206,244,268,308,334,388,421,467,496,510,523,546,581 bps INFO @ Sat, 15 Jan 2022 20:01:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.05_model.r WARNING @ Sat, 15 Jan 2022 20:01:20: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:01:20: #2 You may need to consider one of the other alternative d(s): 61,114,127,188,206,244,268,308,334,388,421,467,496,510,523,546,581 WARNING @ Sat, 15 Jan 2022 20:01:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 20:01:20: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:01:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:01:21: 6000000 INFO @ Sat, 15 Jan 2022 20:01:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:01:24: 1000000 INFO @ Sat, 15 Jan 2022 20:01:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:01:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:01:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.05_summits.bed INFO @ Sat, 15 Jan 2022 20:01:26: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (170 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:01:26: 7000000 INFO @ Sat, 15 Jan 2022 20:01:29: 2000000 INFO @ Sat, 15 Jan 2022 20:01:31: 8000000 INFO @ Sat, 15 Jan 2022 20:01:34: 3000000 INFO @ Sat, 15 Jan 2022 20:01:37: 9000000 INFO @ Sat, 15 Jan 2022 20:01:40: 4000000 INFO @ Sat, 15 Jan 2022 20:01:42: 10000000 INFO @ Sat, 15 Jan 2022 20:01:44: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:01:44: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:01:44: #1 total tags in treatment: 3459994 INFO @ Sat, 15 Jan 2022 20:01:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:01:44: #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 20:01:44: #1 tags after filtering in treatment: 2206891 INFO @ Sat, 15 Jan 2022 20:01:44: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Jan 2022 20:01:44: #1 finished! INFO @ Sat, 15 Jan 2022 20:01:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:01:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:01:44: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:01:44: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 20:01:44: start model_add_line... INFO @ Sat, 15 Jan 2022 20:01:44: start X-correlation... INFO @ Sat, 15 Jan 2022 20:01:44: end of X-cor INFO @ Sat, 15 Jan 2022 20:01:44: #2 finished! INFO @ Sat, 15 Jan 2022 20:01:44: #2 predicted fragment length is 61 bps INFO @ Sat, 15 Jan 2022 20:01:44: #2 alternative fragment length(s) may be 61,114,127,188,206,244,268,308,334,388,421,467,496,510,523,546,581 bps INFO @ Sat, 15 Jan 2022 20:01:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.10_model.r WARNING @ Sat, 15 Jan 2022 20:01:44: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:01:44: #2 You may need to consider one of the other alternative d(s): 61,114,127,188,206,244,268,308,334,388,421,467,496,510,523,546,581 WARNING @ Sat, 15 Jan 2022 20:01:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 20:01:44: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:01:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:01:45: 5000000 INFO @ Sat, 15 Jan 2022 20:01:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:01:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:01:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:01:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.10_summits.bed INFO @ Sat, 15 Jan 2022 20:01:50: Done! INFO @ Sat, 15 Jan 2022 20:01:50: 6000000 pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (25 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:01:55: 7000000 INFO @ Sat, 15 Jan 2022 20:02:00: 8000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:02:05: 9000000 INFO @ Sat, 15 Jan 2022 20:02:10: 10000000 INFO @ Sat, 15 Jan 2022 20:02:11: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:02:11: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:02:11: #1 total tags in treatment: 3459994 INFO @ Sat, 15 Jan 2022 20:02:11: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:02:11: #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 20:02:11: #1 tags after filtering in treatment: 2206891 INFO @ Sat, 15 Jan 2022 20:02:11: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Jan 2022 20:02:11: #1 finished! INFO @ Sat, 15 Jan 2022 20:02:11: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:02:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:02:11: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:02:11: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 20:02:11: start model_add_line... INFO @ Sat, 15 Jan 2022 20:02:11: start X-correlation... INFO @ Sat, 15 Jan 2022 20:02:11: end of X-cor INFO @ Sat, 15 Jan 2022 20:02:11: #2 finished! INFO @ Sat, 15 Jan 2022 20:02:11: #2 predicted fragment length is 61 bps INFO @ Sat, 15 Jan 2022 20:02:11: #2 alternative fragment length(s) may be 61,114,127,188,206,244,268,308,334,388,421,467,496,510,523,546,581 bps INFO @ Sat, 15 Jan 2022 20:02:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.20_model.r WARNING @ Sat, 15 Jan 2022 20:02:11: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:02:11: #2 You may need to consider one of the other alternative d(s): 61,114,127,188,206,244,268,308,334,388,421,467,496,510,523,546,581 WARNING @ Sat, 15 Jan 2022 20:02:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 20:02:11: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:02:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:02:15: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:02:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:02:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:02:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245402/SRX8245402.20_summits.bed INFO @ Sat, 15 Jan 2022 20:02:17: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling