Job ID = 14520763 SRX = SRX8245514 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8485943 spots for SRR11684725/SRR11684725.sra Written 8485943 spots for SRR11684725/SRR11684725.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: 00:03:14 8485943 reads; of these: 8485943 (100.00%) were paired; of these: 5783986 (68.16%) aligned concordantly 0 times 2431038 (28.65%) aligned concordantly exactly 1 time 270919 (3.19%) aligned concordantly >1 times ---- 5783986 pairs aligned concordantly 0 times; of these: 21452 (0.37%) aligned discordantly 1 time ---- 5762534 pairs aligned 0 times concordantly or discordantly; of these: 11525068 mates make up the pairs; of these: 8729695 (75.75%) aligned 0 times 2455917 (21.31%) aligned exactly 1 time 339456 (2.95%) aligned >1 times 48.56% overall alignment rate Time searching: 00:03:14 Overall time: 00:03:14 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_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] 272037 / 2722986 = 0.0999 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 19:56:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.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 19:56:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:56:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:56:07: 1000000 INFO @ Sat, 15 Jan 2022 19:56:13: 2000000 INFO @ Sat, 15 Jan 2022 19:56:19: 3000000 INFO @ Sat, 15 Jan 2022 19:56:24: 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 19:56:30: 5000000 INFO @ Sat, 15 Jan 2022 19:56:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.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 19:56:31: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:56:31: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:56:35: 6000000 INFO @ Sat, 15 Jan 2022 19:56:38: 1000000 INFO @ Sat, 15 Jan 2022 19:56:41: 7000000 INFO @ Sat, 15 Jan 2022 19:56:44: 2000000 INFO @ Sat, 15 Jan 2022 19:56:45: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:56:45: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:56:45: #1 total tags in treatment: 2430515 INFO @ Sat, 15 Jan 2022 19:56:45: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:56:45: #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 19:56:45: #1 tags after filtering in treatment: 1393095 INFO @ Sat, 15 Jan 2022 19:56:45: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 19:56:45: #1 finished! INFO @ Sat, 15 Jan 2022 19:56:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:56:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:56:45: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 19:56:45: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 19:56:45: start model_add_line... INFO @ Sat, 15 Jan 2022 19:56:45: start X-correlation... INFO @ Sat, 15 Jan 2022 19:56:45: end of X-cor INFO @ Sat, 15 Jan 2022 19:56:45: #2 finished! INFO @ Sat, 15 Jan 2022 19:56:45: #2 predicted fragment length is 43 bps INFO @ Sat, 15 Jan 2022 19:56:45: #2 alternative fragment length(s) may be 28,43,69,85,103,122,146,186,201,248,262,265,289,292,387,430,448,468,473,513,530,564,593 bps INFO @ Sat, 15 Jan 2022 19:56:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.05_model.r WARNING @ Sat, 15 Jan 2022 19:56:45: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:56:45: #2 You may need to consider one of the other alternative d(s): 28,43,69,85,103,122,146,186,201,248,262,265,289,292,387,430,448,468,473,513,530,564,593 WARNING @ Sat, 15 Jan 2022 19:56:45: #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 19:56:45: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:56:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:56:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:56:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:56:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:56:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.05_summits.bed INFO @ Sat, 15 Jan 2022 19:56:49: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (21 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:56:49: 3000000 INFO @ Sat, 15 Jan 2022 19:56:55: 4000000 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 19:57:01: 5000000 INFO @ Sat, 15 Jan 2022 19:57:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.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 19:57:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:57:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:57:07: 6000000 INFO @ Sat, 15 Jan 2022 19:57:07: 1000000 INFO @ Sat, 15 Jan 2022 19:57:13: 7000000 INFO @ Sat, 15 Jan 2022 19:57:14: 2000000 INFO @ Sat, 15 Jan 2022 19:57:17: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:57:17: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:57:17: #1 total tags in treatment: 2430515 INFO @ Sat, 15 Jan 2022 19:57:17: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:57:17: #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 19:57:17: #1 tags after filtering in treatment: 1393095 INFO @ Sat, 15 Jan 2022 19:57:17: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 19:57:17: #1 finished! INFO @ Sat, 15 Jan 2022 19:57:17: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:57:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:57:17: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 19:57:17: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 19:57:17: start model_add_line... INFO @ Sat, 15 Jan 2022 19:57:17: start X-correlation... INFO @ Sat, 15 Jan 2022 19:57:17: end of X-cor INFO @ Sat, 15 Jan 2022 19:57:17: #2 finished! INFO @ Sat, 15 Jan 2022 19:57:17: #2 predicted fragment length is 43 bps INFO @ Sat, 15 Jan 2022 19:57:17: #2 alternative fragment length(s) may be 28,43,69,85,103,122,146,186,201,248,262,265,289,292,387,430,448,468,473,513,530,564,593 bps INFO @ Sat, 15 Jan 2022 19:57:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.10_model.r WARNING @ Sat, 15 Jan 2022 19:57:17: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:57:17: #2 You may need to consider one of the other alternative d(s): 28,43,69,85,103,122,146,186,201,248,262,265,289,292,387,430,448,468,473,513,530,564,593 WARNING @ Sat, 15 Jan 2022 19:57:17: #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 19:57:17: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:57:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:57:20: 3000000 INFO @ Sat, 15 Jan 2022 19:57:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:57:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:57:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:57:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.10_summits.bed INFO @ Sat, 15 Jan 2022 19:57:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:57:26: 4000000 INFO @ Sat, 15 Jan 2022 19:57:32: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:57:38: 6000000 INFO @ Sat, 15 Jan 2022 19:57:44: 7000000 INFO @ Sat, 15 Jan 2022 19:57:48: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:57:48: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:57:48: #1 total tags in treatment: 2430515 INFO @ Sat, 15 Jan 2022 19:57:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:57:48: #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 19:57:48: #1 tags after filtering in treatment: 1393095 INFO @ Sat, 15 Jan 2022 19:57:48: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 19:57:48: #1 finished! INFO @ Sat, 15 Jan 2022 19:57:48: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:57:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:57:48: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 19:57:48: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 19:57:48: start model_add_line... INFO @ Sat, 15 Jan 2022 19:57:48: start X-correlation... INFO @ Sat, 15 Jan 2022 19:57:48: end of X-cor INFO @ Sat, 15 Jan 2022 19:57:48: #2 finished! INFO @ Sat, 15 Jan 2022 19:57:48: #2 predicted fragment length is 43 bps INFO @ Sat, 15 Jan 2022 19:57:48: #2 alternative fragment length(s) may be 28,43,69,85,103,122,146,186,201,248,262,265,289,292,387,430,448,468,473,513,530,564,593 bps INFO @ Sat, 15 Jan 2022 19:57:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.20_model.r WARNING @ Sat, 15 Jan 2022 19:57:48: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:57:48: #2 You may need to consider one of the other alternative d(s): 28,43,69,85,103,122,146,186,201,248,262,265,289,292,387,430,448,468,473,513,530,564,593 WARNING @ Sat, 15 Jan 2022 19:57:48: #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 19:57:48: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:57:51: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:57:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:57:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:57:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245514/SRX8245514.20_summits.bed INFO @ Sat, 15 Jan 2022 19:57:52: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 14 millis CompletedMACS2peakCalling