Job ID = 14520783 SRX = SRX8245401 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8837587 spots for SRR11684612/SRR11684612.sra Written 8837587 spots for SRR11684612/SRR11684612.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: 00:06:02 8837587 reads; of these: 8837587 (100.00%) were paired; of these: 4784953 (54.14%) aligned concordantly 0 times 3638860 (41.17%) aligned concordantly exactly 1 time 413774 (4.68%) aligned concordantly >1 times ---- 4784953 pairs aligned concordantly 0 times; of these: 17942 (0.37%) aligned discordantly 1 time ---- 4767011 pairs aligned 0 times concordantly or discordantly; of these: 9534022 mates make up the pairs; of these: 6072042 (63.69%) aligned 0 times 3056817 (32.06%) aligned exactly 1 time 405163 (4.25%) aligned >1 times 65.65% overall alignment rate Time searching: 00:06:02 Overall time: 00:06:02 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] 200302 / 4069850 = 0.0492 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 20:04:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.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 20:04:02: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:04:02: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:04:08: 1000000 INFO @ Sat, 15 Jan 2022 20:04:14: 2000000 INFO @ Sat, 15 Jan 2022 20:04:20: 3000000 INFO @ Sat, 15 Jan 2022 20:04:25: 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 20:04:31: 5000000 INFO @ Sat, 15 Jan 2022 20:04:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.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 20:04:32: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:04:32: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:04:37: 6000000 INFO @ Sat, 15 Jan 2022 20:04:39: 1000000 INFO @ Sat, 15 Jan 2022 20:04:44: 7000000 INFO @ Sat, 15 Jan 2022 20:04:45: 2000000 INFO @ Sat, 15 Jan 2022 20:04:51: 8000000 INFO @ Sat, 15 Jan 2022 20:04:52: 3000000 INFO @ Sat, 15 Jan 2022 20:04:58: 9000000 INFO @ Sat, 15 Jan 2022 20:04:58: 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 20:05:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.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 20:05:02: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:05:02: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:05:05: 10000000 INFO @ Sat, 15 Jan 2022 20:05:05: 5000000 INFO @ Sat, 15 Jan 2022 20:05:09: 1000000 INFO @ Sat, 15 Jan 2022 20:05:13: 6000000 INFO @ Sat, 15 Jan 2022 20:05:13: 11000000 INFO @ Sat, 15 Jan 2022 20:05:14: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:05:14: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:05:14: #1 total tags in treatment: 3852960 INFO @ Sat, 15 Jan 2022 20:05:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:05:14: #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 20:05:14: #1 tags after filtering in treatment: 2374845 INFO @ Sat, 15 Jan 2022 20:05:14: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Jan 2022 20:05:14: #1 finished! INFO @ Sat, 15 Jan 2022 20:05:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:05:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:05:14: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 20:05:14: 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 20:05:14: start model_add_line... INFO @ Sat, 15 Jan 2022 20:05:14: start X-correlation... INFO @ Sat, 15 Jan 2022 20:05:14: end of X-cor INFO @ Sat, 15 Jan 2022 20:05:14: #2 finished! INFO @ Sat, 15 Jan 2022 20:05:14: #2 predicted fragment length is 48 bps INFO @ Sat, 15 Jan 2022 20:05:14: #2 alternative fragment length(s) may be 48,89,122,198,224,239,257,275,321,331,352,415,453,488,512,541,560,590 bps INFO @ Sat, 15 Jan 2022 20:05:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.05_model.r WARNING @ Sat, 15 Jan 2022 20:05:15: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:05:15: #2 You may need to consider one of the other alternative d(s): 48,89,122,198,224,239,257,275,321,331,352,415,453,488,512,541,560,590 WARNING @ Sat, 15 Jan 2022 20:05:15: #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 20:05:15: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:05:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:05:16: 2000000 INFO @ Sat, 15 Jan 2022 20:05:18: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:05:20: 7000000 INFO @ Sat, 15 Jan 2022 20:05:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:05:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:05:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.05_summits.bed INFO @ Sat, 15 Jan 2022 20:05:21: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (89 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:05:22: 3000000 INFO @ Sat, 15 Jan 2022 20:05:27: 8000000 INFO @ Sat, 15 Jan 2022 20:05:29: 4000000 INFO @ Sat, 15 Jan 2022 20:05:33: 9000000 INFO @ Sat, 15 Jan 2022 20:05:35: 5000000 INFO @ Sat, 15 Jan 2022 20:05:40: 10000000 INFO @ Sat, 15 Jan 2022 20:05:42: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:05:47: 11000000 INFO @ Sat, 15 Jan 2022 20:05:49: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:05:49: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:05:49: #1 total tags in treatment: 3852960 INFO @ Sat, 15 Jan 2022 20:05:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:05:49: #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 20:05:49: #1 tags after filtering in treatment: 2374845 INFO @ Sat, 15 Jan 2022 20:05:49: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Jan 2022 20:05:49: #1 finished! INFO @ Sat, 15 Jan 2022 20:05:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:05:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:05:49: 7000000 INFO @ Sat, 15 Jan 2022 20:05:49: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 20:05:49: 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 20:05:49: start model_add_line... INFO @ Sat, 15 Jan 2022 20:05:49: start X-correlation... INFO @ Sat, 15 Jan 2022 20:05:49: end of X-cor INFO @ Sat, 15 Jan 2022 20:05:49: #2 finished! INFO @ Sat, 15 Jan 2022 20:05:49: #2 predicted fragment length is 48 bps INFO @ Sat, 15 Jan 2022 20:05:49: #2 alternative fragment length(s) may be 48,89,122,198,224,239,257,275,321,331,352,415,453,488,512,541,560,590 bps INFO @ Sat, 15 Jan 2022 20:05:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.10_model.r WARNING @ Sat, 15 Jan 2022 20:05:49: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:05:49: #2 You may need to consider one of the other alternative d(s): 48,89,122,198,224,239,257,275,321,331,352,415,453,488,512,541,560,590 WARNING @ Sat, 15 Jan 2022 20:05:49: #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 20:05:49: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:05:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:05:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:05:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:05:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:05:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.10_summits.bed INFO @ Sat, 15 Jan 2022 20:05:54: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:05:55: 8000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:06:01: 9000000 INFO @ Sat, 15 Jan 2022 20:06:07: 10000000 INFO @ Sat, 15 Jan 2022 20:06:13: 11000000 INFO @ Sat, 15 Jan 2022 20:06:14: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:06:14: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:06:14: #1 total tags in treatment: 3852960 INFO @ Sat, 15 Jan 2022 20:06:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:06:14: #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 20:06:15: #1 tags after filtering in treatment: 2374845 INFO @ Sat, 15 Jan 2022 20:06:15: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Jan 2022 20:06:15: #1 finished! INFO @ Sat, 15 Jan 2022 20:06:15: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:06:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:06:15: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 20:06:15: 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 20:06:15: start model_add_line... INFO @ Sat, 15 Jan 2022 20:06:15: start X-correlation... INFO @ Sat, 15 Jan 2022 20:06:15: end of X-cor INFO @ Sat, 15 Jan 2022 20:06:15: #2 finished! INFO @ Sat, 15 Jan 2022 20:06:15: #2 predicted fragment length is 48 bps INFO @ Sat, 15 Jan 2022 20:06:15: #2 alternative fragment length(s) may be 48,89,122,198,224,239,257,275,321,331,352,415,453,488,512,541,560,590 bps INFO @ Sat, 15 Jan 2022 20:06:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.20_model.r WARNING @ Sat, 15 Jan 2022 20:06:15: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:06:15: #2 You may need to consider one of the other alternative d(s): 48,89,122,198,224,239,257,275,321,331,352,415,453,488,512,541,560,590 WARNING @ Sat, 15 Jan 2022 20:06:15: #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 20:06:15: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:06:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:06:18: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:06:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:06:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:06:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245401/SRX8245401.20_summits.bed INFO @ Sat, 15 Jan 2022 20:06:20: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (3 records, 4 fields): 5 millis CompletedMACS2peakCalling