Job ID = 14521134 SRX = SRX8245360 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13714658 spots for SRR11684571/SRR11684571.sra Written 13714658 spots for SRR11684571/SRR11684571.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: 00:09:53 13714658 reads; of these: 13714658 (100.00%) were paired; of these: 6553328 (47.78%) aligned concordantly 0 times 6230663 (45.43%) aligned concordantly exactly 1 time 930667 (6.79%) aligned concordantly >1 times ---- 6553328 pairs aligned concordantly 0 times; of these: 168767 (2.58%) aligned discordantly 1 time ---- 6384561 pairs aligned 0 times concordantly or discordantly; of these: 12769122 mates make up the pairs; of these: 8179122 (64.05%) aligned 0 times 3882321 (30.40%) aligned exactly 1 time 707679 (5.54%) aligned >1 times 70.18% overall alignment rate Time searching: 00:09:53 Overall time: 00:09:53 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] 501486 / 7329158 = 0.0684 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 20:49:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.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 20:49:02: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:49:02: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:49:08: 1000000 INFO @ Sat, 15 Jan 2022 20:49:13: 2000000 INFO @ Sat, 15 Jan 2022 20:49:19: 3000000 INFO @ Sat, 15 Jan 2022 20:49:24: 4000000 INFO @ Sat, 15 Jan 2022 20:49:29: 5000000 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 20:49:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.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 20:49:32: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:49:32: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:49:34: 6000000 INFO @ Sat, 15 Jan 2022 20:49:38: 1000000 INFO @ Sat, 15 Jan 2022 20:49:39: 7000000 INFO @ Sat, 15 Jan 2022 20:49:44: 2000000 INFO @ Sat, 15 Jan 2022 20:49:45: 8000000 INFO @ Sat, 15 Jan 2022 20:49:49: 3000000 INFO @ Sat, 15 Jan 2022 20:49:50: 9000000 INFO @ Sat, 15 Jan 2022 20:49:55: 4000000 INFO @ Sat, 15 Jan 2022 20:49:56: 10000000 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 20:50:00: 5000000 INFO @ Sat, 15 Jan 2022 20:50:01: 11000000 INFO @ Sat, 15 Jan 2022 20:50:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.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 20:50:02: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:50:02: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:50:06: 6000000 INFO @ Sat, 15 Jan 2022 20:50:07: 12000000 INFO @ Sat, 15 Jan 2022 20:50:08: 1000000 INFO @ Sat, 15 Jan 2022 20:50:11: 7000000 INFO @ Sat, 15 Jan 2022 20:50:13: 13000000 INFO @ Sat, 15 Jan 2022 20:50:14: 2000000 INFO @ Sat, 15 Jan 2022 20:50:17: 8000000 INFO @ Sat, 15 Jan 2022 20:50:18: 14000000 INFO @ Sat, 15 Jan 2022 20:50:20: 3000000 INFO @ Sat, 15 Jan 2022 20:50:23: 9000000 INFO @ Sat, 15 Jan 2022 20:50:24: 15000000 INFO @ Sat, 15 Jan 2022 20:50:26: 4000000 INFO @ Sat, 15 Jan 2022 20:50:29: 10000000 INFO @ Sat, 15 Jan 2022 20:50:30: 16000000 INFO @ Sat, 15 Jan 2022 20:50:31: 5000000 INFO @ Sat, 15 Jan 2022 20:50:35: 11000000 INFO @ Sat, 15 Jan 2022 20:50:36: 17000000 INFO @ Sat, 15 Jan 2022 20:50:38: 6000000 INFO @ Sat, 15 Jan 2022 20:50:41: 12000000 INFO @ Sat, 15 Jan 2022 20:50:41: 18000000 INFO @ Sat, 15 Jan 2022 20:50:43: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:50:43: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:50:43: #1 total tags in treatment: 6664308 INFO @ Sat, 15 Jan 2022 20:50:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:50:43: #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 20:50:43: #1 tags after filtering in treatment: 4107519 INFO @ Sat, 15 Jan 2022 20:50:43: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Jan 2022 20:50:43: #1 finished! INFO @ Sat, 15 Jan 2022 20:50:43: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:50:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:50:43: #2 number of paired peaks: 161 WARNING @ Sat, 15 Jan 2022 20:50:43: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 15 Jan 2022 20:50:43: start model_add_line... INFO @ Sat, 15 Jan 2022 20:50:43: start X-correlation... INFO @ Sat, 15 Jan 2022 20:50:43: end of X-cor INFO @ Sat, 15 Jan 2022 20:50:43: #2 finished! INFO @ Sat, 15 Jan 2022 20:50:43: #2 predicted fragment length is 55 bps INFO @ Sat, 15 Jan 2022 20:50:43: #2 alternative fragment length(s) may be 55,67,98,122,140,198,215,229,236,261,319,331,358,426,446,460,491,513,539,562,579 bps INFO @ Sat, 15 Jan 2022 20:50:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.05_model.r WARNING @ Sat, 15 Jan 2022 20:50:43: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:50:43: #2 You may need to consider one of the other alternative d(s): 55,67,98,122,140,198,215,229,236,261,319,331,358,426,446,460,491,513,539,562,579 WARNING @ Sat, 15 Jan 2022 20:50:43: #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 20:50:43: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:50:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:50:44: 7000000 INFO @ Sat, 15 Jan 2022 20:50:46: 13000000 INFO @ Sat, 15 Jan 2022 20:50:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:50:49: 8000000 INFO @ Sat, 15 Jan 2022 20:50:51: 14000000 INFO @ Sat, 15 Jan 2022 20:50:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:50:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:50:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.05_summits.bed INFO @ Sat, 15 Jan 2022 20:50:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:50:54: 9000000 INFO @ Sat, 15 Jan 2022 20:50:56: 15000000 INFO @ Sat, 15 Jan 2022 20:51:00: 10000000 INFO @ Sat, 15 Jan 2022 20:51:02: 16000000 INFO @ Sat, 15 Jan 2022 20:51:05: 11000000 INFO @ Sat, 15 Jan 2022 20:51:07: 17000000 INFO @ Sat, 15 Jan 2022 20:51:10: 12000000 INFO @ Sat, 15 Jan 2022 20:51:12: 18000000 INFO @ Sat, 15 Jan 2022 20:51:14: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:51:14: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:51:14: #1 total tags in treatment: 6664308 INFO @ Sat, 15 Jan 2022 20:51:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:51:14: #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 20:51:14: #1 tags after filtering in treatment: 4107519 INFO @ Sat, 15 Jan 2022 20:51:14: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Jan 2022 20:51:14: #1 finished! INFO @ Sat, 15 Jan 2022 20:51:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:51:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:51:14: #2 number of paired peaks: 161 WARNING @ Sat, 15 Jan 2022 20:51:14: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 15 Jan 2022 20:51:14: start model_add_line... INFO @ Sat, 15 Jan 2022 20:51:14: start X-correlation... INFO @ Sat, 15 Jan 2022 20:51:14: end of X-cor INFO @ Sat, 15 Jan 2022 20:51:14: #2 finished! INFO @ Sat, 15 Jan 2022 20:51:14: #2 predicted fragment length is 55 bps INFO @ Sat, 15 Jan 2022 20:51:14: #2 alternative fragment length(s) may be 55,67,98,122,140,198,215,229,236,261,319,331,358,426,446,460,491,513,539,562,579 bps INFO @ Sat, 15 Jan 2022 20:51:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.10_model.r WARNING @ Sat, 15 Jan 2022 20:51:14: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:51:14: #2 You may need to consider one of the other alternative d(s): 55,67,98,122,140,198,215,229,236,261,319,331,358,426,446,460,491,513,539,562,579 WARNING @ Sat, 15 Jan 2022 20:51:14: #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 20:51:14: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:51:14: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:51:15: 13000000 INFO @ Sat, 15 Jan 2022 20:51:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:51:20: 14000000 INFO @ Sat, 15 Jan 2022 20:51:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:51:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:51:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.10_summits.bed INFO @ Sat, 15 Jan 2022 20:51:23: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (5 records, 4 fields): 54 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:51:25: 15000000 INFO @ Sat, 15 Jan 2022 20:51:30: 16000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:51:35: 17000000 INFO @ Sat, 15 Jan 2022 20:51:40: 18000000 INFO @ Sat, 15 Jan 2022 20:51:41: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:51:41: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:51:41: #1 total tags in treatment: 6664308 INFO @ Sat, 15 Jan 2022 20:51:41: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:51:41: #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 20:51:41: #1 tags after filtering in treatment: 4107519 INFO @ Sat, 15 Jan 2022 20:51:41: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Jan 2022 20:51:41: #1 finished! INFO @ Sat, 15 Jan 2022 20:51:41: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:51:41: #2 number of paired peaks: 161 WARNING @ Sat, 15 Jan 2022 20:51:41: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 15 Jan 2022 20:51:41: start model_add_line... INFO @ Sat, 15 Jan 2022 20:51:41: start X-correlation... INFO @ Sat, 15 Jan 2022 20:51:41: end of X-cor INFO @ Sat, 15 Jan 2022 20:51:41: #2 finished! INFO @ Sat, 15 Jan 2022 20:51:41: #2 predicted fragment length is 55 bps INFO @ Sat, 15 Jan 2022 20:51:41: #2 alternative fragment length(s) may be 55,67,98,122,140,198,215,229,236,261,319,331,358,426,446,460,491,513,539,562,579 bps INFO @ Sat, 15 Jan 2022 20:51:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.20_model.r WARNING @ Sat, 15 Jan 2022 20:51:41: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:51:41: #2 You may need to consider one of the other alternative d(s): 55,67,98,122,140,198,215,229,236,261,319,331,358,426,446,460,491,513,539,562,579 WARNING @ Sat, 15 Jan 2022 20:51:41: #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 20:51:41: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:51:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:51:47: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:51:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:51:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:51:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245360/SRX8245360.20_summits.bed INFO @ Sat, 15 Jan 2022 20:51:49: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling