Job ID = 14521216 SRX = SRX10468514 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4261579 spots for SRR14094825/SRR14094825.sra Written 4261579 spots for SRR14094825/SRR14094825.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: 00:03:43 4261579 reads; of these: 4261579 (100.00%) were paired; of these: 924609 (21.70%) aligned concordantly 0 times 2864906 (67.23%) aligned concordantly exactly 1 time 472064 (11.08%) aligned concordantly >1 times ---- 924609 pairs aligned concordantly 0 times; of these: 32258 (3.49%) aligned discordantly 1 time ---- 892351 pairs aligned 0 times concordantly or discordantly; of these: 1784702 mates make up the pairs; of these: 1710969 (95.87%) aligned 0 times 53247 (2.98%) aligned exactly 1 time 20486 (1.15%) aligned >1 times 79.93% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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] 225744 / 3352785 = 0.0673 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 20:44:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.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 20:44:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:44:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:44:11: 1000000 INFO @ Sat, 15 Jan 2022 20:44:15: 2000000 INFO @ Sat, 15 Jan 2022 20:44:19: 3000000 INFO @ Sat, 15 Jan 2022 20:44:24: 4000000 INFO @ Sat, 15 Jan 2022 20:44:28: 5000000 INFO @ Sat, 15 Jan 2022 20:44:32: 6000000 INFO @ Sat, 15 Jan 2022 20:44:34: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:44:34: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:44:34: #1 total tags in treatment: 3111724 INFO @ Sat, 15 Jan 2022 20:44:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:44:34: #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 20:44:34: #1 tags after filtering in treatment: 2279212 INFO @ Sat, 15 Jan 2022 20:44:34: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 20:44:34: #1 finished! INFO @ Sat, 15 Jan 2022 20:44:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:44:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:44:34: #2 number of paired peaks: 520 WARNING @ Sat, 15 Jan 2022 20:44:34: Fewer paired peaks (520) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 520 pairs to build model! INFO @ Sat, 15 Jan 2022 20:44:34: start model_add_line... INFO @ Sat, 15 Jan 2022 20:44:34: start X-correlation... INFO @ Sat, 15 Jan 2022 20:44:34: end of X-cor INFO @ Sat, 15 Jan 2022 20:44:34: #2 finished! INFO @ Sat, 15 Jan 2022 20:44:34: #2 predicted fragment length is 74 bps INFO @ Sat, 15 Jan 2022 20:44:34: #2 alternative fragment length(s) may be 3,74 bps INFO @ Sat, 15 Jan 2022 20:44:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.05_model.r 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 WARNING @ Sat, 15 Jan 2022 20:44:34: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:44:34: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Sat, 15 Jan 2022 20:44:34: #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 20:44:34: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:44:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:44:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.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 20:44:36: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:44:36: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:44:39: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:44:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:44:41: 1000000 INFO @ Sat, 15 Jan 2022 20:44:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:44:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.05_summits.bed INFO @ Sat, 15 Jan 2022 20:44:42: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1195 records, 4 fields): 179 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:44:47: 2000000 INFO @ Sat, 15 Jan 2022 20:44:52: 3000000 INFO @ Sat, 15 Jan 2022 20:44:58: 4000000 INFO @ Sat, 15 Jan 2022 20:45:03: 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 20:45:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.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 20:45:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:45:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:45:08: 6000000 INFO @ Sat, 15 Jan 2022 20:45:10: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:45:10: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:45:10: #1 total tags in treatment: 3111724 INFO @ Sat, 15 Jan 2022 20:45:10: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:45:10: #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 20:45:10: #1 tags after filtering in treatment: 2279212 INFO @ Sat, 15 Jan 2022 20:45:10: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 20:45:10: #1 finished! INFO @ Sat, 15 Jan 2022 20:45:10: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:45:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:45:11: #2 number of paired peaks: 520 WARNING @ Sat, 15 Jan 2022 20:45:11: Fewer paired peaks (520) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 520 pairs to build model! INFO @ Sat, 15 Jan 2022 20:45:11: start model_add_line... INFO @ Sat, 15 Jan 2022 20:45:11: start X-correlation... INFO @ Sat, 15 Jan 2022 20:45:11: end of X-cor INFO @ Sat, 15 Jan 2022 20:45:11: #2 finished! INFO @ Sat, 15 Jan 2022 20:45:11: #2 predicted fragment length is 74 bps INFO @ Sat, 15 Jan 2022 20:45:11: #2 alternative fragment length(s) may be 3,74 bps INFO @ Sat, 15 Jan 2022 20:45:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.10_model.r WARNING @ Sat, 15 Jan 2022 20:45:11: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:45:11: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Sat, 15 Jan 2022 20:45:11: #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 20:45:11: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:45:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:45:11: 1000000 INFO @ Sat, 15 Jan 2022 20:45:16: 2000000 INFO @ Sat, 15 Jan 2022 20:45:16: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:45:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:45:20: 3000000 INFO @ Sat, 15 Jan 2022 20:45:24: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:45:29: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:45:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:45:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.10_summits.bed INFO @ Sat, 15 Jan 2022 20:45:32: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (687 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:45:33: 6000000 INFO @ Sat, 15 Jan 2022 20:45:35: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:45:35: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:45:35: #1 total tags in treatment: 3111724 INFO @ Sat, 15 Jan 2022 20:45:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:45:35: #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 20:45:35: #1 tags after filtering in treatment: 2279212 INFO @ Sat, 15 Jan 2022 20:45:35: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 20:45:35: #1 finished! INFO @ Sat, 15 Jan 2022 20:45:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:45:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:45:35: #2 number of paired peaks: 520 WARNING @ Sat, 15 Jan 2022 20:45:35: Fewer paired peaks (520) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 520 pairs to build model! INFO @ Sat, 15 Jan 2022 20:45:35: start model_add_line... INFO @ Sat, 15 Jan 2022 20:45:35: start X-correlation... INFO @ Sat, 15 Jan 2022 20:45:35: end of X-cor INFO @ Sat, 15 Jan 2022 20:45:35: #2 finished! INFO @ Sat, 15 Jan 2022 20:45:35: #2 predicted fragment length is 74 bps INFO @ Sat, 15 Jan 2022 20:45:35: #2 alternative fragment length(s) may be 3,74 bps INFO @ Sat, 15 Jan 2022 20:45:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.20_model.r WARNING @ Sat, 15 Jan 2022 20:45:35: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:45:35: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Sat, 15 Jan 2022 20:45:35: #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 20:45:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:45:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:45:40: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:45:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:45:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:45:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468514/SRX10468514.20_summits.bed INFO @ Sat, 15 Jan 2022 20:45:42: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (388 records, 4 fields): 1 millis CompletedMACS2peakCalling