Job ID = 14520762 SRX = SRX8245513 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12944714 spots for SRR11684724/SRR11684724.sra Written 12944714 spots for SRR11684724/SRR11684724.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: 00:08:18 12944714 reads; of these: 12944714 (100.00%) were paired; of these: 6823187 (52.71%) aligned concordantly 0 times 5255103 (40.60%) aligned concordantly exactly 1 time 866424 (6.69%) aligned concordantly >1 times ---- 6823187 pairs aligned concordantly 0 times; of these: 91241 (1.34%) aligned discordantly 1 time ---- 6731946 pairs aligned 0 times concordantly or discordantly; of these: 13463892 mates make up the pairs; of these: 7415310 (55.08%) aligned 0 times 5124076 (38.06%) aligned exactly 1 time 924506 (6.87%) aligned >1 times 71.36% overall alignment rate Time searching: 00:08:18 Overall time: 00:08:18 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] 167228 / 6211732 = 0.0269 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 20:07:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.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 20:07:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:07:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:07:12: 1000000 INFO @ Sat, 15 Jan 2022 20:07:18: 2000000 INFO @ Sat, 15 Jan 2022 20:07:24: 3000000 INFO @ Sat, 15 Jan 2022 20:07:30: 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 20:07:36: 5000000 INFO @ Sat, 15 Jan 2022 20:07:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.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 20:07:36: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:07:36: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:07:42: 1000000 INFO @ Sat, 15 Jan 2022 20:07:42: 6000000 INFO @ Sat, 15 Jan 2022 20:07:47: 2000000 INFO @ Sat, 15 Jan 2022 20:07:48: 7000000 INFO @ Sat, 15 Jan 2022 20:07:53: 3000000 INFO @ Sat, 15 Jan 2022 20:07:55: 8000000 INFO @ Sat, 15 Jan 2022 20:07:58: 4000000 INFO @ Sat, 15 Jan 2022 20:08:01: 9000000 INFO @ Sat, 15 Jan 2022 20:08:04: 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 20:08:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.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 20:08:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:08:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:08:08: 10000000 INFO @ Sat, 15 Jan 2022 20:08:09: 6000000 INFO @ Sat, 15 Jan 2022 20:08:13: 1000000 INFO @ Sat, 15 Jan 2022 20:08:14: 11000000 INFO @ Sat, 15 Jan 2022 20:08:14: 7000000 INFO @ Sat, 15 Jan 2022 20:08:19: 2000000 INFO @ Sat, 15 Jan 2022 20:08:19: 8000000 INFO @ Sat, 15 Jan 2022 20:08:20: 12000000 INFO @ Sat, 15 Jan 2022 20:08:25: 9000000 INFO @ Sat, 15 Jan 2022 20:08:26: 3000000 INFO @ Sat, 15 Jan 2022 20:08:27: 13000000 INFO @ Sat, 15 Jan 2022 20:08:30: 10000000 INFO @ Sat, 15 Jan 2022 20:08:32: 4000000 INFO @ Sat, 15 Jan 2022 20:08:33: 14000000 INFO @ Sat, 15 Jan 2022 20:08:36: 11000000 INFO @ Sat, 15 Jan 2022 20:08:38: 5000000 INFO @ Sat, 15 Jan 2022 20:08:40: 15000000 INFO @ Sat, 15 Jan 2022 20:08:41: 12000000 INFO @ Sat, 15 Jan 2022 20:08:44: 6000000 INFO @ Sat, 15 Jan 2022 20:08:46: 16000000 INFO @ Sat, 15 Jan 2022 20:08:47: 13000000 INFO @ Sat, 15 Jan 2022 20:08:50: 7000000 INFO @ Sat, 15 Jan 2022 20:08:52: 14000000 INFO @ Sat, 15 Jan 2022 20:08:53: 17000000 INFO @ Sat, 15 Jan 2022 20:08:56: 8000000 INFO @ Sat, 15 Jan 2022 20:08:58: 15000000 INFO @ Sat, 15 Jan 2022 20:08:59: 18000000 INFO @ Sat, 15 Jan 2022 20:09:00: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:09:00: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:09:00: #1 total tags in treatment: 5954714 INFO @ Sat, 15 Jan 2022 20:09:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:09:00: #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 20:09:00: #1 tags after filtering in treatment: 3882485 INFO @ Sat, 15 Jan 2022 20:09:00: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 20:09:00: #1 finished! INFO @ Sat, 15 Jan 2022 20:09:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:09:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:09:00: #2 number of paired peaks: 164 WARNING @ Sat, 15 Jan 2022 20:09:00: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Sat, 15 Jan 2022 20:09:00: start model_add_line... INFO @ Sat, 15 Jan 2022 20:09:00: start X-correlation... INFO @ Sat, 15 Jan 2022 20:09:00: end of X-cor INFO @ Sat, 15 Jan 2022 20:09:00: #2 finished! INFO @ Sat, 15 Jan 2022 20:09:00: #2 predicted fragment length is 53 bps INFO @ Sat, 15 Jan 2022 20:09:00: #2 alternative fragment length(s) may be 16,24,53,82,103,159,188,223,240,266,285,289,298,318,338,361,400,427,450,465,483,485,497,533,554,579 bps INFO @ Sat, 15 Jan 2022 20:09:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.05_model.r WARNING @ Sat, 15 Jan 2022 20:09:01: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:09:01: #2 You may need to consider one of the other alternative d(s): 16,24,53,82,103,159,188,223,240,266,285,289,298,318,338,361,400,427,450,465,483,485,497,533,554,579 WARNING @ Sat, 15 Jan 2022 20:09:01: #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 20:09:01: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:09:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:09:03: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:09:03: 16000000 INFO @ Sat, 15 Jan 2022 20:09:06: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:09:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:09:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:09:09: 17000000 INFO @ Sat, 15 Jan 2022 20:09:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.05_summits.bed INFO @ Sat, 15 Jan 2022 20:09:09: Done! INFO @ Sat, 15 Jan 2022 20:09:09: 10000000 pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (47 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:09:14: 18000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:09:15: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:09:15: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:09:15: #1 total tags in treatment: 5954714 INFO @ Sat, 15 Jan 2022 20:09:15: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:09:15: #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 20:09:15: #1 tags after filtering in treatment: 3882485 INFO @ Sat, 15 Jan 2022 20:09:15: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 20:09:15: #1 finished! INFO @ Sat, 15 Jan 2022 20:09:15: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:09:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:09:15: #2 number of paired peaks: 164 WARNING @ Sat, 15 Jan 2022 20:09:15: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Sat, 15 Jan 2022 20:09:15: start model_add_line... INFO @ Sat, 15 Jan 2022 20:09:15: start X-correlation... INFO @ Sat, 15 Jan 2022 20:09:15: end of X-cor INFO @ Sat, 15 Jan 2022 20:09:15: #2 finished! INFO @ Sat, 15 Jan 2022 20:09:15: #2 predicted fragment length is 53 bps INFO @ Sat, 15 Jan 2022 20:09:15: #2 alternative fragment length(s) may be 16,24,53,82,103,159,188,223,240,266,285,289,298,318,338,361,400,427,450,465,483,485,497,533,554,579 bps INFO @ Sat, 15 Jan 2022 20:09:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.10_model.r INFO @ Sat, 15 Jan 2022 20:09:16: 11000000 WARNING @ Sat, 15 Jan 2022 20:09:16: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:09:16: #2 You may need to consider one of the other alternative d(s): 16,24,53,82,103,159,188,223,240,266,285,289,298,318,338,361,400,427,450,465,483,485,497,533,554,579 WARNING @ Sat, 15 Jan 2022 20:09:16: #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 20:09:16: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:09:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:09:21: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:09:22: 12000000 INFO @ Sat, 15 Jan 2022 20:09:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:09:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:09:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.10_summits.bed INFO @ Sat, 15 Jan 2022 20:09:24: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:09:27: 13000000 INFO @ Sat, 15 Jan 2022 20:09:33: 14000000 INFO @ Sat, 15 Jan 2022 20:09:39: 15000000 INFO @ Sat, 15 Jan 2022 20:09:45: 16000000 INFO @ Sat, 15 Jan 2022 20:09:51: 17000000 INFO @ Sat, 15 Jan 2022 20:09:57: 18000000 INFO @ Sat, 15 Jan 2022 20:09:58: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:09:58: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:09:58: #1 total tags in treatment: 5954714 INFO @ Sat, 15 Jan 2022 20:09:58: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:09:58: #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 20:09:58: #1 tags after filtering in treatment: 3882485 INFO @ Sat, 15 Jan 2022 20:09:58: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 20:09:58: #1 finished! INFO @ Sat, 15 Jan 2022 20:09:58: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:09:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:09:58: #2 number of paired peaks: 164 WARNING @ Sat, 15 Jan 2022 20:09:58: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Sat, 15 Jan 2022 20:09:58: start model_add_line... INFO @ Sat, 15 Jan 2022 20:09:58: start X-correlation... INFO @ Sat, 15 Jan 2022 20:09:58: end of X-cor INFO @ Sat, 15 Jan 2022 20:09:58: #2 finished! INFO @ Sat, 15 Jan 2022 20:09:58: #2 predicted fragment length is 53 bps INFO @ Sat, 15 Jan 2022 20:09:58: #2 alternative fragment length(s) may be 16,24,53,82,103,159,188,223,240,266,285,289,298,318,338,361,400,427,450,465,483,485,497,533,554,579 bps INFO @ Sat, 15 Jan 2022 20:09:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.20_model.r WARNING @ Sat, 15 Jan 2022 20:09:58: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:09:58: #2 You may need to consider one of the other alternative d(s): 16,24,53,82,103,159,188,223,240,266,285,289,298,318,338,361,400,427,450,465,483,485,497,533,554,579 WARNING @ Sat, 15 Jan 2022 20:09:58: #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 20:09:58: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:09:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:10:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:10:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:10:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:10:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245513/SRX8245513.20_summits.bed INFO @ Sat, 15 Jan 2022 20:10:06: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling