Job ID = 14521140 SRX = SRX8245366 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18609141 spots for SRR11684577/SRR11684577.sra Written 18609141 spots for SRR11684577/SRR11684577.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: 00:09:42 18609141 reads; of these: 18609141 (100.00%) were paired; of these: 9741114 (52.35%) aligned concordantly 0 times 7833183 (42.09%) aligned concordantly exactly 1 time 1034844 (5.56%) aligned concordantly >1 times ---- 9741114 pairs aligned concordantly 0 times; of these: 173673 (1.78%) aligned discordantly 1 time ---- 9567441 pairs aligned 0 times concordantly or discordantly; of these: 19134882 mates make up the pairs; of these: 13162176 (68.79%) aligned 0 times 5129890 (26.81%) aligned exactly 1 time 842816 (4.40%) aligned >1 times 64.64% overall alignment rate Time searching: 00:09:42 Overall time: 00:09:42 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 12 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] 1267408 / 9040552 = 0.1402 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 20:49:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.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 20:49:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:49:11: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:49:16: 1000000 INFO @ Sat, 15 Jan 2022 20:49:21: 2000000 INFO @ Sat, 15 Jan 2022 20:49:26: 3000000 INFO @ Sat, 15 Jan 2022 20:49:31: 4000000 INFO @ Sat, 15 Jan 2022 20:49:36: 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 20:49:41: 6000000 INFO @ Sat, 15 Jan 2022 20:49:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.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 20:49:41: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:49:41: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:49:46: 7000000 INFO @ Sat, 15 Jan 2022 20:49:47: 1000000 INFO @ Sat, 15 Jan 2022 20:49:51: 8000000 INFO @ Sat, 15 Jan 2022 20:49:53: 2000000 INFO @ Sat, 15 Jan 2022 20:49:57: 9000000 INFO @ Sat, 15 Jan 2022 20:49:58: 3000000 INFO @ Sat, 15 Jan 2022 20:50:02: 10000000 INFO @ Sat, 15 Jan 2022 20:50:04: 4000000 INFO @ Sat, 15 Jan 2022 20:50:08: 11000000 INFO @ Sat, 15 Jan 2022 20:50:09: 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 20:50:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.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 20:50:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:50:11: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:50:13: 12000000 INFO @ Sat, 15 Jan 2022 20:50:15: 6000000 INFO @ Sat, 15 Jan 2022 20:50:17: 1000000 INFO @ Sat, 15 Jan 2022 20:50:19: 13000000 INFO @ Sat, 15 Jan 2022 20:50:20: 7000000 INFO @ Sat, 15 Jan 2022 20:50:23: 2000000 INFO @ Sat, 15 Jan 2022 20:50:25: 14000000 INFO @ Sat, 15 Jan 2022 20:50:25: 8000000 INFO @ Sat, 15 Jan 2022 20:50:28: 3000000 INFO @ Sat, 15 Jan 2022 20:50:31: 15000000 INFO @ Sat, 15 Jan 2022 20:50:31: 9000000 INFO @ Sat, 15 Jan 2022 20:50:34: 4000000 INFO @ Sat, 15 Jan 2022 20:50:36: 10000000 INFO @ Sat, 15 Jan 2022 20:50:36: 16000000 INFO @ Sat, 15 Jan 2022 20:50:40: 5000000 INFO @ Sat, 15 Jan 2022 20:50:42: 11000000 INFO @ Sat, 15 Jan 2022 20:50:42: 17000000 INFO @ Sat, 15 Jan 2022 20:50:45: 6000000 INFO @ Sat, 15 Jan 2022 20:50:47: 12000000 INFO @ Sat, 15 Jan 2022 20:50:48: 18000000 INFO @ Sat, 15 Jan 2022 20:50:50: 7000000 INFO @ Sat, 15 Jan 2022 20:50:53: 13000000 INFO @ Sat, 15 Jan 2022 20:50:53: 19000000 INFO @ Sat, 15 Jan 2022 20:50:56: 8000000 INFO @ Sat, 15 Jan 2022 20:50:59: 14000000 INFO @ Sat, 15 Jan 2022 20:50:59: 20000000 INFO @ Sat, 15 Jan 2022 20:51:02: 9000000 INFO @ Sat, 15 Jan 2022 20:51:05: 15000000 INFO @ Sat, 15 Jan 2022 20:51:05: 21000000 INFO @ Sat, 15 Jan 2022 20:51:08: 10000000 INFO @ Sat, 15 Jan 2022 20:51:08: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:51:08: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:51:08: #1 total tags in treatment: 7609752 INFO @ Sat, 15 Jan 2022 20:51:08: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:51:08: #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 20:51:08: #1 tags after filtering in treatment: 4329514 INFO @ Sat, 15 Jan 2022 20:51:08: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 20:51:08: #1 finished! INFO @ Sat, 15 Jan 2022 20:51:08: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:51:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:51:09: #2 number of paired peaks: 157 WARNING @ Sat, 15 Jan 2022 20:51:09: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Sat, 15 Jan 2022 20:51:09: start model_add_line... INFO @ Sat, 15 Jan 2022 20:51:09: start X-correlation... INFO @ Sat, 15 Jan 2022 20:51:09: end of X-cor INFO @ Sat, 15 Jan 2022 20:51:09: #2 finished! INFO @ Sat, 15 Jan 2022 20:51:09: #2 predicted fragment length is 55 bps INFO @ Sat, 15 Jan 2022 20:51:09: #2 alternative fragment length(s) may be 55,130,165,204,251,273,308,330,361,422,442,499,533,572,588 bps INFO @ Sat, 15 Jan 2022 20:51:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.05_model.r WARNING @ Sat, 15 Jan 2022 20:51:09: #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 20:51:09: #2 You may need to consider one of the other alternative d(s): 55,130,165,204,251,273,308,330,361,422,442,499,533,572,588 WARNING @ Sat, 15 Jan 2022 20:51:09: #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 20:51:09: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:51:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:51:11: 16000000 INFO @ Sat, 15 Jan 2022 20:51:13: 11000000 INFO @ Sat, 15 Jan 2022 20:51:15: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:51:16: 17000000 INFO @ Sat, 15 Jan 2022 20:51:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:51:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:51:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.05_summits.bed INFO @ Sat, 15 Jan 2022 20:51:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (36 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:51:19: 12000000 INFO @ Sat, 15 Jan 2022 20:51:22: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:51:25: 13000000 INFO @ Sat, 15 Jan 2022 20:51:28: 19000000 INFO @ Sat, 15 Jan 2022 20:51:31: 14000000 INFO @ Sat, 15 Jan 2022 20:51:33: 20000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:51:36: 15000000 INFO @ Sat, 15 Jan 2022 20:51:39: 21000000 INFO @ Sat, 15 Jan 2022 20:51:42: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:51:42: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:51:42: #1 total tags in treatment: 7609752 INFO @ Sat, 15 Jan 2022 20:51:42: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:51:42: #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 20:51:42: 16000000 INFO @ Sat, 15 Jan 2022 20:51:42: #1 tags after filtering in treatment: 4329514 INFO @ Sat, 15 Jan 2022 20:51:42: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 20:51:42: #1 finished! INFO @ Sat, 15 Jan 2022 20:51:42: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:51:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:51:42: #2 number of paired peaks: 157 WARNING @ Sat, 15 Jan 2022 20:51:42: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Sat, 15 Jan 2022 20:51:42: start model_add_line... INFO @ Sat, 15 Jan 2022 20:51:42: start X-correlation... INFO @ Sat, 15 Jan 2022 20:51:42: end of X-cor INFO @ Sat, 15 Jan 2022 20:51:42: #2 finished! INFO @ Sat, 15 Jan 2022 20:51:42: #2 predicted fragment length is 55 bps INFO @ Sat, 15 Jan 2022 20:51:42: #2 alternative fragment length(s) may be 55,130,165,204,251,273,308,330,361,422,442,499,533,572,588 bps INFO @ Sat, 15 Jan 2022 20:51:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.10_model.r WARNING @ Sat, 15 Jan 2022 20:51:42: #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 20:51:42: #2 You may need to consider one of the other alternative d(s): 55,130,165,204,251,273,308,330,361,422,442,499,533,572,588 WARNING @ Sat, 15 Jan 2022 20:51:42: #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 20:51:42: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:51:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:51:47: 17000000 INFO @ Sat, 15 Jan 2022 20:51:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:51:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:51:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:51:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.10_summits.bed INFO @ Sat, 15 Jan 2022 20:51:50: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (4 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:51:52: 18000000 INFO @ Sat, 15 Jan 2022 20:51:57: 19000000 INFO @ Sat, 15 Jan 2022 20:52:02: 20000000 INFO @ Sat, 15 Jan 2022 20:52:07: 21000000 INFO @ Sat, 15 Jan 2022 20:52:10: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:52:10: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:52:10: #1 total tags in treatment: 7609752 INFO @ Sat, 15 Jan 2022 20:52:10: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:52:10: #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 20:52:10: #1 tags after filtering in treatment: 4329514 INFO @ Sat, 15 Jan 2022 20:52:10: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 20:52:10: #1 finished! INFO @ Sat, 15 Jan 2022 20:52:10: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:52:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:52:10: #2 number of paired peaks: 157 WARNING @ Sat, 15 Jan 2022 20:52:10: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Sat, 15 Jan 2022 20:52:10: start model_add_line... INFO @ Sat, 15 Jan 2022 20:52:10: start X-correlation... INFO @ Sat, 15 Jan 2022 20:52:10: end of X-cor INFO @ Sat, 15 Jan 2022 20:52:10: #2 finished! INFO @ Sat, 15 Jan 2022 20:52:10: #2 predicted fragment length is 55 bps INFO @ Sat, 15 Jan 2022 20:52:10: #2 alternative fragment length(s) may be 55,130,165,204,251,273,308,330,361,422,442,499,533,572,588 bps INFO @ Sat, 15 Jan 2022 20:52:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.20_model.r WARNING @ Sat, 15 Jan 2022 20:52:10: #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 20:52:10: #2 You may need to consider one of the other alternative d(s): 55,130,165,204,251,273,308,330,361,422,442,499,533,572,588 WARNING @ Sat, 15 Jan 2022 20:52:10: #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 20:52:10: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:52:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:52:16: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:52:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:52:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:52:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245366/SRX8245366.20_summits.bed INFO @ Sat, 15 Jan 2022 20:52:18: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling