Job ID = 14521268 SRX = SRX8245397 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9238536 spots for SRR11684608/SRR11684608.sra Written 9238536 spots for SRR11684608/SRR11684608.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: 00:08:28 9238536 reads; of these: 9238536 (100.00%) were paired; of these: 5081275 (55.00%) aligned concordantly 0 times 3844596 (41.61%) aligned concordantly exactly 1 time 312665 (3.38%) aligned concordantly >1 times ---- 5081275 pairs aligned concordantly 0 times; of these: 24156 (0.48%) aligned discordantly 1 time ---- 5057119 pairs aligned 0 times concordantly or discordantly; of these: 10114238 mates make up the pairs; of these: 6161397 (60.92%) aligned 0 times 3547185 (35.07%) aligned exactly 1 time 405656 (4.01%) aligned >1 times 66.65% overall alignment rate Time searching: 00:08:28 Overall time: 00:08:28 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] 380222 / 4179079 = 0.0910 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 20:59:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.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 20:59:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:59:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:00:06: 1000000 INFO @ Sat, 15 Jan 2022 21:00:16: 2000000 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 21:00:25: 3000000 INFO @ Sat, 15 Jan 2022 21:00:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.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 21:00:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:00:26: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:00:34: 1000000 INFO @ Sat, 15 Jan 2022 21:00:35: 4000000 INFO @ Sat, 15 Jan 2022 21:00:41: 2000000 INFO @ Sat, 15 Jan 2022 21:00:46: 5000000 INFO @ Sat, 15 Jan 2022 21:00:48: 3000000 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 21:00:55: 4000000 INFO @ Sat, 15 Jan 2022 21:00:56: 6000000 INFO @ Sat, 15 Jan 2022 21:00:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.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 21:00:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:00:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:01:03: 5000000 INFO @ Sat, 15 Jan 2022 21:01:05: 1000000 INFO @ Sat, 15 Jan 2022 21:01:06: 7000000 INFO @ Sat, 15 Jan 2022 21:01:11: 6000000 INFO @ Sat, 15 Jan 2022 21:01:14: 2000000 INFO @ Sat, 15 Jan 2022 21:01:16: 8000000 INFO @ Sat, 15 Jan 2022 21:01:18: 7000000 INFO @ Sat, 15 Jan 2022 21:01:23: 3000000 INFO @ Sat, 15 Jan 2022 21:01:25: 8000000 INFO @ Sat, 15 Jan 2022 21:01:27: 9000000 INFO @ Sat, 15 Jan 2022 21:01:32: 4000000 INFO @ Sat, 15 Jan 2022 21:01:33: 9000000 INFO @ Sat, 15 Jan 2022 21:01:37: 10000000 INFO @ Sat, 15 Jan 2022 21:01:40: 10000000 INFO @ Sat, 15 Jan 2022 21:01:41: 5000000 INFO @ Sat, 15 Jan 2022 21:01:48: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:01:48: 11000000 INFO @ Sat, 15 Jan 2022 21:01:51: 6000000 INFO @ Sat, 15 Jan 2022 21:01:53: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:01:53: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:01:53: #1 total tags in treatment: 3781014 INFO @ Sat, 15 Jan 2022 21:01:53: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:01:53: #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 21:01:53: #1 tags after filtering in treatment: 1749739 INFO @ Sat, 15 Jan 2022 21:01:53: #1 Redundant rate of treatment: 0.54 INFO @ Sat, 15 Jan 2022 21:01:53: #1 finished! INFO @ Sat, 15 Jan 2022 21:01:53: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:01:53: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 21:01:53: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 21:01:53: start model_add_line... INFO @ Sat, 15 Jan 2022 21:01:53: start X-correlation... INFO @ Sat, 15 Jan 2022 21:01:53: end of X-cor INFO @ Sat, 15 Jan 2022 21:01:53: #2 finished! INFO @ Sat, 15 Jan 2022 21:01:53: #2 predicted fragment length is 46 bps INFO @ Sat, 15 Jan 2022 21:01:53: #2 alternative fragment length(s) may be 24,46,62,121,140,189,201,240,256,289,316,348,371,395,406,422,450,474,494,517,567 bps INFO @ Sat, 15 Jan 2022 21:01:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.10_model.r WARNING @ Sat, 15 Jan 2022 21:01:53: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:01:53: #2 You may need to consider one of the other alternative d(s): 24,46,62,121,140,189,201,240,256,289,316,348,371,395,406,422,450,474,494,517,567 WARNING @ Sat, 15 Jan 2022 21:01:53: #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 21:01:53: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:01:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:01:54: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:01:54: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:01:54: #1 total tags in treatment: 3781014 INFO @ Sat, 15 Jan 2022 21:01:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:01:54: #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 21:01:54: #1 tags after filtering in treatment: 1749739 INFO @ Sat, 15 Jan 2022 21:01:54: #1 Redundant rate of treatment: 0.54 INFO @ Sat, 15 Jan 2022 21:01:54: #1 finished! INFO @ Sat, 15 Jan 2022 21:01:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:01:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:01:54: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 21:01:54: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 21:01:54: start model_add_line... INFO @ Sat, 15 Jan 2022 21:01:54: start X-correlation... INFO @ Sat, 15 Jan 2022 21:01:54: end of X-cor INFO @ Sat, 15 Jan 2022 21:01:54: #2 finished! INFO @ Sat, 15 Jan 2022 21:01:54: #2 predicted fragment length is 46 bps INFO @ Sat, 15 Jan 2022 21:01:54: #2 alternative fragment length(s) may be 24,46,62,121,140,189,201,240,256,289,316,348,371,395,406,422,450,474,494,517,567 bps INFO @ Sat, 15 Jan 2022 21:01:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.05_model.r WARNING @ Sat, 15 Jan 2022 21:01:54: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:01:54: #2 You may need to consider one of the other alternative d(s): 24,46,62,121,140,189,201,240,256,289,316,348,371,395,406,422,450,474,494,517,567 WARNING @ Sat, 15 Jan 2022 21:01:54: #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 21:01:54: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:01:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:01:57: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:01:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:01:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:01:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:01:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.10_summits.bed INFO @ Sat, 15 Jan 2022 21:01:59: Done! pass1 - making usageList (5 chroms): 2 millis pass2 - checking and writing primary data (6 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:01:59: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:02:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:02:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:02:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.05_summits.bed INFO @ Sat, 15 Jan 2022 21:02:01: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (66 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:02:08: 8000000 INFO @ Sat, 15 Jan 2022 21:02:17: 9000000 INFO @ Sat, 15 Jan 2022 21:02:26: 10000000 INFO @ Sat, 15 Jan 2022 21:02:36: 11000000 INFO @ Sat, 15 Jan 2022 21:02:42: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:02:42: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:02:42: #1 total tags in treatment: 3781014 INFO @ Sat, 15 Jan 2022 21:02:42: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:02:42: #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 21:02:42: #1 tags after filtering in treatment: 1749739 INFO @ Sat, 15 Jan 2022 21:02:42: #1 Redundant rate of treatment: 0.54 INFO @ Sat, 15 Jan 2022 21:02:42: #1 finished! INFO @ Sat, 15 Jan 2022 21:02:42: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:02:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:02:42: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 21:02:42: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 21:02:42: start model_add_line... INFO @ Sat, 15 Jan 2022 21:02:42: start X-correlation... INFO @ Sat, 15 Jan 2022 21:02:42: end of X-cor INFO @ Sat, 15 Jan 2022 21:02:42: #2 finished! INFO @ Sat, 15 Jan 2022 21:02:42: #2 predicted fragment length is 46 bps INFO @ Sat, 15 Jan 2022 21:02:42: #2 alternative fragment length(s) may be 24,46,62,121,140,189,201,240,256,289,316,348,371,395,406,422,450,474,494,517,567 bps INFO @ Sat, 15 Jan 2022 21:02:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.20_model.r WARNING @ Sat, 15 Jan 2022 21:02:42: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:02:42: #2 You may need to consider one of the other alternative d(s): 24,46,62,121,140,189,201,240,256,289,316,348,371,395,406,422,450,474,494,517,567 WARNING @ Sat, 15 Jan 2022 21:02:42: #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 21:02:42: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:02:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:02:47: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:02:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:02:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:02:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245397/SRX8245397.20_summits.bed INFO @ Sat, 15 Jan 2022 21:02:49: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 5 millis CompletedMACS2peakCalling