Job ID = 14520431 SRX = SRX11781026 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:05:21 prefetch.2.10.7: 1) Downloading 'SRR15480969'... 2022-01-15T10:05:21 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:05:43 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:05:43 prefetch.2.10.7: 'SRR15480969' is valid 2022-01-15T10:05:43 prefetch.2.10.7: 1) 'SRR15480969' was downloaded successfully 2022-01-15T10:05:43 prefetch.2.10.7: 'SRR15480969' has 0 unresolved dependencies Read 6277372 spots for SRR15480969/SRR15480969.sra Written 6277372 spots for SRR15480969/SRR15480969.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: 00:04:30 6277372 reads; of these: 6277372 (100.00%) were paired; of these: 1209361 (19.27%) aligned concordantly 0 times 2780792 (44.30%) aligned concordantly exactly 1 time 2287219 (36.44%) aligned concordantly >1 times ---- 1209361 pairs aligned concordantly 0 times; of these: 127538 (10.55%) aligned discordantly 1 time ---- 1081823 pairs aligned 0 times concordantly or discordantly; of these: 2163646 mates make up the pairs; of these: 1639211 (75.76%) aligned 0 times 196918 (9.10%) aligned exactly 1 time 327517 (15.14%) aligned >1 times 86.94% overall alignment rate Time searching: 00:04:30 Overall time: 00:04:30 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] 981021 / 5151655 = 0.1904 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 19:13:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.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 19:13:46: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:13:46: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:13:51: 1000000 INFO @ Sat, 15 Jan 2022 19:13:55: 2000000 INFO @ Sat, 15 Jan 2022 19:13:59: 3000000 INFO @ Sat, 15 Jan 2022 19:14:04: 4000000 INFO @ Sat, 15 Jan 2022 19:14:08: 5000000 INFO @ Sat, 15 Jan 2022 19:14:13: 6000000 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 19:14:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.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 19:14:16: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:14:16: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:14:17: 7000000 INFO @ Sat, 15 Jan 2022 19:14:21: 1000000 INFO @ Sat, 15 Jan 2022 19:14:22: 8000000 INFO @ Sat, 15 Jan 2022 19:14:25: 2000000 INFO @ Sat, 15 Jan 2022 19:14:27: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:14:27: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:14:27: #1 total tags in treatment: 4105522 INFO @ Sat, 15 Jan 2022 19:14:27: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:14:27: #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 19:14:27: #1 tags after filtering in treatment: 1978601 INFO @ Sat, 15 Jan 2022 19:14:27: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 15 Jan 2022 19:14:27: #1 finished! INFO @ Sat, 15 Jan 2022 19:14:27: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:14:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:14:27: #2 number of paired peaks: 195 WARNING @ Sat, 15 Jan 2022 19:14:27: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Sat, 15 Jan 2022 19:14:27: start model_add_line... INFO @ Sat, 15 Jan 2022 19:14:27: start X-correlation... INFO @ Sat, 15 Jan 2022 19:14:27: end of X-cor INFO @ Sat, 15 Jan 2022 19:14:27: #2 finished! INFO @ Sat, 15 Jan 2022 19:14:27: #2 predicted fragment length is 157 bps INFO @ Sat, 15 Jan 2022 19:14:27: #2 alternative fragment length(s) may be 3,157,592 bps INFO @ Sat, 15 Jan 2022 19:14:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.05_model.r WARNING @ Sat, 15 Jan 2022 19:14:27: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:14:27: #2 You may need to consider one of the other alternative d(s): 3,157,592 WARNING @ Sat, 15 Jan 2022 19:14:27: #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 19:14:27: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:14:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:14:30: 3000000 INFO @ Sat, 15 Jan 2022 19:14:31: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:14:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:14:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:14:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.05_summits.bed INFO @ Sat, 15 Jan 2022 19:14:33: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (212 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:14:34: 4000000 INFO @ Sat, 15 Jan 2022 19:14:39: 5000000 INFO @ Sat, 15 Jan 2022 19:14:43: 6000000 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 19:14:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.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 19:14:46: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:14:46: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:14:48: 7000000 INFO @ Sat, 15 Jan 2022 19:14:51: 1000000 INFO @ Sat, 15 Jan 2022 19:14:52: 8000000 INFO @ Sat, 15 Jan 2022 19:14:56: 2000000 INFO @ Sat, 15 Jan 2022 19:14:57: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:14:57: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:14:57: #1 total tags in treatment: 4105522 INFO @ Sat, 15 Jan 2022 19:14:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:14:57: #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 19:14:57: #1 tags after filtering in treatment: 1978601 INFO @ Sat, 15 Jan 2022 19:14:57: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 15 Jan 2022 19:14:57: #1 finished! INFO @ Sat, 15 Jan 2022 19:14:57: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:14:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:14:57: #2 number of paired peaks: 195 WARNING @ Sat, 15 Jan 2022 19:14:57: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Sat, 15 Jan 2022 19:14:57: start model_add_line... INFO @ Sat, 15 Jan 2022 19:14:57: start X-correlation... INFO @ Sat, 15 Jan 2022 19:14:57: end of X-cor INFO @ Sat, 15 Jan 2022 19:14:57: #2 finished! INFO @ Sat, 15 Jan 2022 19:14:57: #2 predicted fragment length is 157 bps INFO @ Sat, 15 Jan 2022 19:14:57: #2 alternative fragment length(s) may be 3,157,592 bps INFO @ Sat, 15 Jan 2022 19:14:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.10_model.r WARNING @ Sat, 15 Jan 2022 19:14:57: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:14:57: #2 You may need to consider one of the other alternative d(s): 3,157,592 WARNING @ Sat, 15 Jan 2022 19:14:57: #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 19:14:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:14:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:15:00: 3000000 INFO @ Sat, 15 Jan 2022 19:15:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:15:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:15:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:15:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.10_summits.bed INFO @ Sat, 15 Jan 2022 19:15:03: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (72 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:15:05: 4000000 INFO @ Sat, 15 Jan 2022 19:15:10: 5000000 INFO @ Sat, 15 Jan 2022 19:15:14: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:15:19: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:15:24: 8000000 INFO @ Sat, 15 Jan 2022 19:15:28: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:15:28: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:15:28: #1 total tags in treatment: 4105522 INFO @ Sat, 15 Jan 2022 19:15:28: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:15:28: #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 19:15:28: #1 tags after filtering in treatment: 1978601 INFO @ Sat, 15 Jan 2022 19:15:28: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 15 Jan 2022 19:15:28: #1 finished! INFO @ Sat, 15 Jan 2022 19:15:28: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:15:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:15:28: #2 number of paired peaks: 195 WARNING @ Sat, 15 Jan 2022 19:15:28: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Sat, 15 Jan 2022 19:15:28: start model_add_line... INFO @ Sat, 15 Jan 2022 19:15:28: start X-correlation... INFO @ Sat, 15 Jan 2022 19:15:28: end of X-cor INFO @ Sat, 15 Jan 2022 19:15:28: #2 finished! INFO @ Sat, 15 Jan 2022 19:15:28: #2 predicted fragment length is 157 bps INFO @ Sat, 15 Jan 2022 19:15:28: #2 alternative fragment length(s) may be 3,157,592 bps INFO @ Sat, 15 Jan 2022 19:15:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.20_model.r WARNING @ Sat, 15 Jan 2022 19:15:28: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:15:28: #2 You may need to consider one of the other alternative d(s): 3,157,592 WARNING @ Sat, 15 Jan 2022 19:15:28: #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 19:15:28: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:15:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:15:33: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:15:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:15:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:15:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781026/SRX11781026.20_summits.bed INFO @ Sat, 15 Jan 2022 19:15:34: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (16 records, 4 fields): 2 millis CompletedMACS2peakCalling