Job ID = 14520592 SRX = SRX11781070 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:25:04 prefetch.2.10.7: 1) Downloading 'SRR15481013'... 2022-01-15T10:25:04 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:28:18 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:28:18 prefetch.2.10.7: 1) 'SRR15481013' was downloaded successfully 2022-01-15T10:28:18 prefetch.2.10.7: 'SRR15481013' has 0 unresolved dependencies Read 13434210 spots for SRR15481013/SRR15481013.sra Written 13434210 spots for SRR15481013/SRR15481013.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: 00:31:05 13434210 reads; of these: 13434210 (100.00%) were paired; of these: 1886978 (14.05%) aligned concordantly 0 times 5517957 (41.07%) aligned concordantly exactly 1 time 6029275 (44.88%) aligned concordantly >1 times ---- 1886978 pairs aligned concordantly 0 times; of these: 53127 (2.82%) aligned discordantly 1 time ---- 1833851 pairs aligned 0 times concordantly or discordantly; of these: 3667702 mates make up the pairs; of these: 2666459 (72.70%) aligned 0 times 489532 (13.35%) aligned exactly 1 time 511711 (13.95%) aligned >1 times 90.08% overall alignment rate Time searching: 00:31:05 Overall time: 00:31:05 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] 1450649 / 11599586 = 0.1251 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 20:09:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.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 20:09:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:09:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:09:10: 1000000 INFO @ Sat, 15 Jan 2022 20:09:18: 2000000 INFO @ Sat, 15 Jan 2022 20:09:26: 3000000 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 20:09:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.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 20:09:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:09:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:09:35: 4000000 INFO @ Sat, 15 Jan 2022 20:09:41: 1000000 INFO @ Sat, 15 Jan 2022 20:09:45: 5000000 INFO @ Sat, 15 Jan 2022 20:09:49: 2000000 INFO @ Sat, 15 Jan 2022 20:09:54: 6000000 INFO @ Sat, 15 Jan 2022 20:09:58: 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 20:10:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.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 20:10:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:10:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:10:04: 7000000 INFO @ Sat, 15 Jan 2022 20:10:06: 4000000 INFO @ Sat, 15 Jan 2022 20:10:11: 1000000 INFO @ Sat, 15 Jan 2022 20:10:13: 8000000 INFO @ Sat, 15 Jan 2022 20:10:14: 5000000 INFO @ Sat, 15 Jan 2022 20:10:19: 2000000 INFO @ Sat, 15 Jan 2022 20:10:23: 6000000 INFO @ Sat, 15 Jan 2022 20:10:23: 9000000 INFO @ Sat, 15 Jan 2022 20:10:28: 3000000 INFO @ Sat, 15 Jan 2022 20:10:31: 7000000 INFO @ Sat, 15 Jan 2022 20:10:33: 10000000 INFO @ Sat, 15 Jan 2022 20:10:36: 4000000 INFO @ Sat, 15 Jan 2022 20:10:39: 8000000 INFO @ Sat, 15 Jan 2022 20:10:42: 11000000 INFO @ Sat, 15 Jan 2022 20:10:44: 5000000 INFO @ Sat, 15 Jan 2022 20:10:48: 9000000 INFO @ Sat, 15 Jan 2022 20:10:52: 12000000 INFO @ Sat, 15 Jan 2022 20:10:52: 6000000 INFO @ Sat, 15 Jan 2022 20:10:56: 10000000 INFO @ Sat, 15 Jan 2022 20:11:00: 7000000 INFO @ Sat, 15 Jan 2022 20:11:02: 13000000 INFO @ Sat, 15 Jan 2022 20:11:04: 11000000 INFO @ Sat, 15 Jan 2022 20:11:09: 8000000 INFO @ Sat, 15 Jan 2022 20:11:11: 14000000 INFO @ Sat, 15 Jan 2022 20:11:12: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:11:17: 9000000 INFO @ Sat, 15 Jan 2022 20:11:21: 15000000 INFO @ Sat, 15 Jan 2022 20:11:21: 13000000 INFO @ Sat, 15 Jan 2022 20:11:25: 10000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:11:29: 14000000 INFO @ Sat, 15 Jan 2022 20:11:30: 16000000 INFO @ Sat, 15 Jan 2022 20:11:33: 11000000 INFO @ Sat, 15 Jan 2022 20:11:37: 15000000 INFO @ Sat, 15 Jan 2022 20:11:40: 17000000 INFO @ Sat, 15 Jan 2022 20:11:42: 12000000 INFO @ Sat, 15 Jan 2022 20:11:46: 16000000 INFO @ Sat, 15 Jan 2022 20:11:49: 18000000 INFO @ Sat, 15 Jan 2022 20:11:50: 13000000 INFO @ Sat, 15 Jan 2022 20:11:54: 17000000 INFO @ Sat, 15 Jan 2022 20:11:58: 14000000 INFO @ Sat, 15 Jan 2022 20:11:59: 19000000 INFO @ Sat, 15 Jan 2022 20:12:02: 18000000 INFO @ Sat, 15 Jan 2022 20:12:06: 15000000 INFO @ Sat, 15 Jan 2022 20:12:09: 20000000 INFO @ Sat, 15 Jan 2022 20:12:11: 19000000 INFO @ Sat, 15 Jan 2022 20:12:14: 16000000 INFO @ Sat, 15 Jan 2022 20:12:18: 21000000 INFO @ Sat, 15 Jan 2022 20:12:19: 20000000 INFO @ Sat, 15 Jan 2022 20:12:21: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:12:21: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:12:21: #1 total tags in treatment: 10099583 INFO @ Sat, 15 Jan 2022 20:12:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:12:21: #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 20:12:21: #1 tags after filtering in treatment: 4019932 INFO @ Sat, 15 Jan 2022 20:12:21: #1 Redundant rate of treatment: 0.60 INFO @ Sat, 15 Jan 2022 20:12:21: #1 finished! INFO @ Sat, 15 Jan 2022 20:12:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:12:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:12:21: #2 number of paired peaks: 165 WARNING @ Sat, 15 Jan 2022 20:12:21: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Sat, 15 Jan 2022 20:12:21: start model_add_line... INFO @ Sat, 15 Jan 2022 20:12:21: start X-correlation... INFO @ Sat, 15 Jan 2022 20:12:21: end of X-cor INFO @ Sat, 15 Jan 2022 20:12:21: #2 finished! INFO @ Sat, 15 Jan 2022 20:12:21: #2 predicted fragment length is 66 bps INFO @ Sat, 15 Jan 2022 20:12:21: #2 alternative fragment length(s) may be 29,66,140,158,165,196,226,258,303,338,378,390,415,431,450,483,518,520,526,539,568 bps INFO @ Sat, 15 Jan 2022 20:12:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.05_model.r WARNING @ Sat, 15 Jan 2022 20:12:21: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:12:21: #2 You may need to consider one of the other alternative d(s): 29,66,140,158,165,196,226,258,303,338,378,390,415,431,450,483,518,520,526,539,568 WARNING @ Sat, 15 Jan 2022 20:12:21: #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 20:12:21: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:12:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:12:22: 17000000 INFO @ Sat, 15 Jan 2022 20:12:27: 21000000 INFO @ Sat, 15 Jan 2022 20:12:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:12:29: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:12:29: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:12:29: #1 total tags in treatment: 10099583 INFO @ Sat, 15 Jan 2022 20:12:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:12:29: #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 20:12:29: #1 tags after filtering in treatment: 4019932 INFO @ Sat, 15 Jan 2022 20:12:29: #1 Redundant rate of treatment: 0.60 INFO @ Sat, 15 Jan 2022 20:12:29: #1 finished! INFO @ Sat, 15 Jan 2022 20:12:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:12:30: #2 number of paired peaks: 165 WARNING @ Sat, 15 Jan 2022 20:12:30: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Sat, 15 Jan 2022 20:12:30: start model_add_line... INFO @ Sat, 15 Jan 2022 20:12:30: start X-correlation... INFO @ Sat, 15 Jan 2022 20:12:30: end of X-cor INFO @ Sat, 15 Jan 2022 20:12:30: #2 finished! INFO @ Sat, 15 Jan 2022 20:12:30: #2 predicted fragment length is 66 bps INFO @ Sat, 15 Jan 2022 20:12:30: #2 alternative fragment length(s) may be 29,66,140,158,165,196,226,258,303,338,378,390,415,431,450,483,518,520,526,539,568 bps INFO @ Sat, 15 Jan 2022 20:12:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.10_model.r WARNING @ Sat, 15 Jan 2022 20:12:30: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:12:30: #2 You may need to consider one of the other alternative d(s): 29,66,140,158,165,196,226,258,303,338,378,390,415,431,450,483,518,520,526,539,568 WARNING @ Sat, 15 Jan 2022 20:12:30: #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 20:12:30: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:12:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:12:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:12:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:12:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.05_summits.bed INFO @ Sat, 15 Jan 2022 20:12:30: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (196 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:12:30: 18000000 INFO @ Sat, 15 Jan 2022 20:12:36: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:12:38: 19000000 INFO @ Sat, 15 Jan 2022 20:12:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:12:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:12:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.10_summits.bed INFO @ Sat, 15 Jan 2022 20:12:39: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (74 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:12:45: 20000000 INFO @ Sat, 15 Jan 2022 20:12:52: 21000000 INFO @ Sat, 15 Jan 2022 20:12:54: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:12:54: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:12:54: #1 total tags in treatment: 10099583 INFO @ Sat, 15 Jan 2022 20:12:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:12:54: #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 20:12:54: #1 tags after filtering in treatment: 4019932 INFO @ Sat, 15 Jan 2022 20:12:54: #1 Redundant rate of treatment: 0.60 INFO @ Sat, 15 Jan 2022 20:12:54: #1 finished! INFO @ Sat, 15 Jan 2022 20:12:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:12:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:12:55: #2 number of paired peaks: 165 WARNING @ Sat, 15 Jan 2022 20:12:55: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Sat, 15 Jan 2022 20:12:55: start model_add_line... INFO @ Sat, 15 Jan 2022 20:12:55: start X-correlation... INFO @ Sat, 15 Jan 2022 20:12:55: end of X-cor INFO @ Sat, 15 Jan 2022 20:12:55: #2 finished! INFO @ Sat, 15 Jan 2022 20:12:55: #2 predicted fragment length is 66 bps INFO @ Sat, 15 Jan 2022 20:12:55: #2 alternative fragment length(s) may be 29,66,140,158,165,196,226,258,303,338,378,390,415,431,450,483,518,520,526,539,568 bps INFO @ Sat, 15 Jan 2022 20:12:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.20_model.r WARNING @ Sat, 15 Jan 2022 20:12:55: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:12:55: #2 You may need to consider one of the other alternative d(s): 29,66,140,158,165,196,226,258,303,338,378,390,415,431,450,483,518,520,526,539,568 WARNING @ Sat, 15 Jan 2022 20:12:55: #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 20:12:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:12:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:13:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:13:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:13:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:13:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781070/SRX11781070.20_summits.bed INFO @ Sat, 15 Jan 2022 20:13:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (12 records, 4 fields): 1 millis CompletedMACS2peakCalling