Job ID = 14520596 SRX = SRX11781074 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:25:19 prefetch.2.10.7: 1) Downloading 'SRR15481017'... 2022-01-15T10:25:19 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:26:18 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:26:18 prefetch.2.10.7: 1) 'SRR15481017' was downloaded successfully 2022-01-15T10:26:18 prefetch.2.10.7: 'SRR15481017' has 0 unresolved dependencies Read 11953464 spots for SRR15481017/SRR15481017.sra Written 11953464 spots for SRR15481017/SRR15481017.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: 00:22:54 11953464 reads; of these: 11953464 (100.00%) were paired; of these: 2280358 (19.08%) aligned concordantly 0 times 5547238 (46.41%) aligned concordantly exactly 1 time 4125868 (34.52%) aligned concordantly >1 times ---- 2280358 pairs aligned concordantly 0 times; of these: 60326 (2.65%) aligned discordantly 1 time ---- 2220032 pairs aligned 0 times concordantly or discordantly; of these: 4440064 mates make up the pairs; of these: 3329788 (74.99%) aligned 0 times 653147 (14.71%) aligned exactly 1 time 457129 (10.30%) aligned >1 times 86.07% overall alignment rate Time searching: 00:22:54 Overall time: 00:22:54 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] 905000 / 9732749 = 0.0930 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 19:58:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.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 19:58:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:58:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:58:06: 1000000 INFO @ Sat, 15 Jan 2022 19:58:13: 2000000 INFO @ Sat, 15 Jan 2022 19:58:20: 3000000 INFO @ Sat, 15 Jan 2022 19:58:27: 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 19:58:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.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 19:58:30: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:58:30: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:58:34: 5000000 INFO @ Sat, 15 Jan 2022 19:58:37: 1000000 INFO @ Sat, 15 Jan 2022 19:58:41: 6000000 INFO @ Sat, 15 Jan 2022 19:58:44: 2000000 INFO @ Sat, 15 Jan 2022 19:58:49: 7000000 INFO @ Sat, 15 Jan 2022 19:58:52: 3000000 INFO @ Sat, 15 Jan 2022 19:58:56: 8000000 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 19:59:00: 4000000 INFO @ Sat, 15 Jan 2022 19:59:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.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 19:59:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:59:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:59:04: 9000000 INFO @ Sat, 15 Jan 2022 19:59:06: 5000000 INFO @ Sat, 15 Jan 2022 19:59:07: 1000000 INFO @ Sat, 15 Jan 2022 19:59:12: 10000000 INFO @ Sat, 15 Jan 2022 19:59:13: 6000000 INFO @ Sat, 15 Jan 2022 19:59:15: 2000000 INFO @ Sat, 15 Jan 2022 19:59:20: 7000000 INFO @ Sat, 15 Jan 2022 19:59:20: 11000000 INFO @ Sat, 15 Jan 2022 19:59:23: 3000000 INFO @ Sat, 15 Jan 2022 19:59:27: 8000000 INFO @ Sat, 15 Jan 2022 19:59:28: 12000000 INFO @ Sat, 15 Jan 2022 19:59:31: 4000000 INFO @ Sat, 15 Jan 2022 19:59:35: 9000000 INFO @ Sat, 15 Jan 2022 19:59:35: 13000000 INFO @ Sat, 15 Jan 2022 19:59:38: 5000000 INFO @ Sat, 15 Jan 2022 19:59:42: 10000000 INFO @ Sat, 15 Jan 2022 19:59:43: 14000000 INFO @ Sat, 15 Jan 2022 19:59:46: 6000000 INFO @ Sat, 15 Jan 2022 19:59:50: 15000000 INFO @ Sat, 15 Jan 2022 19:59:50: 11000000 INFO @ Sat, 15 Jan 2022 19:59:53: 7000000 INFO @ Sat, 15 Jan 2022 19:59:57: 16000000 INFO @ Sat, 15 Jan 2022 19:59:58: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:00:01: 8000000 INFO @ Sat, 15 Jan 2022 20:00:05: 17000000 INFO @ Sat, 15 Jan 2022 20:00:06: 13000000 INFO @ Sat, 15 Jan 2022 20:00:09: 9000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:00:12: 18000000 INFO @ Sat, 15 Jan 2022 20:00:14: 14000000 INFO @ Sat, 15 Jan 2022 20:00:16: 10000000 INFO @ Sat, 15 Jan 2022 20:00:18: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:00:18: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:00:18: #1 total tags in treatment: 8770373 INFO @ Sat, 15 Jan 2022 20:00:18: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:00:18: #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 20:00:18: #1 tags after filtering in treatment: 3756670 INFO @ Sat, 15 Jan 2022 20:00:18: #1 Redundant rate of treatment: 0.57 INFO @ Sat, 15 Jan 2022 20:00:18: #1 finished! INFO @ Sat, 15 Jan 2022 20:00:18: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:00:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:00:18: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:00:18: 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 20:00:18: start model_add_line... INFO @ Sat, 15 Jan 2022 20:00:18: start X-correlation... INFO @ Sat, 15 Jan 2022 20:00:18: end of X-cor INFO @ Sat, 15 Jan 2022 20:00:18: #2 finished! INFO @ Sat, 15 Jan 2022 20:00:18: #2 predicted fragment length is 61 bps INFO @ Sat, 15 Jan 2022 20:00:18: #2 alternative fragment length(s) may be 16,61,118,140,165,227,243,273,299,330,368,389,402,420,472,487,492,501,527,547,562,582 bps INFO @ Sat, 15 Jan 2022 20:00:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.05_model.r WARNING @ Sat, 15 Jan 2022 20:00:19: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:00:19: #2 You may need to consider one of the other alternative d(s): 16,61,118,140,165,227,243,273,299,330,368,389,402,420,472,487,492,501,527,547,562,582 WARNING @ Sat, 15 Jan 2022 20:00:19: #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 20:00:19: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:00:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:00:21: 15000000 INFO @ Sat, 15 Jan 2022 20:00:24: 11000000 INFO @ Sat, 15 Jan 2022 20:00:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:00:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:00:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:00:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.05_summits.bed INFO @ Sat, 15 Jan 2022 20:00:27: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (162 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:00:29: 16000000 INFO @ Sat, 15 Jan 2022 20:00:31: 12000000 INFO @ Sat, 15 Jan 2022 20:00:37: 17000000 INFO @ Sat, 15 Jan 2022 20:00:39: 13000000 INFO @ Sat, 15 Jan 2022 20:00:45: 18000000 INFO @ Sat, 15 Jan 2022 20:00:46: 14000000 INFO @ Sat, 15 Jan 2022 20:00:51: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:00:51: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:00:51: #1 total tags in treatment: 8770373 INFO @ Sat, 15 Jan 2022 20:00:51: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:00:51: #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 20:00:51: #1 tags after filtering in treatment: 3756670 INFO @ Sat, 15 Jan 2022 20:00:51: #1 Redundant rate of treatment: 0.57 INFO @ Sat, 15 Jan 2022 20:00:51: #1 finished! INFO @ Sat, 15 Jan 2022 20:00:51: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:00:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:00:51: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:00:51: 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 20:00:51: start model_add_line... INFO @ Sat, 15 Jan 2022 20:00:51: start X-correlation... INFO @ Sat, 15 Jan 2022 20:00:51: end of X-cor INFO @ Sat, 15 Jan 2022 20:00:51: #2 finished! INFO @ Sat, 15 Jan 2022 20:00:51: #2 predicted fragment length is 61 bps INFO @ Sat, 15 Jan 2022 20:00:51: #2 alternative fragment length(s) may be 16,61,118,140,165,227,243,273,299,330,368,389,402,420,472,487,492,501,527,547,562,582 bps INFO @ Sat, 15 Jan 2022 20:00:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.10_model.r INFO @ Sat, 15 Jan 2022 20:00:53: 15000000 WARNING @ Sat, 15 Jan 2022 20:00:55: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:00:55: #2 You may need to consider one of the other alternative d(s): 16,61,118,140,165,227,243,273,299,330,368,389,402,420,472,487,492,501,527,547,562,582 WARNING @ Sat, 15 Jan 2022 20:00:55: #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 20:00:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:00:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:00:59: 16000000 INFO @ Sat, 15 Jan 2022 20:01:00: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:01:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:01:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:01:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.10_summits.bed INFO @ Sat, 15 Jan 2022 20:01:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (56 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:01:06: 17000000 INFO @ Sat, 15 Jan 2022 20:01:13: 18000000 INFO @ Sat, 15 Jan 2022 20:01:18: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:01:18: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:01:18: #1 total tags in treatment: 8770373 INFO @ Sat, 15 Jan 2022 20:01:18: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:01:18: #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 20:01:18: #1 tags after filtering in treatment: 3756670 INFO @ Sat, 15 Jan 2022 20:01:18: #1 Redundant rate of treatment: 0.57 INFO @ Sat, 15 Jan 2022 20:01:18: #1 finished! INFO @ Sat, 15 Jan 2022 20:01:18: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:01:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:01:18: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:01:18: 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 20:01:18: start model_add_line... INFO @ Sat, 15 Jan 2022 20:01:18: start X-correlation... INFO @ Sat, 15 Jan 2022 20:01:18: end of X-cor INFO @ Sat, 15 Jan 2022 20:01:18: #2 finished! INFO @ Sat, 15 Jan 2022 20:01:18: #2 predicted fragment length is 61 bps INFO @ Sat, 15 Jan 2022 20:01:18: #2 alternative fragment length(s) may be 16,61,118,140,165,227,243,273,299,330,368,389,402,420,472,487,492,501,527,547,562,582 bps INFO @ Sat, 15 Jan 2022 20:01:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.20_model.r WARNING @ Sat, 15 Jan 2022 20:01:18: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:01:18: #2 You may need to consider one of the other alternative d(s): 16,61,118,140,165,227,243,273,299,330,368,389,402,420,472,487,492,501,527,547,562,582 WARNING @ Sat, 15 Jan 2022 20:01:18: #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 20:01:18: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:01:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:01:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:01:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:01:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:01:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781074/SRX11781074.20_summits.bed INFO @ Sat, 15 Jan 2022 20:01:26: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 1 millis CompletedMACS2peakCalling