Job ID = 14520483 SRX = SRX11781047 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:12:53 prefetch.2.10.7: 1) Downloading 'SRR15480990'... 2022-01-15T10:12:53 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:13:19 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:13:20 prefetch.2.10.7: 'SRR15480990' is valid 2022-01-15T10:13:20 prefetch.2.10.7: 1) 'SRR15480990' was downloaded successfully 2022-01-15T10:13:20 prefetch.2.10.7: 'SRR15480990' has 0 unresolved dependencies Read 6531768 spots for SRR15480990/SRR15480990.sra Written 6531768 spots for SRR15480990/SRR15480990.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: 00:05:42 6531768 reads; of these: 6531768 (100.00%) were paired; of these: 1310788 (20.07%) aligned concordantly 0 times 3869458 (59.24%) aligned concordantly exactly 1 time 1351522 (20.69%) aligned concordantly >1 times ---- 1310788 pairs aligned concordantly 0 times; of these: 241191 (18.40%) aligned discordantly 1 time ---- 1069597 pairs aligned 0 times concordantly or discordantly; of these: 2139194 mates make up the pairs; of these: 1484931 (69.42%) aligned 0 times 389948 (18.23%) aligned exactly 1 time 264315 (12.36%) aligned >1 times 88.63% overall alignment rate Time searching: 00:05:42 Overall time: 00:05:42 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 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] 431158 / 5423639 = 0.0795 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 19:23:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.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 19:23:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:23:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:24:02: 1000000 INFO @ Sat, 15 Jan 2022 19:24:10: 2000000 INFO @ Sat, 15 Jan 2022 19:24:17: 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 19:24:23: 4000000 INFO @ Sat, 15 Jan 2022 19:24:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.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 19:24:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:24:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:24:32: 5000000 INFO @ Sat, 15 Jan 2022 19:24:33: 1000000 INFO @ Sat, 15 Jan 2022 19:24:40: 6000000 INFO @ Sat, 15 Jan 2022 19:24:41: 2000000 INFO @ Sat, 15 Jan 2022 19:24:49: 7000000 INFO @ Sat, 15 Jan 2022 19:24:50: 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 19:24:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.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 19:24:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:24:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:24:58: 8000000 INFO @ Sat, 15 Jan 2022 19:24:59: 4000000 INFO @ Sat, 15 Jan 2022 19:25:03: 1000000 INFO @ Sat, 15 Jan 2022 19:25:06: 9000000 INFO @ Sat, 15 Jan 2022 19:25:07: 5000000 INFO @ Sat, 15 Jan 2022 19:25:12: 2000000 INFO @ Sat, 15 Jan 2022 19:25:15: 10000000 INFO @ Sat, 15 Jan 2022 19:25:16: 6000000 INFO @ Sat, 15 Jan 2022 19:25:21: 3000000 INFO @ Sat, 15 Jan 2022 19:25:21: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:25:21: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:25:21: #1 total tags in treatment: 4803064 INFO @ Sat, 15 Jan 2022 19:25:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:25:21: #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 19:25:21: #1 tags after filtering in treatment: 3396646 INFO @ Sat, 15 Jan 2022 19:25:21: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 19:25:21: #1 finished! INFO @ Sat, 15 Jan 2022 19:25:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:25:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:25:21: #2 number of paired peaks: 146 WARNING @ Sat, 15 Jan 2022 19:25:21: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Sat, 15 Jan 2022 19:25:21: start model_add_line... INFO @ Sat, 15 Jan 2022 19:25:21: start X-correlation... INFO @ Sat, 15 Jan 2022 19:25:21: end of X-cor INFO @ Sat, 15 Jan 2022 19:25:21: #2 finished! INFO @ Sat, 15 Jan 2022 19:25:21: #2 predicted fragment length is 99 bps INFO @ Sat, 15 Jan 2022 19:25:21: #2 alternative fragment length(s) may be 76,97,99,168,195,240,423,585 bps INFO @ Sat, 15 Jan 2022 19:25:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.05_model.r WARNING @ Sat, 15 Jan 2022 19:25:21: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:25:21: #2 You may need to consider one of the other alternative d(s): 76,97,99,168,195,240,423,585 WARNING @ Sat, 15 Jan 2022 19:25:21: #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 19:25:21: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:25:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:25:25: 7000000 INFO @ Sat, 15 Jan 2022 19:25:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:25:29: 4000000 INFO @ Sat, 15 Jan 2022 19:25:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:25:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:25:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.05_summits.bed INFO @ Sat, 15 Jan 2022 19:25:31: Done! pass1 - making usageList (16 chroms): 0 millis BedGraph に変換しました。 BigWig に変換中... pass2 - checking and writing primary data (82 records, 4 fields): 1594 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:25:33: 8000000 INFO @ Sat, 15 Jan 2022 19:25:37: 5000000 INFO @ Sat, 15 Jan 2022 19:25:42: 9000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:25:46: 6000000 INFO @ Sat, 15 Jan 2022 19:25:50: 10000000 INFO @ Sat, 15 Jan 2022 19:25:55: 7000000 INFO @ Sat, 15 Jan 2022 19:25:56: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:25:56: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:25:56: #1 total tags in treatment: 4803064 INFO @ Sat, 15 Jan 2022 19:25:56: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:25:56: #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 19:25:56: #1 tags after filtering in treatment: 3396646 INFO @ Sat, 15 Jan 2022 19:25:56: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 19:25:56: #1 finished! INFO @ Sat, 15 Jan 2022 19:25:56: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:25:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:25:56: #2 number of paired peaks: 146 WARNING @ Sat, 15 Jan 2022 19:25:56: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Sat, 15 Jan 2022 19:25:56: start model_add_line... INFO @ Sat, 15 Jan 2022 19:25:56: start X-correlation... INFO @ Sat, 15 Jan 2022 19:25:56: end of X-cor INFO @ Sat, 15 Jan 2022 19:25:56: #2 finished! INFO @ Sat, 15 Jan 2022 19:25:56: #2 predicted fragment length is 99 bps INFO @ Sat, 15 Jan 2022 19:25:56: #2 alternative fragment length(s) may be 76,97,99,168,195,240,423,585 bps INFO @ Sat, 15 Jan 2022 19:25:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.10_model.r WARNING @ Sat, 15 Jan 2022 19:25:56: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:25:56: #2 You may need to consider one of the other alternative d(s): 76,97,99,168,195,240,423,585 WARNING @ Sat, 15 Jan 2022 19:25:56: #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 19:25:56: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:25:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:26:02: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:26:03: 8000000 INFO @ Sat, 15 Jan 2022 19:26:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:26:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:26:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.10_summits.bed INFO @ Sat, 15 Jan 2022 19:26:04: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:26:10: 9000000 INFO @ Sat, 15 Jan 2022 19:26:18: 10000000 INFO @ Sat, 15 Jan 2022 19:26:22: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:26:22: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:26:22: #1 total tags in treatment: 4803064 INFO @ Sat, 15 Jan 2022 19:26:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:26:22: #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 19:26:22: #1 tags after filtering in treatment: 3396646 INFO @ Sat, 15 Jan 2022 19:26:22: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 19:26:22: #1 finished! INFO @ Sat, 15 Jan 2022 19:26:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:26:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:26:22: #2 number of paired peaks: 146 WARNING @ Sat, 15 Jan 2022 19:26:22: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Sat, 15 Jan 2022 19:26:22: start model_add_line... INFO @ Sat, 15 Jan 2022 19:26:22: start X-correlation... INFO @ Sat, 15 Jan 2022 19:26:22: end of X-cor INFO @ Sat, 15 Jan 2022 19:26:22: #2 finished! INFO @ Sat, 15 Jan 2022 19:26:22: #2 predicted fragment length is 99 bps INFO @ Sat, 15 Jan 2022 19:26:22: #2 alternative fragment length(s) may be 76,97,99,168,195,240,423,585 bps INFO @ Sat, 15 Jan 2022 19:26:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.20_model.r WARNING @ Sat, 15 Jan 2022 19:26:23: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:26:23: #2 You may need to consider one of the other alternative d(s): 76,97,99,168,195,240,423,585 WARNING @ Sat, 15 Jan 2022 19:26:23: #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 19:26:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:26:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:26:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:26:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:26:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:26:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781047/SRX11781047.20_summits.bed INFO @ Sat, 15 Jan 2022 19:26:31: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (6 records, 4 fields): 18 millis CompletedMACS2peakCalling