Job ID = 7099372 SRX = SRX6911504 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6559476 spots for SRR10191131/SRR10191131.sra Written 6559476 spots for SRR10191131/SRR10191131.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: 00:07:32 6559476 reads; of these: 6559476 (100.00%) were paired; of these: 3132319 (47.75%) aligned concordantly 0 times 3118144 (47.54%) aligned concordantly exactly 1 time 309013 (4.71%) aligned concordantly >1 times ---- 3132319 pairs aligned concordantly 0 times; of these: 1678882 (53.60%) aligned discordantly 1 time ---- 1453437 pairs aligned 0 times concordantly or discordantly; of these: 2906874 mates make up the pairs; of these: 1964382 (67.58%) aligned 0 times 502768 (17.30%) aligned exactly 1 time 439724 (15.13%) aligned >1 times 85.03% overall alignment rate Time searching: 00:07:32 Overall time: 00:07:32 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] 352005 / 5104931 = 0.0690 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 12:15:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.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 @ Wed, 22 Jul 2020 12:15:53: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:15:53: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:16:00: 1000000 INFO @ Wed, 22 Jul 2020 12:16:06: 2000000 INFO @ Wed, 22 Jul 2020 12:16:11: 3000000 INFO @ Wed, 22 Jul 2020 12:16:17: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 12:16:23: 5000000 INFO @ Wed, 22 Jul 2020 12:16:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.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 @ Wed, 22 Jul 2020 12:16:23: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:16:23: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:16:30: 6000000 INFO @ Wed, 22 Jul 2020 12:16:31: 1000000 INFO @ Wed, 22 Jul 2020 12:16:36: 7000000 INFO @ Wed, 22 Jul 2020 12:16:37: 2000000 INFO @ Wed, 22 Jul 2020 12:16:43: 8000000 INFO @ Wed, 22 Jul 2020 12:16:44: 3000000 INFO @ Wed, 22 Jul 2020 12:16:49: 9000000 INFO @ Wed, 22 Jul 2020 12:16:51: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 12:16:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.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 @ Wed, 22 Jul 2020 12:16:53: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:16:53: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:16:56: 10000000 INFO @ Wed, 22 Jul 2020 12:16:58: 5000000 INFO @ Wed, 22 Jul 2020 12:16:59: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:16:59: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:16:59: #1 total tags in treatment: 3166160 INFO @ Wed, 22 Jul 2020 12:16:59: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:16:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:16:59: #1 tags after filtering in treatment: 2012747 INFO @ Wed, 22 Jul 2020 12:16:59: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Jul 2020 12:16:59: #1 finished! INFO @ Wed, 22 Jul 2020 12:16:59: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:16:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:16:59: #2 number of paired peaks: 475 WARNING @ Wed, 22 Jul 2020 12:16:59: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Wed, 22 Jul 2020 12:16:59: start model_add_line... INFO @ Wed, 22 Jul 2020 12:16:59: start X-correlation... INFO @ Wed, 22 Jul 2020 12:16:59: end of X-cor INFO @ Wed, 22 Jul 2020 12:16:59: #2 finished! INFO @ Wed, 22 Jul 2020 12:16:59: #2 predicted fragment length is 215 bps INFO @ Wed, 22 Jul 2020 12:16:59: #2 alternative fragment length(s) may be 0,134,185,203,215,232,260,274,294 bps INFO @ Wed, 22 Jul 2020 12:16:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.05_model.r INFO @ Wed, 22 Jul 2020 12:16:59: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:16:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:17:00: 1000000 INFO @ Wed, 22 Jul 2020 12:17:04: 6000000 INFO @ Wed, 22 Jul 2020 12:17:08: 2000000 INFO @ Wed, 22 Jul 2020 12:17:09: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:17:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.05_peaks.xls INFO @ Wed, 22 Jul 2020 12:17:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:17:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.05_summits.bed INFO @ Wed, 22 Jul 2020 12:17:11: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (147 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 12:17:11: 7000000 INFO @ Wed, 22 Jul 2020 12:17:15: 3000000 INFO @ Wed, 22 Jul 2020 12:17:17: 8000000 INFO @ Wed, 22 Jul 2020 12:17:22: 4000000 INFO @ Wed, 22 Jul 2020 12:17:24: 9000000 INFO @ Wed, 22 Jul 2020 12:17:29: 5000000 INFO @ Wed, 22 Jul 2020 12:17:30: 10000000 INFO @ Wed, 22 Jul 2020 12:17:33: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:17:33: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:17:33: #1 total tags in treatment: 3166160 INFO @ Wed, 22 Jul 2020 12:17:33: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:17:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:17:33: #1 tags after filtering in treatment: 2012747 INFO @ Wed, 22 Jul 2020 12:17:33: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Jul 2020 12:17:33: #1 finished! INFO @ Wed, 22 Jul 2020 12:17:33: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:17:33: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 12:17:33: #2 number of paired peaks: 475 WARNING @ Wed, 22 Jul 2020 12:17:33: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Wed, 22 Jul 2020 12:17:33: start model_add_line... INFO @ Wed, 22 Jul 2020 12:17:33: start X-correlation... INFO @ Wed, 22 Jul 2020 12:17:33: end of X-cor INFO @ Wed, 22 Jul 2020 12:17:33: #2 finished! INFO @ Wed, 22 Jul 2020 12:17:33: #2 predicted fragment length is 215 bps INFO @ Wed, 22 Jul 2020 12:17:33: #2 alternative fragment length(s) may be 0,134,185,203,215,232,260,274,294 bps INFO @ Wed, 22 Jul 2020 12:17:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.10_model.r INFO @ Wed, 22 Jul 2020 12:17:33: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:17:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:17:36: 6000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 12:17:42: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:17:43: 7000000 INFO @ Wed, 22 Jul 2020 12:17:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.10_peaks.xls INFO @ Wed, 22 Jul 2020 12:17:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:17:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.10_summits.bed INFO @ Wed, 22 Jul 2020 12:17:44: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (43 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 12:17:49: 8000000 INFO @ Wed, 22 Jul 2020 12:17:56: 9000000 INFO @ Wed, 22 Jul 2020 12:18:03: 10000000 INFO @ Wed, 22 Jul 2020 12:18:06: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:18:06: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:18:06: #1 total tags in treatment: 3166160 INFO @ Wed, 22 Jul 2020 12:18:06: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:18:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:18:06: #1 tags after filtering in treatment: 2012747 INFO @ Wed, 22 Jul 2020 12:18:06: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Jul 2020 12:18:06: #1 finished! INFO @ Wed, 22 Jul 2020 12:18:06: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:18:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:18:06: #2 number of paired peaks: 475 WARNING @ Wed, 22 Jul 2020 12:18:06: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Wed, 22 Jul 2020 12:18:06: start model_add_line... INFO @ Wed, 22 Jul 2020 12:18:06: start X-correlation... INFO @ Wed, 22 Jul 2020 12:18:06: end of X-cor INFO @ Wed, 22 Jul 2020 12:18:06: #2 finished! INFO @ Wed, 22 Jul 2020 12:18:06: #2 predicted fragment length is 215 bps INFO @ Wed, 22 Jul 2020 12:18:06: #2 alternative fragment length(s) may be 0,134,185,203,215,232,260,274,294 bps INFO @ Wed, 22 Jul 2020 12:18:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.20_model.r INFO @ Wed, 22 Jul 2020 12:18:06: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:18:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:18:15: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:18:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.20_peaks.xls INFO @ Wed, 22 Jul 2020 12:18:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:18:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911504/SRX6911504.20_summits.bed INFO @ Wed, 22 Jul 2020 12:18:17: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (11 records, 4 fields): 1 millis CompletedMACS2peakCalling