Job ID = 14520380 SRX = SRX11781119 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:01:21 prefetch.2.10.7: 1) Downloading 'SRR15481062'... 2022-01-15T10:01:21 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:02:04 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:02:04 prefetch.2.10.7: 1) 'SRR15481062' was downloaded successfully 2022-01-15T10:02:04 prefetch.2.10.7: 'SRR15481062' has 0 unresolved dependencies Read 9383940 spots for SRR15481062/SRR15481062.sra Written 9383940 spots for SRR15481062/SRR15481062.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: 00:04:35 9383940 reads; of these: 9383940 (100.00%) were paired; of these: 5426414 (57.83%) aligned concordantly 0 times 3534390 (37.66%) aligned concordantly exactly 1 time 423136 (4.51%) aligned concordantly >1 times ---- 5426414 pairs aligned concordantly 0 times; of these: 347156 (6.40%) aligned discordantly 1 time ---- 5079258 pairs aligned 0 times concordantly or discordantly; of these: 10158516 mates make up the pairs; of these: 6318814 (62.20%) aligned 0 times 3298401 (32.47%) aligned exactly 1 time 541301 (5.33%) aligned >1 times 66.33% overall alignment rate Time searching: 00:04:35 Overall time: 00:04:35 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] 528223 / 4304021 = 0.1227 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 19:10:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.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 19:10:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:10:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:10:54: 1000000 INFO @ Sat, 15 Jan 2022 19:11:01: 2000000 INFO @ Sat, 15 Jan 2022 19:11:08: 3000000 INFO @ Sat, 15 Jan 2022 19:11:14: 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 19:11:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.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 19:11:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:11:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:11:21: 5000000 INFO @ Sat, 15 Jan 2022 19:11:25: 1000000 INFO @ Sat, 15 Jan 2022 19:11:29: 6000000 INFO @ Sat, 15 Jan 2022 19:11:33: 2000000 INFO @ Sat, 15 Jan 2022 19:11:37: 7000000 INFO @ Sat, 15 Jan 2022 19:11:41: 3000000 INFO @ Sat, 15 Jan 2022 19:11:44: 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 19:11:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.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 19:11:47: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:11:47: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:11:48: 4000000 INFO @ Sat, 15 Jan 2022 19:11:52: 9000000 INFO @ Sat, 15 Jan 2022 19:11:54: 1000000 INFO @ Sat, 15 Jan 2022 19:11:55: 5000000 INFO @ Sat, 15 Jan 2022 19:12:00: 10000000 INFO @ Sat, 15 Jan 2022 19:12:01: 2000000 INFO @ Sat, 15 Jan 2022 19:12:03: 6000000 INFO @ Sat, 15 Jan 2022 19:12:08: 11000000 INFO @ Sat, 15 Jan 2022 19:12:08: 3000000 INFO @ Sat, 15 Jan 2022 19:12:10: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:12:10: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:12:10: #1 total tags in treatment: 3458883 INFO @ Sat, 15 Jan 2022 19:12:10: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:12:10: #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 19:12:11: #1 tags after filtering in treatment: 2740824 INFO @ Sat, 15 Jan 2022 19:12:11: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:12:11: #1 finished! INFO @ Sat, 15 Jan 2022 19:12:11: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:12:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:12:11: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 19:12:11: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 19:12:11: start model_add_line... INFO @ Sat, 15 Jan 2022 19:12:11: start X-correlation... INFO @ Sat, 15 Jan 2022 19:12:11: end of X-cor INFO @ Sat, 15 Jan 2022 19:12:11: #2 finished! INFO @ Sat, 15 Jan 2022 19:12:11: #2 predicted fragment length is 252 bps INFO @ Sat, 15 Jan 2022 19:12:11: #2 alternative fragment length(s) may be 77,99,168,186,212,236,238,252,365,481,581 bps INFO @ Sat, 15 Jan 2022 19:12:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.05_model.r INFO @ Sat, 15 Jan 2022 19:12:11: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:12:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:12:11: 7000000 INFO @ Sat, 15 Jan 2022 19:12:16: 4000000 INFO @ Sat, 15 Jan 2022 19:12:16: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:12:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:12:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:12:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.05_summits.bed INFO @ Sat, 15 Jan 2022 19:12:18: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (37 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:12:18: 8000000 INFO @ Sat, 15 Jan 2022 19:12:23: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:12:26: 9000000 INFO @ Sat, 15 Jan 2022 19:12:29: 6000000 INFO @ Sat, 15 Jan 2022 19:12:34: 10000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:12:36: 7000000 INFO @ Sat, 15 Jan 2022 19:12:42: 11000000 INFO @ Sat, 15 Jan 2022 19:12:43: 8000000 INFO @ Sat, 15 Jan 2022 19:12:45: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:12:45: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:12:45: #1 total tags in treatment: 3458883 INFO @ Sat, 15 Jan 2022 19:12:45: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:12:45: #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 19:12:45: #1 tags after filtering in treatment: 2740824 INFO @ Sat, 15 Jan 2022 19:12:45: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:12:45: #1 finished! INFO @ Sat, 15 Jan 2022 19:12:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:12:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:12:45: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 19:12:45: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 19:12:45: start model_add_line... INFO @ Sat, 15 Jan 2022 19:12:45: start X-correlation... INFO @ Sat, 15 Jan 2022 19:12:45: end of X-cor INFO @ Sat, 15 Jan 2022 19:12:45: #2 finished! INFO @ Sat, 15 Jan 2022 19:12:45: #2 predicted fragment length is 252 bps INFO @ Sat, 15 Jan 2022 19:12:45: #2 alternative fragment length(s) may be 77,99,168,186,212,236,238,252,365,481,581 bps INFO @ Sat, 15 Jan 2022 19:12:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.10_model.r INFO @ Sat, 15 Jan 2022 19:12:45: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:12:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:12:49: 9000000 INFO @ Sat, 15 Jan 2022 19:12:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:12:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:12:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:12:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.10_summits.bed INFO @ Sat, 15 Jan 2022 19:12:52: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (15 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:12:56: 10000000 INFO @ Sat, 15 Jan 2022 19:13:02: 11000000 INFO @ Sat, 15 Jan 2022 19:13:04: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:13:04: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:13:04: #1 total tags in treatment: 3458883 INFO @ Sat, 15 Jan 2022 19:13:04: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:13:04: #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 19:13:04: #1 tags after filtering in treatment: 2740824 INFO @ Sat, 15 Jan 2022 19:13:04: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:13:04: #1 finished! INFO @ Sat, 15 Jan 2022 19:13:04: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:13:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:13:04: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 19:13:04: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 19:13:04: start model_add_line... INFO @ Sat, 15 Jan 2022 19:13:04: start X-correlation... INFO @ Sat, 15 Jan 2022 19:13:04: end of X-cor INFO @ Sat, 15 Jan 2022 19:13:04: #2 finished! INFO @ Sat, 15 Jan 2022 19:13:04: #2 predicted fragment length is 252 bps INFO @ Sat, 15 Jan 2022 19:13:04: #2 alternative fragment length(s) may be 77,99,168,186,212,236,238,252,365,481,581 bps INFO @ Sat, 15 Jan 2022 19:13:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.20_model.r INFO @ Sat, 15 Jan 2022 19:13:04: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:13:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:13:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:13:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:13:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:13:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781119/SRX11781119.20_summits.bed INFO @ Sat, 15 Jan 2022 19:13:12: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 18 millis CompletedMACS2peakCalling