Job ID = 14520395 SRX = SRX11781125 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:01:51 prefetch.2.10.7: 1) Downloading 'SRR15481068'... 2022-01-15T10:01:51 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:02:05 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:02:06 prefetch.2.10.7: 'SRR15481068' is valid 2022-01-15T10:02:06 prefetch.2.10.7: 1) 'SRR15481068' was downloaded successfully 2022-01-15T10:02:06 prefetch.2.10.7: 'SRR15481068' has 0 unresolved dependencies Read 6155357 spots for SRR15481068/SRR15481068.sra Written 6155357 spots for SRR15481068/SRR15481068.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: 00:03:29 6155357 reads; of these: 6155357 (100.00%) were paired; of these: 3947658 (64.13%) aligned concordantly 0 times 2012943 (32.70%) aligned concordantly exactly 1 time 194756 (3.16%) aligned concordantly >1 times ---- 3947658 pairs aligned concordantly 0 times; of these: 37318 (0.95%) aligned discordantly 1 time ---- 3910340 pairs aligned 0 times concordantly or discordantly; of these: 7820680 mates make up the pairs; of these: 4284105 (54.78%) aligned 0 times 3168842 (40.52%) aligned exactly 1 time 367733 (4.70%) aligned >1 times 65.20% overall alignment rate Time searching: 00:03:29 Overall time: 00:03:29 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_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] 207963 / 2244188 = 0.0927 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 19:08:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.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 19:08:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:08:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:08:49: 1000000 INFO @ Sat, 15 Jan 2022 19:08:56: 2000000 INFO @ Sat, 15 Jan 2022 19:09:02: 3000000 INFO @ Sat, 15 Jan 2022 19:09:08: 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 19:09:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.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 19:09:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:09:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:09:15: 5000000 INFO @ Sat, 15 Jan 2022 19:09:20: 1000000 INFO @ Sat, 15 Jan 2022 19:09:21: 6000000 INFO @ Sat, 15 Jan 2022 19:09:26: 2000000 INFO @ Sat, 15 Jan 2022 19:09:28: 7000000 INFO @ Sat, 15 Jan 2022 19:09:32: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:09:32: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:09:32: #1 total tags in treatment: 2001637 INFO @ Sat, 15 Jan 2022 19:09:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:09:32: #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 19:09:32: #1 tags after filtering in treatment: 1589497 INFO @ Sat, 15 Jan 2022 19:09:32: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:09:32: #1 finished! INFO @ Sat, 15 Jan 2022 19:09:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:09:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:09:32: #2 number of paired peaks: 181 WARNING @ Sat, 15 Jan 2022 19:09:32: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Sat, 15 Jan 2022 19:09:32: start model_add_line... INFO @ Sat, 15 Jan 2022 19:09:32: start X-correlation... INFO @ Sat, 15 Jan 2022 19:09:32: end of X-cor INFO @ Sat, 15 Jan 2022 19:09:32: #2 finished! INFO @ Sat, 15 Jan 2022 19:09:32: #2 predicted fragment length is 245 bps INFO @ Sat, 15 Jan 2022 19:09:32: #2 alternative fragment length(s) may be 1,245,281 bps INFO @ Sat, 15 Jan 2022 19:09:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.05_model.r INFO @ Sat, 15 Jan 2022 19:09:32: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:09:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:09:33: 3000000 INFO @ Sat, 15 Jan 2022 19:09:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:09:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:09:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:09:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.05_summits.bed INFO @ Sat, 15 Jan 2022 19:09:38: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (29 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:09:39: 4000000 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 19:09:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.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 19:09:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:09:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:09:46: 5000000 INFO @ Sat, 15 Jan 2022 19:09:48: 1000000 INFO @ Sat, 15 Jan 2022 19:09:52: 6000000 INFO @ Sat, 15 Jan 2022 19:09:54: 2000000 INFO @ Sat, 15 Jan 2022 19:09:59: 3000000 INFO @ Sat, 15 Jan 2022 19:09:59: 7000000 INFO @ Sat, 15 Jan 2022 19:10:03: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:10:03: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:10:03: #1 total tags in treatment: 2001637 INFO @ Sat, 15 Jan 2022 19:10:03: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:10:03: #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 19:10:03: #1 tags after filtering in treatment: 1589497 INFO @ Sat, 15 Jan 2022 19:10:03: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:10:03: #1 finished! INFO @ Sat, 15 Jan 2022 19:10:03: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:10:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:10:03: #2 number of paired peaks: 181 WARNING @ Sat, 15 Jan 2022 19:10:03: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Sat, 15 Jan 2022 19:10:03: start model_add_line... INFO @ Sat, 15 Jan 2022 19:10:03: start X-correlation... INFO @ Sat, 15 Jan 2022 19:10:03: end of X-cor INFO @ Sat, 15 Jan 2022 19:10:03: #2 finished! INFO @ Sat, 15 Jan 2022 19:10:03: #2 predicted fragment length is 245 bps INFO @ Sat, 15 Jan 2022 19:10:03: #2 alternative fragment length(s) may be 1,245,281 bps INFO @ Sat, 15 Jan 2022 19:10:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.10_model.r INFO @ Sat, 15 Jan 2022 19:10:03: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:10:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:10:04: 4000000 INFO @ Sat, 15 Jan 2022 19:10:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:10:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:10:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:10:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.10_summits.bed INFO @ Sat, 15 Jan 2022 19:10:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:10:10: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:10:15: 6000000 INFO @ Sat, 15 Jan 2022 19:10:20: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:10:23: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:10:23: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:10:23: #1 total tags in treatment: 2001637 INFO @ Sat, 15 Jan 2022 19:10:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:10:23: #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 19:10:23: #1 tags after filtering in treatment: 1589497 INFO @ Sat, 15 Jan 2022 19:10:23: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:10:23: #1 finished! INFO @ Sat, 15 Jan 2022 19:10:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:10:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:10:24: #2 number of paired peaks: 181 WARNING @ Sat, 15 Jan 2022 19:10:24: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Sat, 15 Jan 2022 19:10:24: start model_add_line... INFO @ Sat, 15 Jan 2022 19:10:24: start X-correlation... INFO @ Sat, 15 Jan 2022 19:10:24: end of X-cor INFO @ Sat, 15 Jan 2022 19:10:24: #2 finished! INFO @ Sat, 15 Jan 2022 19:10:24: #2 predicted fragment length is 245 bps INFO @ Sat, 15 Jan 2022 19:10:24: #2 alternative fragment length(s) may be 1,245,281 bps INFO @ Sat, 15 Jan 2022 19:10:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.20_model.r INFO @ Sat, 15 Jan 2022 19:10:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:10:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:10:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:10:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:10:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:10:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781125/SRX11781125.20_summits.bed INFO @ Sat, 15 Jan 2022 19:10:30: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 27 millis CompletedMACS2peakCalling