Job ID = 14520379 SRX = SRX11781118 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:01:06 prefetch.2.10.7: 1) Downloading 'SRR15481061'... 2022-01-15T10:01:06 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:01:36 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:01:36 prefetch.2.10.7: 'SRR15481061' is valid 2022-01-15T10:01:36 prefetch.2.10.7: 1) 'SRR15481061' was downloaded successfully 2022-01-15T10:01:36 prefetch.2.10.7: 'SRR15481061' has 0 unresolved dependencies Read 6092215 spots for SRR15481061/SRR15481061.sra Written 6092215 spots for SRR15481061/SRR15481061.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: 00:03:03 6092215 reads; of these: 6092215 (100.00%) were paired; of these: 3400539 (55.82%) aligned concordantly 0 times 2320165 (38.08%) aligned concordantly exactly 1 time 371511 (6.10%) aligned concordantly >1 times ---- 3400539 pairs aligned concordantly 0 times; of these: 88531 (2.60%) aligned discordantly 1 time ---- 3312008 pairs aligned 0 times concordantly or discordantly; of these: 6624016 mates make up the pairs; of these: 4012343 (60.57%) aligned 0 times 2195658 (33.15%) aligned exactly 1 time 416015 (6.28%) aligned >1 times 67.07% overall alignment rate Time searching: 00:03:03 Overall time: 00:03:03 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] 188930 / 2779821 = 0.0680 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 19:07:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.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 19:07:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:07:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:07:44: 1000000 INFO @ Sat, 15 Jan 2022 19:07:49: 2000000 INFO @ Sat, 15 Jan 2022 19:07:53: 3000000 INFO @ Sat, 15 Jan 2022 19:07:58: 4000000 INFO @ Sat, 15 Jan 2022 19:08:02: 5000000 INFO @ Sat, 15 Jan 2022 19:08:07: 6000000 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 19:08:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.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 19:08:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:08:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:08:12: 7000000 INFO @ Sat, 15 Jan 2022 19:08:15: 1000000 INFO @ Sat, 15 Jan 2022 19:08:16: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:08:16: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:08:16: #1 total tags in treatment: 2506504 INFO @ Sat, 15 Jan 2022 19:08:16: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:08:16: #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 19:08:16: #1 tags after filtering in treatment: 2044920 INFO @ Sat, 15 Jan 2022 19:08:16: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 15 Jan 2022 19:08:16: #1 finished! INFO @ Sat, 15 Jan 2022 19:08:16: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:08:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:08:16: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 19:08:16: 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 19:08:16: start model_add_line... INFO @ Sat, 15 Jan 2022 19:08:16: start X-correlation... INFO @ Sat, 15 Jan 2022 19:08:16: end of X-cor INFO @ Sat, 15 Jan 2022 19:08:16: #2 finished! INFO @ Sat, 15 Jan 2022 19:08:16: #2 predicted fragment length is 288 bps INFO @ Sat, 15 Jan 2022 19:08:16: #2 alternative fragment length(s) may be 0,241,273,288,332,408 bps INFO @ Sat, 15 Jan 2022 19:08:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.05_model.r INFO @ Sat, 15 Jan 2022 19:08:16: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:08:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:08:20: 2000000 INFO @ Sat, 15 Jan 2022 19:08:21: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:08:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:08:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:08:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.05_summits.bed INFO @ Sat, 15 Jan 2022 19:08:23: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (25 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:08:25: 3000000 INFO @ Sat, 15 Jan 2022 19:08:30: 4000000 INFO @ Sat, 15 Jan 2022 19:08:34: 5000000 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 19:08:39: 6000000 INFO @ Sat, 15 Jan 2022 19:08:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.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 19:08:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:08:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:08:45: 7000000 INFO @ Sat, 15 Jan 2022 19:08:46: 1000000 INFO @ Sat, 15 Jan 2022 19:08:49: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:08:49: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:08:49: #1 total tags in treatment: 2506504 INFO @ Sat, 15 Jan 2022 19:08:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:08:49: #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 19:08:49: #1 tags after filtering in treatment: 2044920 INFO @ Sat, 15 Jan 2022 19:08:49: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 15 Jan 2022 19:08:49: #1 finished! INFO @ Sat, 15 Jan 2022 19:08:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:08:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:08:49: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 19:08:49: 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 19:08:49: start model_add_line... INFO @ Sat, 15 Jan 2022 19:08:49: start X-correlation... INFO @ Sat, 15 Jan 2022 19:08:49: end of X-cor INFO @ Sat, 15 Jan 2022 19:08:49: #2 finished! INFO @ Sat, 15 Jan 2022 19:08:49: #2 predicted fragment length is 288 bps INFO @ Sat, 15 Jan 2022 19:08:49: #2 alternative fragment length(s) may be 0,241,273,288,332,408 bps INFO @ Sat, 15 Jan 2022 19:08:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.10_model.r INFO @ Sat, 15 Jan 2022 19:08:49: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:08:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:08:52: 2000000 INFO @ Sat, 15 Jan 2022 19:08:54: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:08:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:08:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:08:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.10_summits.bed INFO @ Sat, 15 Jan 2022 19:08:56: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (12 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:08:58: 3000000 INFO @ Sat, 15 Jan 2022 19:09:04: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:09:10: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:09:15: 6000000 INFO @ Sat, 15 Jan 2022 19:09:21: 7000000 INFO @ Sat, 15 Jan 2022 19:09:25: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:09:25: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:09:25: #1 total tags in treatment: 2506504 INFO @ Sat, 15 Jan 2022 19:09:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:09:25: #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 19:09:26: #1 tags after filtering in treatment: 2044920 INFO @ Sat, 15 Jan 2022 19:09:26: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 15 Jan 2022 19:09:26: #1 finished! INFO @ Sat, 15 Jan 2022 19:09:26: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:09:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:09:26: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 19:09:26: 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 19:09:26: start model_add_line... INFO @ Sat, 15 Jan 2022 19:09:26: start X-correlation... INFO @ Sat, 15 Jan 2022 19:09:26: end of X-cor INFO @ Sat, 15 Jan 2022 19:09:26: #2 finished! INFO @ Sat, 15 Jan 2022 19:09:26: #2 predicted fragment length is 288 bps INFO @ Sat, 15 Jan 2022 19:09:26: #2 alternative fragment length(s) may be 0,241,273,288,332,408 bps INFO @ Sat, 15 Jan 2022 19:09:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.20_model.r INFO @ Sat, 15 Jan 2022 19:09:26: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:09:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:09:31: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:09:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:09:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:09:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781118/SRX11781118.20_summits.bed INFO @ Sat, 15 Jan 2022 19:09:32: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis CompletedMACS2peakCalling