Job ID = 14520368 SRX = SRX11781113 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:00:51 prefetch.2.10.7: 1) Downloading 'SRR15481056'... 2022-01-15T10:00:51 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:01:32 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:01:32 prefetch.2.10.7: 1) 'SRR15481056' was downloaded successfully 2022-01-15T10:01:32 prefetch.2.10.7: 'SRR15481056' has 0 unresolved dependencies Read 9965518 spots for SRR15481056/SRR15481056.sra Written 9965518 spots for SRR15481056/SRR15481056.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: 00:06:58 9965518 reads; of these: 9965518 (100.00%) were paired; of these: 6526247 (65.49%) aligned concordantly 0 times 2325594 (23.34%) aligned concordantly exactly 1 time 1113677 (11.18%) aligned concordantly >1 times ---- 6526247 pairs aligned concordantly 0 times; of these: 22963 (0.35%) aligned discordantly 1 time ---- 6503284 pairs aligned 0 times concordantly or discordantly; of these: 13006568 mates make up the pairs; of these: 8964315 (68.92%) aligned 0 times 2705001 (20.80%) aligned exactly 1 time 1337252 (10.28%) aligned >1 times 55.02% overall alignment rate Time searching: 00:06:58 Overall time: 00:06:58 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] 818389 / 3461473 = 0.2364 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 19:12:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.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 19:12:02: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:12:02: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:12:08: 1000000 INFO @ Sat, 15 Jan 2022 19:12:13: 2000000 INFO @ Sat, 15 Jan 2022 19:12:19: 3000000 INFO @ Sat, 15 Jan 2022 19:12:24: 4000000 INFO @ Sat, 15 Jan 2022 19:12:30: 5000000 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 19:12:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.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 19:12:32: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:12:32: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:12:35: 6000000 INFO @ Sat, 15 Jan 2022 19:12:38: 1000000 INFO @ Sat, 15 Jan 2022 19:12:42: 7000000 INFO @ Sat, 15 Jan 2022 19:12:43: 2000000 INFO @ Sat, 15 Jan 2022 19:12:48: 8000000 INFO @ Sat, 15 Jan 2022 19:12:48: 3000000 INFO @ Sat, 15 Jan 2022 19:12:54: 4000000 INFO @ Sat, 15 Jan 2022 19:12:55: 9000000 INFO @ Sat, 15 Jan 2022 19:12:57: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:12:57: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:12:57: #1 total tags in treatment: 2625062 INFO @ Sat, 15 Jan 2022 19:12:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:12:57: #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 19:12:57: #1 tags after filtering in treatment: 1746322 INFO @ Sat, 15 Jan 2022 19:12:57: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 19:12:57: #1 finished! INFO @ Sat, 15 Jan 2022 19:12:57: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:12:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:12:57: #2 number of paired peaks: 129 WARNING @ Sat, 15 Jan 2022 19:12:57: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 15 Jan 2022 19:12:57: start model_add_line... INFO @ Sat, 15 Jan 2022 19:12:57: start X-correlation... INFO @ Sat, 15 Jan 2022 19:12:57: end of X-cor INFO @ Sat, 15 Jan 2022 19:12:57: #2 finished! INFO @ Sat, 15 Jan 2022 19:12:57: #2 predicted fragment length is 181 bps INFO @ Sat, 15 Jan 2022 19:12:57: #2 alternative fragment length(s) may be 1,30,93,124,160,181,215,238,572,576,579 bps INFO @ Sat, 15 Jan 2022 19:12:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.05_model.r INFO @ Sat, 15 Jan 2022 19:12:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:12:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:12:59: 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 19:13:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.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 19:13:02: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:13:02: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:13:02: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:13:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:13:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:13:04: 6000000 INFO @ Sat, 15 Jan 2022 19:13:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.05_summits.bed INFO @ Sat, 15 Jan 2022 19:13:05: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (347 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:13:08: 1000000 INFO @ Sat, 15 Jan 2022 19:13:10: 7000000 INFO @ Sat, 15 Jan 2022 19:13:14: 2000000 INFO @ Sat, 15 Jan 2022 19:13:15: 8000000 INFO @ Sat, 15 Jan 2022 19:13:20: 3000000 INFO @ Sat, 15 Jan 2022 19:13:21: 9000000 INFO @ Sat, 15 Jan 2022 19:13:22: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:13:22: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:13:22: #1 total tags in treatment: 2625062 INFO @ Sat, 15 Jan 2022 19:13:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:13:22: #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 19:13:22: #1 tags after filtering in treatment: 1746322 INFO @ Sat, 15 Jan 2022 19:13:22: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 19:13:22: #1 finished! INFO @ Sat, 15 Jan 2022 19:13:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:13:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:13:23: #2 number of paired peaks: 129 WARNING @ Sat, 15 Jan 2022 19:13:23: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 15 Jan 2022 19:13:23: start model_add_line... INFO @ Sat, 15 Jan 2022 19:13:23: start X-correlation... INFO @ Sat, 15 Jan 2022 19:13:23: end of X-cor INFO @ Sat, 15 Jan 2022 19:13:23: #2 finished! INFO @ Sat, 15 Jan 2022 19:13:23: #2 predicted fragment length is 181 bps INFO @ Sat, 15 Jan 2022 19:13:23: #2 alternative fragment length(s) may be 1,30,93,124,160,181,215,238,572,576,579 bps INFO @ Sat, 15 Jan 2022 19:13:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.10_model.r INFO @ Sat, 15 Jan 2022 19:13:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:13:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:13:26: 4000000 INFO @ Sat, 15 Jan 2022 19:13:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:13:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.10_peaks.xls BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:13:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:13:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.10_summits.bed INFO @ Sat, 15 Jan 2022 19:13:30: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (157 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:13:31: 5000000 INFO @ Sat, 15 Jan 2022 19:13:37: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:13:42: 7000000 INFO @ Sat, 15 Jan 2022 19:13:48: 8000000 INFO @ Sat, 15 Jan 2022 19:13:53: 9000000 INFO @ Sat, 15 Jan 2022 19:13:55: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:13:55: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:13:55: #1 total tags in treatment: 2625062 INFO @ Sat, 15 Jan 2022 19:13:55: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:13:55: #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 19:13:55: #1 tags after filtering in treatment: 1746322 INFO @ Sat, 15 Jan 2022 19:13:55: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 19:13:55: #1 finished! INFO @ Sat, 15 Jan 2022 19:13:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:13:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:13:55: #2 number of paired peaks: 129 WARNING @ Sat, 15 Jan 2022 19:13:55: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 15 Jan 2022 19:13:55: start model_add_line... INFO @ Sat, 15 Jan 2022 19:13:55: start X-correlation... INFO @ Sat, 15 Jan 2022 19:13:55: end of X-cor INFO @ Sat, 15 Jan 2022 19:13:55: #2 finished! INFO @ Sat, 15 Jan 2022 19:13:55: #2 predicted fragment length is 181 bps INFO @ Sat, 15 Jan 2022 19:13:55: #2 alternative fragment length(s) may be 1,30,93,124,160,181,215,238,572,576,579 bps INFO @ Sat, 15 Jan 2022 19:13:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.20_model.r INFO @ Sat, 15 Jan 2022 19:13:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:14:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:14:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:14:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:14:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781113/SRX11781113.20_summits.bed INFO @ Sat, 15 Jan 2022 19:14:02: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (49 records, 4 fields): 2 millis CompletedMACS2peakCalling