Job ID = 14520436 SRX = SRX11781141 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:05:51 prefetch.2.10.7: 1) Downloading 'SRR15481084'... 2022-01-15T10:05:51 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:06:07 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:06:07 prefetch.2.10.7: 'SRR15481084' is valid 2022-01-15T10:06:07 prefetch.2.10.7: 1) 'SRR15481084' was downloaded successfully 2022-01-15T10:06:07 prefetch.2.10.7: 'SRR15481084' has 0 unresolved dependencies Read 6532351 spots for SRR15481084/SRR15481084.sra Written 6532351 spots for SRR15481084/SRR15481084.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: 00:02:41 6532351 reads; of these: 6532351 (100.00%) were paired; of these: 4248528 (65.04%) aligned concordantly 0 times 2006757 (30.72%) aligned concordantly exactly 1 time 277066 (4.24%) aligned concordantly >1 times ---- 4248528 pairs aligned concordantly 0 times; of these: 48638 (1.14%) aligned discordantly 1 time ---- 4199890 pairs aligned 0 times concordantly or discordantly; of these: 8399780 mates make up the pairs; of these: 4636969 (55.20%) aligned 0 times 3276329 (39.00%) aligned exactly 1 time 486482 (5.79%) aligned >1 times 64.51% overall alignment rate Time searching: 00:02:41 Overall time: 00:02:41 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] 294863 / 2331567 = 0.1265 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 19:11:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.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 19:11:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:11:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:11:29: 1000000 INFO @ Sat, 15 Jan 2022 19:11:34: 2000000 INFO @ Sat, 15 Jan 2022 19:11:39: 3000000 INFO @ Sat, 15 Jan 2022 19:11:43: 4000000 INFO @ Sat, 15 Jan 2022 19:11:48: 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 19:11:53: 6000000 INFO @ Sat, 15 Jan 2022 19:11:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.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 19:11:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:11:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:11:58: 7000000 INFO @ Sat, 15 Jan 2022 19:12:00: 1000000 INFO @ Sat, 15 Jan 2022 19:12:03: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:12:03: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:12:03: #1 total tags in treatment: 1992268 INFO @ Sat, 15 Jan 2022 19:12:03: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:12:03: #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 19:12:03: #1 tags after filtering in treatment: 1366915 INFO @ Sat, 15 Jan 2022 19:12:03: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 19:12:03: #1 finished! INFO @ Sat, 15 Jan 2022 19:12:03: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:12:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:12:03: #2 number of paired peaks: 177 WARNING @ Sat, 15 Jan 2022 19:12:03: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sat, 15 Jan 2022 19:12:03: start model_add_line... INFO @ Sat, 15 Jan 2022 19:12:03: start X-correlation... INFO @ Sat, 15 Jan 2022 19:12:03: end of X-cor INFO @ Sat, 15 Jan 2022 19:12:03: #2 finished! INFO @ Sat, 15 Jan 2022 19:12:03: #2 predicted fragment length is 245 bps INFO @ Sat, 15 Jan 2022 19:12:03: #2 alternative fragment length(s) may be 0,206,216,223,230,245,287 bps INFO @ Sat, 15 Jan 2022 19:12:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.05_model.r INFO @ Sat, 15 Jan 2022 19:12:03: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:12:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:12:05: 2000000 INFO @ Sat, 15 Jan 2022 19:12:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:12:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:12:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:12:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.05_summits.bed INFO @ Sat, 15 Jan 2022 19:12:08: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (23 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:12:10: 3000000 INFO @ Sat, 15 Jan 2022 19:12:15: 4000000 INFO @ Sat, 15 Jan 2022 19:12:20: 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 19:12:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.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 19:12:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:12:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:12:26: 6000000 INFO @ Sat, 15 Jan 2022 19:12:31: 1000000 INFO @ Sat, 15 Jan 2022 19:12:32: 7000000 INFO @ Sat, 15 Jan 2022 19:12:37: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:12:37: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:12:37: #1 total tags in treatment: 1992268 INFO @ Sat, 15 Jan 2022 19:12:37: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:12:37: #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 19:12:37: #1 tags after filtering in treatment: 1366915 INFO @ Sat, 15 Jan 2022 19:12:37: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 19:12:37: #1 finished! INFO @ Sat, 15 Jan 2022 19:12:37: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:12:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:12:37: #2 number of paired peaks: 177 WARNING @ Sat, 15 Jan 2022 19:12:37: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sat, 15 Jan 2022 19:12:37: start model_add_line... INFO @ Sat, 15 Jan 2022 19:12:37: start X-correlation... INFO @ Sat, 15 Jan 2022 19:12:37: end of X-cor INFO @ Sat, 15 Jan 2022 19:12:37: #2 finished! INFO @ Sat, 15 Jan 2022 19:12:37: #2 predicted fragment length is 245 bps INFO @ Sat, 15 Jan 2022 19:12:37: #2 alternative fragment length(s) may be 0,206,216,223,230,245,287 bps INFO @ Sat, 15 Jan 2022 19:12:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.10_model.r INFO @ Sat, 15 Jan 2022 19:12:38: 2000000 INFO @ Sat, 15 Jan 2022 19:12:38: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:12:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:12:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:12:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:12:44: 3000000 INFO @ Sat, 15 Jan 2022 19:12:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:12:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.10_summits.bed INFO @ Sat, 15 Jan 2022 19:12:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:12:49: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:12:55: 5000000 INFO @ Sat, 15 Jan 2022 19:13:01: 6000000 INFO @ Sat, 15 Jan 2022 19:13:06: 7000000 INFO @ Sat, 15 Jan 2022 19:13:11: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:13:11: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:13:11: #1 total tags in treatment: 1992268 INFO @ Sat, 15 Jan 2022 19:13:11: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:13:11: #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 19:13:11: #1 tags after filtering in treatment: 1366915 INFO @ Sat, 15 Jan 2022 19:13:11: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 19:13:11: #1 finished! INFO @ Sat, 15 Jan 2022 19:13:11: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:13:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:13:11: #2 number of paired peaks: 177 WARNING @ Sat, 15 Jan 2022 19:13:11: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sat, 15 Jan 2022 19:13:11: start model_add_line... INFO @ Sat, 15 Jan 2022 19:13:11: start X-correlation... INFO @ Sat, 15 Jan 2022 19:13:11: end of X-cor INFO @ Sat, 15 Jan 2022 19:13:11: #2 finished! INFO @ Sat, 15 Jan 2022 19:13:11: #2 predicted fragment length is 245 bps INFO @ Sat, 15 Jan 2022 19:13:11: #2 alternative fragment length(s) may be 0,206,216,223,230,245,287 bps INFO @ Sat, 15 Jan 2022 19:13:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.20_model.r INFO @ Sat, 15 Jan 2022 19:13:11: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:13:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:13:14: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:13:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:13:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:13:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781141/SRX11781141.20_summits.bed INFO @ Sat, 15 Jan 2022 19:13:16: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis CompletedMACS2peakCalling