Job ID = 14520399 SRX = SRX11781127 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:02:06 prefetch.2.10.7: 1) Downloading 'SRR15481070'... 2022-01-15T10:02:06 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:02:15 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:02:15 prefetch.2.10.7: 'SRR15481070' is valid 2022-01-15T10:02:15 prefetch.2.10.7: 1) 'SRR15481070' was downloaded successfully 2022-01-15T10:02:15 prefetch.2.10.7: 'SRR15481070' has 0 unresolved dependencies Read 3768393 spots for SRR15481070/SRR15481070.sra Written 3768393 spots for SRR15481070/SRR15481070.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: 00:02:03 3768393 reads; of these: 3768393 (100.00%) were paired; of these: 2447649 (64.95%) aligned concordantly 0 times 1219355 (32.36%) aligned concordantly exactly 1 time 101389 (2.69%) aligned concordantly >1 times ---- 2447649 pairs aligned concordantly 0 times; of these: 42742 (1.75%) aligned discordantly 1 time ---- 2404907 pairs aligned 0 times concordantly or discordantly; of these: 4809814 mates make up the pairs; of these: 2627490 (54.63%) aligned 0 times 1963807 (40.83%) aligned exactly 1 time 218517 (4.54%) aligned >1 times 65.14% overall alignment rate Time searching: 00:02:03 Overall time: 00:02:03 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] 114469 / 1362940 = 0.0840 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 19:06:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.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 19:06:22: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:06:22: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:06:28: 1000000 INFO @ Sat, 15 Jan 2022 19:06:33: 2000000 INFO @ Sat, 15 Jan 2022 19:06:38: 3000000 INFO @ Sat, 15 Jan 2022 19:06:43: 4000000 INFO @ Sat, 15 Jan 2022 19:06:47: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:06:47: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:06:47: #1 total tags in treatment: 1208232 INFO @ Sat, 15 Jan 2022 19:06:47: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:06:47: #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 19:06:47: #1 tags after filtering in treatment: 948856 INFO @ Sat, 15 Jan 2022 19:06:47: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:06:47: #1 finished! INFO @ Sat, 15 Jan 2022 19:06:47: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:06:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:06:47: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 19:06:47: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 15 Jan 2022 19:06:47: start model_add_line... INFO @ Sat, 15 Jan 2022 19:06:47: start X-correlation... INFO @ Sat, 15 Jan 2022 19:06:47: end of X-cor INFO @ Sat, 15 Jan 2022 19:06:47: #2 finished! INFO @ Sat, 15 Jan 2022 19:06:47: #2 predicted fragment length is 267 bps INFO @ Sat, 15 Jan 2022 19:06:47: #2 alternative fragment length(s) may be 1,226,267 bps INFO @ Sat, 15 Jan 2022 19:06:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.05_model.r INFO @ Sat, 15 Jan 2022 19:06:47: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:06:47: #3 Pre-compute pvalue-qvalue table... 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 19:06:51: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:06:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:06:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:06:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.05_summits.bed INFO @ Sat, 15 Jan 2022 19:06:52: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (29 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:06:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.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 19:06:52: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:06:52: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:06:58: 1000000 INFO @ Sat, 15 Jan 2022 19:07:03: 2000000 INFO @ Sat, 15 Jan 2022 19:07:08: 3000000 INFO @ Sat, 15 Jan 2022 19:07:14: 4000000 INFO @ Sat, 15 Jan 2022 19:07:17: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:07:17: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:07:17: #1 total tags in treatment: 1208232 INFO @ Sat, 15 Jan 2022 19:07:17: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:07:17: #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 19:07:17: #1 tags after filtering in treatment: 948856 INFO @ Sat, 15 Jan 2022 19:07:17: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:07:17: #1 finished! INFO @ Sat, 15 Jan 2022 19:07:17: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:07:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:07:17: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 19:07:17: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 15 Jan 2022 19:07:17: start model_add_line... INFO @ Sat, 15 Jan 2022 19:07:17: start X-correlation... INFO @ Sat, 15 Jan 2022 19:07:17: end of X-cor INFO @ Sat, 15 Jan 2022 19:07:17: #2 finished! INFO @ Sat, 15 Jan 2022 19:07:17: #2 predicted fragment length is 267 bps INFO @ Sat, 15 Jan 2022 19:07:17: #2 alternative fragment length(s) may be 1,226,267 bps INFO @ Sat, 15 Jan 2022 19:07:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.10_model.r INFO @ Sat, 15 Jan 2022 19:07:18: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:07:18: #3 Pre-compute pvalue-qvalue table... 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 19:07:21: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:07:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:07:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:07:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.10_summits.bed INFO @ Sat, 15 Jan 2022 19:07:22: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (11 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:07:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.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 19:07:22: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:07:22: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:07:28: 1000000 INFO @ Sat, 15 Jan 2022 19:07:33: 2000000 INFO @ Sat, 15 Jan 2022 19:07:38: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:07:44: 4000000 INFO @ Sat, 15 Jan 2022 19:07:48: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:07:48: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:07:48: #1 total tags in treatment: 1208232 INFO @ Sat, 15 Jan 2022 19:07:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:07:48: #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 19:07:48: #1 tags after filtering in treatment: 948856 INFO @ Sat, 15 Jan 2022 19:07:48: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:07:48: #1 finished! INFO @ Sat, 15 Jan 2022 19:07:48: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:07:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:07:48: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 19:07:48: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 15 Jan 2022 19:07:48: start model_add_line... INFO @ Sat, 15 Jan 2022 19:07:48: start X-correlation... INFO @ Sat, 15 Jan 2022 19:07:48: end of X-cor INFO @ Sat, 15 Jan 2022 19:07:48: #2 finished! INFO @ Sat, 15 Jan 2022 19:07:48: #2 predicted fragment length is 267 bps INFO @ Sat, 15 Jan 2022 19:07:48: #2 alternative fragment length(s) may be 1,226,267 bps INFO @ Sat, 15 Jan 2022 19:07:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.20_model.r INFO @ Sat, 15 Jan 2022 19:07:48: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:07:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:07:51: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:07:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:07:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:07:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781127/SRX11781127.20_summits.bed INFO @ Sat, 15 Jan 2022 19:07:52: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis CompletedMACS2peakCalling