Job ID = 7113504 SRX = SRX8462171 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T05:39:56 prefetch.2.10.7: 1) Downloading 'SRR11915630'... 2020-07-22T05:39:56 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:42:01 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:42:02 prefetch.2.10.7: 'SRR11915630' is valid 2020-07-22T05:42:02 prefetch.2.10.7: 1) 'SRR11915630' was downloaded successfully 2020-07-22T05:42:02 prefetch.2.10.7: 'SRR11915630' has 0 unresolved dependencies Read 5710241 spots for SRR11915630/SRR11915630.sra Written 5710241 spots for SRR11915630/SRR11915630.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: 00:05:23 5710241 reads; of these: 5710241 (100.00%) were paired; of these: 875290 (15.33%) aligned concordantly 0 times 4035722 (70.68%) aligned concordantly exactly 1 time 799229 (14.00%) aligned concordantly >1 times ---- 875290 pairs aligned concordantly 0 times; of these: 37448 (4.28%) aligned discordantly 1 time ---- 837842 pairs aligned 0 times concordantly or discordantly; of these: 1675684 mates make up the pairs; of these: 1551844 (92.61%) aligned 0 times 87052 (5.20%) aligned exactly 1 time 36788 (2.20%) aligned >1 times 86.41% overall alignment rate Time searching: 00:05:23 Overall time: 00:05:23 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] 2424563 / 4869584 = 0.4979 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 14:51:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.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 @ Wed, 22 Jul 2020 14:51:21: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:51:21: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:51:27: 1000000 INFO @ Wed, 22 Jul 2020 14:51:32: 2000000 INFO @ Wed, 22 Jul 2020 14:51:38: 3000000 INFO @ Wed, 22 Jul 2020 14:51:44: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 14:51:50: 5000000 INFO @ Wed, 22 Jul 2020 14:51:50: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 14:51:50: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 14:51:50: #1 total tags in treatment: 2416979 INFO @ Wed, 22 Jul 2020 14:51:50: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:51:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 14:51:50: #1 tags after filtering in treatment: 1778922 INFO @ Wed, 22 Jul 2020 14:51:50: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 22 Jul 2020 14:51:50: #1 finished! INFO @ Wed, 22 Jul 2020 14:51:50: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:51:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:51:50: #2 number of paired peaks: 148 WARNING @ Wed, 22 Jul 2020 14:51:50: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Wed, 22 Jul 2020 14:51:50: start model_add_line... INFO @ Wed, 22 Jul 2020 14:51:50: start X-correlation... INFO @ Wed, 22 Jul 2020 14:51:50: end of X-cor INFO @ Wed, 22 Jul 2020 14:51:50: #2 finished! INFO @ Wed, 22 Jul 2020 14:51:50: #2 predicted fragment length is 280 bps INFO @ Wed, 22 Jul 2020 14:51:50: #2 alternative fragment length(s) may be 280 bps INFO @ Wed, 22 Jul 2020 14:51:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.05_model.r INFO @ Wed, 22 Jul 2020 14:51:50: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:51:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:51:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.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 @ Wed, 22 Jul 2020 14:51:51: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:51:51: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:51:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:51:57: 1000000 INFO @ Wed, 22 Jul 2020 14:51:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.05_peaks.xls INFO @ Wed, 22 Jul 2020 14:51:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:51:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.05_summits.bed INFO @ Wed, 22 Jul 2020 14:51:58: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (745 records, 4 fields): 84 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 14:52:02: 2000000 INFO @ Wed, 22 Jul 2020 14:52:08: 3000000 INFO @ Wed, 22 Jul 2020 14:52:14: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 14:52:20: 5000000 INFO @ Wed, 22 Jul 2020 14:52:20: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 14:52:20: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 14:52:20: #1 total tags in treatment: 2416979 INFO @ Wed, 22 Jul 2020 14:52:20: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:52:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 14:52:20: #1 tags after filtering in treatment: 1778922 INFO @ Wed, 22 Jul 2020 14:52:20: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 22 Jul 2020 14:52:20: #1 finished! INFO @ Wed, 22 Jul 2020 14:52:20: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:52:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:52:20: #2 number of paired peaks: 148 WARNING @ Wed, 22 Jul 2020 14:52:20: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Wed, 22 Jul 2020 14:52:20: start model_add_line... INFO @ Wed, 22 Jul 2020 14:52:20: start X-correlation... INFO @ Wed, 22 Jul 2020 14:52:20: end of X-cor INFO @ Wed, 22 Jul 2020 14:52:20: #2 finished! INFO @ Wed, 22 Jul 2020 14:52:20: #2 predicted fragment length is 280 bps INFO @ Wed, 22 Jul 2020 14:52:20: #2 alternative fragment length(s) may be 280 bps INFO @ Wed, 22 Jul 2020 14:52:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.10_model.r INFO @ Wed, 22 Jul 2020 14:52:20: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:52:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:52:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.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 @ Wed, 22 Jul 2020 14:52:21: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:52:21: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:52:25: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:52:27: 1000000 INFO @ Wed, 22 Jul 2020 14:52:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.10_peaks.xls INFO @ Wed, 22 Jul 2020 14:52:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:52:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.10_summits.bed INFO @ Wed, 22 Jul 2020 14:52:27: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (487 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 14:52:33: 2000000 INFO @ Wed, 22 Jul 2020 14:52:39: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 14:52:45: 4000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 14:52:51: 5000000 INFO @ Wed, 22 Jul 2020 14:52:51: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 14:52:51: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 14:52:51: #1 total tags in treatment: 2416979 INFO @ Wed, 22 Jul 2020 14:52:51: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:52:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 14:52:51: #1 tags after filtering in treatment: 1778922 INFO @ Wed, 22 Jul 2020 14:52:51: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 22 Jul 2020 14:52:51: #1 finished! INFO @ Wed, 22 Jul 2020 14:52:51: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:52:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:52:51: #2 number of paired peaks: 148 WARNING @ Wed, 22 Jul 2020 14:52:51: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Wed, 22 Jul 2020 14:52:51: start model_add_line... INFO @ Wed, 22 Jul 2020 14:52:51: start X-correlation... INFO @ Wed, 22 Jul 2020 14:52:51: end of X-cor INFO @ Wed, 22 Jul 2020 14:52:51: #2 finished! INFO @ Wed, 22 Jul 2020 14:52:51: #2 predicted fragment length is 280 bps INFO @ Wed, 22 Jul 2020 14:52:51: #2 alternative fragment length(s) may be 280 bps INFO @ Wed, 22 Jul 2020 14:52:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.20_model.r INFO @ Wed, 22 Jul 2020 14:52:51: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:52:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:52:57: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:52:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.20_peaks.xls INFO @ Wed, 22 Jul 2020 14:52:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:52:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8462171/SRX8462171.20_summits.bed INFO @ Wed, 22 Jul 2020 14:52:59: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (355 records, 4 fields): 2 millis CompletedMACS2peakCalling