Job ID = 10223938 SRX = SRX7496389 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11861015 spots for SRR10823000/SRR10823000.sra Written 11861015 spots for SRR10823000/SRR10823000.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 11861015 reads; of these: 11861015 (100.00%) were paired; of these: 9894896 (83.42%) aligned concordantly 0 times 1705191 (14.38%) aligned concordantly exactly 1 time 260928 (2.20%) aligned concordantly >1 times ---- 9894896 pairs aligned concordantly 0 times; of these: 24375 (0.25%) aligned discordantly 1 time ---- 9870521 pairs aligned 0 times concordantly or discordantly; of these: 19741042 mates make up the pairs; of these: 18422232 (93.32%) aligned 0 times 1169510 (5.92%) aligned exactly 1 time 149300 (0.76%) aligned >1 times 22.34% 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] 311856 / 1990270 = 0.1567 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 @ Fri, 16 Oct 2020 08:57:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.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 @ Fri, 16 Oct 2020 08:57:18: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:57:18: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:57:23: 1000000 INFO @ Fri, 16 Oct 2020 08:57:28: 2000000 INFO @ Fri, 16 Oct 2020 08:57:33: 3000000 INFO @ Fri, 16 Oct 2020 08:57:39: 4000000 INFO @ Fri, 16 Oct 2020 08:57:42: #1 tag size is determined as 37 bps INFO @ Fri, 16 Oct 2020 08:57:42: #1 tag size = 37 INFO @ Fri, 16 Oct 2020 08:57:42: #1 total tags in treatment: 1655061 INFO @ Fri, 16 Oct 2020 08:57:42: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:57:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:57:42: #1 tags after filtering in treatment: 859088 INFO @ Fri, 16 Oct 2020 08:57:42: #1 Redundant rate of treatment: 0.48 INFO @ Fri, 16 Oct 2020 08:57:42: #1 finished! INFO @ Fri, 16 Oct 2020 08:57:42: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:57:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:57:42: #2 number of paired peaks: 101 WARNING @ Fri, 16 Oct 2020 08:57:42: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Fri, 16 Oct 2020 08:57:42: start model_add_line... INFO @ Fri, 16 Oct 2020 08:57:42: start X-correlation... INFO @ Fri, 16 Oct 2020 08:57:42: end of X-cor INFO @ Fri, 16 Oct 2020 08:57:42: #2 finished! INFO @ Fri, 16 Oct 2020 08:57:42: #2 predicted fragment length is 188 bps INFO @ Fri, 16 Oct 2020 08:57:42: #2 alternative fragment length(s) may be 188,230 bps INFO @ Fri, 16 Oct 2020 08:57:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.05_model.r INFO @ Fri, 16 Oct 2020 08:57:42: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:57:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:57:45: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:57:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.05_peaks.xls INFO @ Fri, 16 Oct 2020 08:57:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:57:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.05_summits.bed INFO @ Fri, 16 Oct 2020 08:57:46: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (1972 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 @ Fri, 16 Oct 2020 08:57:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.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 @ Fri, 16 Oct 2020 08:57:48: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:57:48: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:57:53: 1000000 INFO @ Fri, 16 Oct 2020 08:57:59: 2000000 INFO @ Fri, 16 Oct 2020 08:58:04: 3000000 INFO @ Fri, 16 Oct 2020 08:58:09: 4000000 INFO @ Fri, 16 Oct 2020 08:58:13: #1 tag size is determined as 37 bps INFO @ Fri, 16 Oct 2020 08:58:13: #1 tag size = 37 INFO @ Fri, 16 Oct 2020 08:58:13: #1 total tags in treatment: 1655061 INFO @ Fri, 16 Oct 2020 08:58:13: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:58:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:58:13: #1 tags after filtering in treatment: 859088 INFO @ Fri, 16 Oct 2020 08:58:13: #1 Redundant rate of treatment: 0.48 INFO @ Fri, 16 Oct 2020 08:58:13: #1 finished! INFO @ Fri, 16 Oct 2020 08:58:13: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:58:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:58:13: #2 number of paired peaks: 101 WARNING @ Fri, 16 Oct 2020 08:58:13: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Fri, 16 Oct 2020 08:58:13: start model_add_line... INFO @ Fri, 16 Oct 2020 08:58:13: start X-correlation... INFO @ Fri, 16 Oct 2020 08:58:13: end of X-cor INFO @ Fri, 16 Oct 2020 08:58:13: #2 finished! INFO @ Fri, 16 Oct 2020 08:58:13: #2 predicted fragment length is 188 bps INFO @ Fri, 16 Oct 2020 08:58:13: #2 alternative fragment length(s) may be 188,230 bps INFO @ Fri, 16 Oct 2020 08:58:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.10_model.r INFO @ Fri, 16 Oct 2020 08:58:13: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:58:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:58:15: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:58:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.10_peaks.xls INFO @ Fri, 16 Oct 2020 08:58:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:58:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.10_summits.bed INFO @ Fri, 16 Oct 2020 08:58:16: Done! BedGraph に変換中... pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (1161 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 @ Fri, 16 Oct 2020 08:58:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.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 @ Fri, 16 Oct 2020 08:58:18: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:58:18: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:58:23: 1000000 INFO @ Fri, 16 Oct 2020 08:58:27: 2000000 INFO @ Fri, 16 Oct 2020 08:58:31: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:58:36: 4000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:58:39: #1 tag size is determined as 37 bps INFO @ Fri, 16 Oct 2020 08:58:39: #1 tag size = 37 INFO @ Fri, 16 Oct 2020 08:58:39: #1 total tags in treatment: 1655061 INFO @ Fri, 16 Oct 2020 08:58:39: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:58:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:58:39: #1 tags after filtering in treatment: 859088 INFO @ Fri, 16 Oct 2020 08:58:39: #1 Redundant rate of treatment: 0.48 INFO @ Fri, 16 Oct 2020 08:58:39: #1 finished! INFO @ Fri, 16 Oct 2020 08:58:39: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:58:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:58:39: #2 number of paired peaks: 101 WARNING @ Fri, 16 Oct 2020 08:58:39: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Fri, 16 Oct 2020 08:58:39: start model_add_line... INFO @ Fri, 16 Oct 2020 08:58:39: start X-correlation... INFO @ Fri, 16 Oct 2020 08:58:39: end of X-cor INFO @ Fri, 16 Oct 2020 08:58:39: #2 finished! INFO @ Fri, 16 Oct 2020 08:58:39: #2 predicted fragment length is 188 bps INFO @ Fri, 16 Oct 2020 08:58:39: #2 alternative fragment length(s) may be 188,230 bps INFO @ Fri, 16 Oct 2020 08:58:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.20_model.r INFO @ Fri, 16 Oct 2020 08:58:39: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:58:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:58:42: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:58:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.20_peaks.xls INFO @ Fri, 16 Oct 2020 08:58:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:58:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496389/SRX7496389.20_summits.bed INFO @ Fri, 16 Oct 2020 08:58:43: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (487 records, 4 fields): 2 millis CompletedMACS2peakCalling