Job ID = 10224050 SRX = SRX8952607 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11823839 spots for SRR12458279/SRR12458279.sra Written 11823839 spots for SRR12458279/SRR12458279.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: 00:02:51 11823839 reads; of these: 11823839 (100.00%) were paired; of these: 8910140 (75.36%) aligned concordantly 0 times 2552137 (21.58%) aligned concordantly exactly 1 time 361562 (3.06%) aligned concordantly >1 times ---- 8910140 pairs aligned concordantly 0 times; of these: 442957 (4.97%) aligned discordantly 1 time ---- 8467183 pairs aligned 0 times concordantly or discordantly; of these: 16934366 mates make up the pairs; of these: 15187487 (89.68%) aligned 0 times 1416799 (8.37%) aligned exactly 1 time 330080 (1.95%) aligned >1 times 35.78% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 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] 625935 / 3282168 = 0.1907 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 09:20:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.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 09:20:21: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:20:21: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:20:26: 1000000 INFO @ Fri, 16 Oct 2020 09:20:31: 2000000 INFO @ Fri, 16 Oct 2020 09:20:36: 3000000 INFO @ Fri, 16 Oct 2020 09:20:41: 4000000 INFO @ Fri, 16 Oct 2020 09:20:46: 5000000 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 09:20:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.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 09:20:51: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:20:51: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:20:52: 6000000 INFO @ Fri, 16 Oct 2020 09:20:57: 1000000 INFO @ Fri, 16 Oct 2020 09:20:57: 7000000 INFO @ Fri, 16 Oct 2020 09:20:58: #1 tag size is determined as 44 bps INFO @ Fri, 16 Oct 2020 09:20:58: #1 tag size = 44 INFO @ Fri, 16 Oct 2020 09:20:58: #1 total tags in treatment: 2421795 INFO @ Fri, 16 Oct 2020 09:20:58: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:20:58: #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 09:20:58: #1 tags after filtering in treatment: 1897803 INFO @ Fri, 16 Oct 2020 09:20:58: #1 Redundant rate of treatment: 0.22 INFO @ Fri, 16 Oct 2020 09:20:58: #1 finished! INFO @ Fri, 16 Oct 2020 09:20:58: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:20:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:20:58: #2 number of paired peaks: 136 WARNING @ Fri, 16 Oct 2020 09:20:58: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Fri, 16 Oct 2020 09:20:58: start model_add_line... INFO @ Fri, 16 Oct 2020 09:20:58: start X-correlation... INFO @ Fri, 16 Oct 2020 09:20:58: end of X-cor INFO @ Fri, 16 Oct 2020 09:20:58: #2 finished! INFO @ Fri, 16 Oct 2020 09:20:58: #2 predicted fragment length is 248 bps INFO @ Fri, 16 Oct 2020 09:20:58: #2 alternative fragment length(s) may be 248 bps INFO @ Fri, 16 Oct 2020 09:20:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.05_model.r INFO @ Fri, 16 Oct 2020 09:20:58: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:20:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:21:02: 2000000 INFO @ Fri, 16 Oct 2020 09:21:03: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:21:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:21:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:21:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.05_summits.bed INFO @ Fri, 16 Oct 2020 09:21:05: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (837 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:21:06: 3000000 INFO @ Fri, 16 Oct 2020 09:21:11: 4000000 INFO @ Fri, 16 Oct 2020 09:21:16: 5000000 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 @ Fri, 16 Oct 2020 09:21:20: 6000000 INFO @ Fri, 16 Oct 2020 09:21:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.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 09:21:21: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:21:21: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:21:25: 7000000 INFO @ Fri, 16 Oct 2020 09:21:26: 1000000 INFO @ Fri, 16 Oct 2020 09:21:26: #1 tag size is determined as 44 bps INFO @ Fri, 16 Oct 2020 09:21:26: #1 tag size = 44 INFO @ Fri, 16 Oct 2020 09:21:26: #1 total tags in treatment: 2421795 INFO @ Fri, 16 Oct 2020 09:21:26: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:21:26: #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 09:21:26: #1 tags after filtering in treatment: 1897803 INFO @ Fri, 16 Oct 2020 09:21:26: #1 Redundant rate of treatment: 0.22 INFO @ Fri, 16 Oct 2020 09:21:26: #1 finished! INFO @ Fri, 16 Oct 2020 09:21:26: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:21:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:21:27: #2 number of paired peaks: 136 WARNING @ Fri, 16 Oct 2020 09:21:27: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Fri, 16 Oct 2020 09:21:27: start model_add_line... INFO @ Fri, 16 Oct 2020 09:21:27: start X-correlation... INFO @ Fri, 16 Oct 2020 09:21:27: end of X-cor INFO @ Fri, 16 Oct 2020 09:21:27: #2 finished! INFO @ Fri, 16 Oct 2020 09:21:27: #2 predicted fragment length is 248 bps INFO @ Fri, 16 Oct 2020 09:21:27: #2 alternative fragment length(s) may be 248 bps INFO @ Fri, 16 Oct 2020 09:21:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.10_model.r INFO @ Fri, 16 Oct 2020 09:21:27: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:21:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:21:31: 2000000 INFO @ Fri, 16 Oct 2020 09:21:32: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:21:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:21:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:21:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.10_summits.bed INFO @ Fri, 16 Oct 2020 09:21:33: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (620 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:21:36: 3000000 INFO @ Fri, 16 Oct 2020 09:21:41: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:21:46: 5000000 INFO @ Fri, 16 Oct 2020 09:21:50: 6000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:21:55: 7000000 INFO @ Fri, 16 Oct 2020 09:21:56: #1 tag size is determined as 44 bps INFO @ Fri, 16 Oct 2020 09:21:56: #1 tag size = 44 INFO @ Fri, 16 Oct 2020 09:21:56: #1 total tags in treatment: 2421795 INFO @ Fri, 16 Oct 2020 09:21:56: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:21:56: #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 09:21:56: #1 tags after filtering in treatment: 1897803 INFO @ Fri, 16 Oct 2020 09:21:56: #1 Redundant rate of treatment: 0.22 INFO @ Fri, 16 Oct 2020 09:21:56: #1 finished! INFO @ Fri, 16 Oct 2020 09:21:56: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:21:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:21:56: #2 number of paired peaks: 136 WARNING @ Fri, 16 Oct 2020 09:21:56: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Fri, 16 Oct 2020 09:21:56: start model_add_line... INFO @ Fri, 16 Oct 2020 09:21:56: start X-correlation... INFO @ Fri, 16 Oct 2020 09:21:56: end of X-cor INFO @ Fri, 16 Oct 2020 09:21:56: #2 finished! INFO @ Fri, 16 Oct 2020 09:21:56: #2 predicted fragment length is 248 bps INFO @ Fri, 16 Oct 2020 09:21:56: #2 alternative fragment length(s) may be 248 bps INFO @ Fri, 16 Oct 2020 09:21:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.20_model.r INFO @ Fri, 16 Oct 2020 09:21:56: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:21:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:22:01: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:22:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:22:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:22:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952607/SRX8952607.20_summits.bed INFO @ Fri, 16 Oct 2020 09:22:02: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (442 records, 4 fields): 1 millis CompletedMACS2peakCalling