Job ID = 10224078 SRX = SRX8952634 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4011523 spots for SRR12458252/SRR12458252.sra Written 4011523 spots for SRR12458252/SRR12458252.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: 00:01:20 4011523 reads; of these: 4011523 (100.00%) were paired; of these: 2868707 (71.51%) aligned concordantly 0 times 1027378 (25.61%) aligned concordantly exactly 1 time 115438 (2.88%) aligned concordantly >1 times ---- 2868707 pairs aligned concordantly 0 times; of these: 342179 (11.93%) aligned discordantly 1 time ---- 2526528 pairs aligned 0 times concordantly or discordantly; of these: 5053056 mates make up the pairs; of these: 3936833 (77.91%) aligned 0 times 972502 (19.25%) aligned exactly 1 time 143721 (2.84%) aligned >1 times 50.93% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 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] 415737 / 1462308 = 0.2843 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 09:23:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.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 09:23:24: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:23:24: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:23:29: 1000000 INFO @ Fri, 16 Oct 2020 09:23:33: 2000000 INFO @ Fri, 16 Oct 2020 09:23:39: 3000000 INFO @ Fri, 16 Oct 2020 09:23:40: #1 tag size is determined as 41 bps INFO @ Fri, 16 Oct 2020 09:23:40: #1 tag size = 41 INFO @ Fri, 16 Oct 2020 09:23:40: #1 total tags in treatment: 930514 INFO @ Fri, 16 Oct 2020 09:23:40: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:23:40: #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 09:23:40: #1 tags after filtering in treatment: 862445 INFO @ Fri, 16 Oct 2020 09:23:40: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 16 Oct 2020 09:23:40: #1 finished! INFO @ Fri, 16 Oct 2020 09:23:40: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:23:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:23:40: #2 number of paired peaks: 202 WARNING @ Fri, 16 Oct 2020 09:23:40: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Fri, 16 Oct 2020 09:23:40: start model_add_line... INFO @ Fri, 16 Oct 2020 09:23:40: start X-correlation... INFO @ Fri, 16 Oct 2020 09:23:40: end of X-cor INFO @ Fri, 16 Oct 2020 09:23:40: #2 finished! INFO @ Fri, 16 Oct 2020 09:23:40: #2 predicted fragment length is 288 bps INFO @ Fri, 16 Oct 2020 09:23:40: #2 alternative fragment length(s) may be 24,60,86,196,221,258,288,325,363,422 bps INFO @ Fri, 16 Oct 2020 09:23:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.05_model.r INFO @ Fri, 16 Oct 2020 09:23:40: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:23:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:23:42: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:23:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:23:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:23:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.05_summits.bed INFO @ Fri, 16 Oct 2020 09:23:43: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (156 records, 4 fields): 2 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 09:23:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.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 09:23:54: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:23:54: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:23:58: 1000000 INFO @ Fri, 16 Oct 2020 09:24:02: 2000000 INFO @ Fri, 16 Oct 2020 09:24:07: 3000000 INFO @ Fri, 16 Oct 2020 09:24:08: #1 tag size is determined as 41 bps INFO @ Fri, 16 Oct 2020 09:24:08: #1 tag size = 41 INFO @ Fri, 16 Oct 2020 09:24:08: #1 total tags in treatment: 930514 INFO @ Fri, 16 Oct 2020 09:24:08: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:24:08: #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 09:24:08: #1 tags after filtering in treatment: 862445 INFO @ Fri, 16 Oct 2020 09:24:08: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 16 Oct 2020 09:24:08: #1 finished! INFO @ Fri, 16 Oct 2020 09:24:08: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:24:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:24:08: #2 number of paired peaks: 202 WARNING @ Fri, 16 Oct 2020 09:24:08: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Fri, 16 Oct 2020 09:24:08: start model_add_line... INFO @ Fri, 16 Oct 2020 09:24:08: start X-correlation... INFO @ Fri, 16 Oct 2020 09:24:08: end of X-cor INFO @ Fri, 16 Oct 2020 09:24:08: #2 finished! INFO @ Fri, 16 Oct 2020 09:24:08: #2 predicted fragment length is 288 bps INFO @ Fri, 16 Oct 2020 09:24:08: #2 alternative fragment length(s) may be 24,60,86,196,221,258,288,325,363,422 bps INFO @ Fri, 16 Oct 2020 09:24:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.10_model.r INFO @ Fri, 16 Oct 2020 09:24:08: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:24:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:24:10: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:24:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:24:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:24:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.10_summits.bed INFO @ Fri, 16 Oct 2020 09:24:11: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (98 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 09:24:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.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 09:24:24: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:24:24: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:24:28: 1000000 INFO @ Fri, 16 Oct 2020 09:24:32: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:24:36: 3000000 INFO @ Fri, 16 Oct 2020 09:24:37: #1 tag size is determined as 41 bps INFO @ Fri, 16 Oct 2020 09:24:37: #1 tag size = 41 INFO @ Fri, 16 Oct 2020 09:24:37: #1 total tags in treatment: 930514 INFO @ Fri, 16 Oct 2020 09:24:37: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:24:37: #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 09:24:37: #1 tags after filtering in treatment: 862445 INFO @ Fri, 16 Oct 2020 09:24:37: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 16 Oct 2020 09:24:37: #1 finished! INFO @ Fri, 16 Oct 2020 09:24:37: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:24:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:24:37: #2 number of paired peaks: 202 WARNING @ Fri, 16 Oct 2020 09:24:37: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Fri, 16 Oct 2020 09:24:37: start model_add_line... INFO @ Fri, 16 Oct 2020 09:24:37: start X-correlation... INFO @ Fri, 16 Oct 2020 09:24:37: end of X-cor INFO @ Fri, 16 Oct 2020 09:24:37: #2 finished! INFO @ Fri, 16 Oct 2020 09:24:37: #2 predicted fragment length is 288 bps INFO @ Fri, 16 Oct 2020 09:24:37: #2 alternative fragment length(s) may be 24,60,86,196,221,258,288,325,363,422 bps INFO @ Fri, 16 Oct 2020 09:24:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.20_model.r INFO @ Fri, 16 Oct 2020 09:24:37: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:24:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:24:39: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:24:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:24:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:24:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952634/SRX8952634.20_summits.bed INFO @ Fri, 16 Oct 2020 09:24:41: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (45 records, 4 fields): 1 millis CompletedMACS2peakCalling