Job ID = 14521288 SRX = SRX10468530 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2693369 spots for SRR14094841/SRR14094841.sra Written 2693369 spots for SRR14094841/SRR14094841.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: 00:00:58 2693369 reads; of these: 2693369 (100.00%) were paired; of these: 1095996 (40.69%) aligned concordantly 0 times 1354459 (50.29%) aligned concordantly exactly 1 time 242914 (9.02%) aligned concordantly >1 times ---- 1095996 pairs aligned concordantly 0 times; of these: 8400 (0.77%) aligned discordantly 1 time ---- 1087596 pairs aligned 0 times concordantly or discordantly; of these: 2175192 mates make up the pairs; of these: 2137180 (98.25%) aligned 0 times 27500 (1.26%) aligned exactly 1 time 10512 (0.48%) aligned >1 times 60.33% overall alignment rate Time searching: 00:00:58 Overall time: 00:00:58 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] 59805 / 1598718 = 0.0374 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 20:48:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.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 20:48:23: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:48:23: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:48:28: 1000000 INFO @ Sat, 15 Jan 2022 20:48:33: 2000000 INFO @ Sat, 15 Jan 2022 20:48:38: 3000000 INFO @ Sat, 15 Jan 2022 20:48:39: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:48:39: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:48:39: #1 total tags in treatment: 1537591 INFO @ Sat, 15 Jan 2022 20:48:39: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:48:39: #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 20:48:39: #1 tags after filtering in treatment: 1241541 INFO @ Sat, 15 Jan 2022 20:48:39: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 20:48:39: #1 finished! INFO @ Sat, 15 Jan 2022 20:48:39: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:48:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:48:39: #2 number of paired peaks: 605 WARNING @ Sat, 15 Jan 2022 20:48:39: Fewer paired peaks (605) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 605 pairs to build model! INFO @ Sat, 15 Jan 2022 20:48:39: start model_add_line... INFO @ Sat, 15 Jan 2022 20:48:39: start X-correlation... INFO @ Sat, 15 Jan 2022 20:48:39: end of X-cor INFO @ Sat, 15 Jan 2022 20:48:39: #2 finished! INFO @ Sat, 15 Jan 2022 20:48:39: #2 predicted fragment length is 60 bps INFO @ Sat, 15 Jan 2022 20:48:39: #2 alternative fragment length(s) may be 3,60,69,77 bps INFO @ Sat, 15 Jan 2022 20:48:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.05_model.r INFO @ Sat, 15 Jan 2022 20:48:39: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:48:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:48:41: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:48:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:48:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:48:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.05_summits.bed INFO @ Sat, 15 Jan 2022 20:48:43: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (836 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 20:48:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.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 20:48:53: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:48:53: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:48:58: 1000000 INFO @ Sat, 15 Jan 2022 20:49:03: 2000000 INFO @ Sat, 15 Jan 2022 20:49:08: 3000000 INFO @ Sat, 15 Jan 2022 20:49:09: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:49:09: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:49:09: #1 total tags in treatment: 1537591 INFO @ Sat, 15 Jan 2022 20:49:09: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:49:09: #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 20:49:09: #1 tags after filtering in treatment: 1241541 INFO @ Sat, 15 Jan 2022 20:49:09: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 20:49:09: #1 finished! INFO @ Sat, 15 Jan 2022 20:49:09: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:49:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:49:09: #2 number of paired peaks: 605 WARNING @ Sat, 15 Jan 2022 20:49:09: Fewer paired peaks (605) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 605 pairs to build model! INFO @ Sat, 15 Jan 2022 20:49:09: start model_add_line... INFO @ Sat, 15 Jan 2022 20:49:09: start X-correlation... INFO @ Sat, 15 Jan 2022 20:49:09: end of X-cor INFO @ Sat, 15 Jan 2022 20:49:09: #2 finished! INFO @ Sat, 15 Jan 2022 20:49:09: #2 predicted fragment length is 60 bps INFO @ Sat, 15 Jan 2022 20:49:09: #2 alternative fragment length(s) may be 3,60,69,77 bps INFO @ Sat, 15 Jan 2022 20:49:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.10_model.r INFO @ Sat, 15 Jan 2022 20:49:09: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:49:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:49:12: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:49:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:49:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:49:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.10_summits.bed INFO @ Sat, 15 Jan 2022 20:49:13: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (423 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 20:49:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.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 20:49:23: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:49:23: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:49:27: 1000000 INFO @ Sat, 15 Jan 2022 20:49:31: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:49:36: 3000000 INFO @ Sat, 15 Jan 2022 20:49:36: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:49:36: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:49:36: #1 total tags in treatment: 1537591 INFO @ Sat, 15 Jan 2022 20:49:36: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:49:36: #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 20:49:36: #1 tags after filtering in treatment: 1241541 INFO @ Sat, 15 Jan 2022 20:49:36: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 20:49:36: #1 finished! INFO @ Sat, 15 Jan 2022 20:49:36: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:49:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:49:36: #2 number of paired peaks: 605 WARNING @ Sat, 15 Jan 2022 20:49:36: Fewer paired peaks (605) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 605 pairs to build model! INFO @ Sat, 15 Jan 2022 20:49:36: start model_add_line... INFO @ Sat, 15 Jan 2022 20:49:36: start X-correlation... INFO @ Sat, 15 Jan 2022 20:49:36: end of X-cor INFO @ Sat, 15 Jan 2022 20:49:36: #2 finished! INFO @ Sat, 15 Jan 2022 20:49:36: #2 predicted fragment length is 60 bps INFO @ Sat, 15 Jan 2022 20:49:36: #2 alternative fragment length(s) may be 3,60,69,77 bps INFO @ Sat, 15 Jan 2022 20:49:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.20_model.r INFO @ Sat, 15 Jan 2022 20:49:36: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:49:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:49:39: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:49:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:49:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:49:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468530/SRX10468530.20_summits.bed INFO @ Sat, 15 Jan 2022 20:49:40: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (174 records, 4 fields): 2 millis CompletedMACS2peakCalling