Job ID = 14520800 SRX = SRX8245527 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3589571 spots for SRR11684738/SRR11684738.sra Written 3589571 spots for SRR11684738/SRR11684738.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: 00:01:50 3589571 reads; of these: 3589571 (100.00%) were paired; of these: 2225965 (62.01%) aligned concordantly 0 times 1216426 (33.89%) aligned concordantly exactly 1 time 147180 (4.10%) aligned concordantly >1 times ---- 2225965 pairs aligned concordantly 0 times; of these: 8300 (0.37%) aligned discordantly 1 time ---- 2217665 pairs aligned 0 times concordantly or discordantly; of these: 4435330 mates make up the pairs; of these: 2409191 (54.32%) aligned 0 times 1784864 (40.24%) aligned exactly 1 time 241275 (5.44%) aligned >1 times 66.44% overall alignment rate Time searching: 00:01:50 Overall time: 00:01:50 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] 11172 / 1371629 = 0.0081 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 19:55:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.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 19:55:51: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:55:51: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:55:57: 1000000 INFO @ Sat, 15 Jan 2022 19:56:02: 2000000 INFO @ Sat, 15 Jan 2022 19:56:07: 3000000 INFO @ Sat, 15 Jan 2022 19:56:12: 4000000 INFO @ Sat, 15 Jan 2022 19:56:16: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:56:16: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:56:16: #1 total tags in treatment: 1352458 INFO @ Sat, 15 Jan 2022 19:56:16: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:56:16: #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 19:56:16: #1 tags after filtering in treatment: 1067450 INFO @ Sat, 15 Jan 2022 19:56:16: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:56:16: #1 finished! INFO @ Sat, 15 Jan 2022 19:56:16: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:56:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:56:16: #2 number of paired peaks: 185 WARNING @ Sat, 15 Jan 2022 19:56:16: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sat, 15 Jan 2022 19:56:16: start model_add_line... INFO @ Sat, 15 Jan 2022 19:56:16: start X-correlation... INFO @ Sat, 15 Jan 2022 19:56:16: end of X-cor INFO @ Sat, 15 Jan 2022 19:56:16: #2 finished! INFO @ Sat, 15 Jan 2022 19:56:16: #2 predicted fragment length is 192 bps INFO @ Sat, 15 Jan 2022 19:56:16: #2 alternative fragment length(s) may be 0,126,166,192,206,227,264,567,579 bps INFO @ Sat, 15 Jan 2022 19:56:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.05_model.r INFO @ Sat, 15 Jan 2022 19:56:16: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:56:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:56:19: #3 Call peaks for each chromosome... 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 19:56:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:56:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:56:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.05_summits.bed INFO @ Sat, 15 Jan 2022 19:56:20: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (20 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:56:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.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 19:56:21: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:56:21: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:56:27: 1000000 INFO @ Sat, 15 Jan 2022 19:56:34: 2000000 INFO @ Sat, 15 Jan 2022 19:56:41: 3000000 INFO @ Sat, 15 Jan 2022 19:56:47: 4000000 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 19:56:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.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 19:56:51: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:56:51: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:56:52: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:56:52: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:56:52: #1 total tags in treatment: 1352458 INFO @ Sat, 15 Jan 2022 19:56:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:56:52: #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 19:56:52: #1 tags after filtering in treatment: 1067450 INFO @ Sat, 15 Jan 2022 19:56:52: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:56:52: #1 finished! INFO @ Sat, 15 Jan 2022 19:56:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:56:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:56:52: #2 number of paired peaks: 185 WARNING @ Sat, 15 Jan 2022 19:56:52: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sat, 15 Jan 2022 19:56:52: start model_add_line... INFO @ Sat, 15 Jan 2022 19:56:52: start X-correlation... INFO @ Sat, 15 Jan 2022 19:56:52: end of X-cor INFO @ Sat, 15 Jan 2022 19:56:52: #2 finished! INFO @ Sat, 15 Jan 2022 19:56:52: #2 predicted fragment length is 192 bps INFO @ Sat, 15 Jan 2022 19:56:52: #2 alternative fragment length(s) may be 0,126,166,192,206,227,264,567,579 bps INFO @ Sat, 15 Jan 2022 19:56:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.10_model.r INFO @ Sat, 15 Jan 2022 19:56:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:56:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:56:55: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:56:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:56:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:56:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.10_summits.bed INFO @ Sat, 15 Jan 2022 19:56:56: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (11 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:56:57: 1000000 INFO @ Sat, 15 Jan 2022 19:57:03: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:57:08: 3000000 INFO @ Sat, 15 Jan 2022 19:57:14: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:57:18: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:57:18: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:57:18: #1 total tags in treatment: 1352458 INFO @ Sat, 15 Jan 2022 19:57:18: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:57:18: #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 19:57:18: #1 tags after filtering in treatment: 1067450 INFO @ Sat, 15 Jan 2022 19:57:18: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:57:18: #1 finished! INFO @ Sat, 15 Jan 2022 19:57:18: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:57:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:57:18: #2 number of paired peaks: 185 WARNING @ Sat, 15 Jan 2022 19:57:18: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sat, 15 Jan 2022 19:57:18: start model_add_line... INFO @ Sat, 15 Jan 2022 19:57:18: start X-correlation... INFO @ Sat, 15 Jan 2022 19:57:18: end of X-cor INFO @ Sat, 15 Jan 2022 19:57:18: #2 finished! INFO @ Sat, 15 Jan 2022 19:57:18: #2 predicted fragment length is 192 bps INFO @ Sat, 15 Jan 2022 19:57:18: #2 alternative fragment length(s) may be 0,126,166,192,206,227,264,567,579 bps INFO @ Sat, 15 Jan 2022 19:57:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.20_model.r INFO @ Sat, 15 Jan 2022 19:57:18: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:57:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:57:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:57:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:57:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:57:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245527/SRX8245527.20_summits.bed INFO @ Sat, 15 Jan 2022 19:57:21: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling