Job ID = 14519716 SRX = SRX8754201 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1877060 spots for SRR12246272/SRR12246272.sra Written 1877060 spots for SRR12246272/SRR12246272.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: 00:00:53 1877060 reads; of these: 1877060 (100.00%) were paired; of these: 297135 (15.83%) aligned concordantly 0 times 1348344 (71.83%) aligned concordantly exactly 1 time 231581 (12.34%) aligned concordantly >1 times ---- 297135 pairs aligned concordantly 0 times; of these: 192267 (64.71%) aligned discordantly 1 time ---- 104868 pairs aligned 0 times concordantly or discordantly; of these: 209736 mates make up the pairs; of these: 105083 (50.10%) aligned 0 times 31640 (15.09%) aligned exactly 1 time 73013 (34.81%) aligned >1 times 97.20% overall alignment rate Time searching: 00:00:53 Overall time: 00:00:53 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] 14662 / 1768278 = 0.0083 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 17:33:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.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 17:33:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:33:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:33:10: 1000000 INFO @ Sat, 15 Jan 2022 17:33:15: 2000000 INFO @ Sat, 15 Jan 2022 17:33:19: 3000000 INFO @ Sat, 15 Jan 2022 17:33:22: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 17:33:22: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 17:33:22: #1 total tags in treatment: 1566444 INFO @ Sat, 15 Jan 2022 17:33:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:33:22: #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 17:33:22: #1 tags after filtering in treatment: 1394510 INFO @ Sat, 15 Jan 2022 17:33:22: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 15 Jan 2022 17:33:22: #1 finished! INFO @ Sat, 15 Jan 2022 17:33:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:33:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:33:22: #2 number of paired peaks: 116 WARNING @ Sat, 15 Jan 2022 17:33:22: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Sat, 15 Jan 2022 17:33:22: start model_add_line... INFO @ Sat, 15 Jan 2022 17:33:22: start X-correlation... INFO @ Sat, 15 Jan 2022 17:33:22: end of X-cor INFO @ Sat, 15 Jan 2022 17:33:22: #2 finished! INFO @ Sat, 15 Jan 2022 17:33:22: #2 predicted fragment length is 268 bps INFO @ Sat, 15 Jan 2022 17:33:22: #2 alternative fragment length(s) may be 2,213,268,297,322 bps INFO @ Sat, 15 Jan 2022 17:33:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.05_model.r INFO @ Sat, 15 Jan 2022 17:33:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:33:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:33:25: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:33:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:33:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:33:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.05_summits.bed INFO @ Sat, 15 Jan 2022 17:33:27: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (33 records, 4 fields): 2 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 17:33:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.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 17:33:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:33:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:33:41: 1000000 INFO @ Sat, 15 Jan 2022 17:33:46: 2000000 INFO @ Sat, 15 Jan 2022 17:33:51: 3000000 INFO @ Sat, 15 Jan 2022 17:33:54: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 17:33:54: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 17:33:54: #1 total tags in treatment: 1566444 INFO @ Sat, 15 Jan 2022 17:33:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:33:54: #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 17:33:54: #1 tags after filtering in treatment: 1394510 INFO @ Sat, 15 Jan 2022 17:33:54: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 15 Jan 2022 17:33:54: #1 finished! INFO @ Sat, 15 Jan 2022 17:33:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:33:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:33:54: #2 number of paired peaks: 116 WARNING @ Sat, 15 Jan 2022 17:33:54: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Sat, 15 Jan 2022 17:33:54: start model_add_line... INFO @ Sat, 15 Jan 2022 17:33:54: start X-correlation... INFO @ Sat, 15 Jan 2022 17:33:54: end of X-cor INFO @ Sat, 15 Jan 2022 17:33:54: #2 finished! INFO @ Sat, 15 Jan 2022 17:33:54: #2 predicted fragment length is 268 bps INFO @ Sat, 15 Jan 2022 17:33:54: #2 alternative fragment length(s) may be 2,213,268,297,322 bps INFO @ Sat, 15 Jan 2022 17:33:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.10_model.r INFO @ Sat, 15 Jan 2022 17:33:54: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:33:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:33:57: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:33:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:33:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:33:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.10_summits.bed INFO @ Sat, 15 Jan 2022 17:33:58: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (20 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 17:34:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.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 17:34:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:34:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:34:10: 1000000 INFO @ Sat, 15 Jan 2022 17:34:15: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:34:19: 3000000 INFO @ Sat, 15 Jan 2022 17:34:22: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 17:34:22: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 17:34:22: #1 total tags in treatment: 1566444 INFO @ Sat, 15 Jan 2022 17:34:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:34:22: #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 17:34:22: #1 tags after filtering in treatment: 1394510 INFO @ Sat, 15 Jan 2022 17:34:22: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 15 Jan 2022 17:34:22: #1 finished! INFO @ Sat, 15 Jan 2022 17:34:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:34:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:34:22: #2 number of paired peaks: 116 WARNING @ Sat, 15 Jan 2022 17:34:22: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Sat, 15 Jan 2022 17:34:22: start model_add_line... INFO @ Sat, 15 Jan 2022 17:34:22: start X-correlation... INFO @ Sat, 15 Jan 2022 17:34:22: end of X-cor INFO @ Sat, 15 Jan 2022 17:34:22: #2 finished! INFO @ Sat, 15 Jan 2022 17:34:22: #2 predicted fragment length is 268 bps INFO @ Sat, 15 Jan 2022 17:34:22: #2 alternative fragment length(s) may be 2,213,268,297,322 bps INFO @ Sat, 15 Jan 2022 17:34:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.20_model.r INFO @ Sat, 15 Jan 2022 17:34:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:34:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:34:25: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:34:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:34:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:34:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8754201/SRX8754201.20_summits.bed INFO @ Sat, 15 Jan 2022 17:34:27: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (5 records, 4 fields): 2 millis CompletedMACS2peakCalling