Job ID = 10223957 SRX = SRX7496406 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4163176 spots for SRR10823017/SRR10823017.sra Written 4163176 spots for SRR10823017/SRR10823017.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: 00:00:33 4163176 reads; of these: 4163176 (100.00%) were paired; of these: 3822911 (91.83%) aligned concordantly 0 times 284081 (6.82%) aligned concordantly exactly 1 time 56184 (1.35%) aligned concordantly >1 times ---- 3822911 pairs aligned concordantly 0 times; of these: 1389 (0.04%) aligned discordantly 1 time ---- 3821522 pairs aligned 0 times concordantly or discordantly; of these: 7643044 mates make up the pairs; of these: 7357892 (96.27%) aligned 0 times 244897 (3.20%) aligned exactly 1 time 40255 (0.53%) aligned >1 times 11.63% overall alignment rate Time searching: 00:00:33 Overall time: 00:00:33 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] 16742 / 341568 = 0.0490 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 08:58:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.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 08:58:23: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:58:23: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:58:28: #1 tag size is determined as 37 bps INFO @ Fri, 16 Oct 2020 08:58:28: #1 tag size = 37 INFO @ Fri, 16 Oct 2020 08:58:28: #1 total tags in treatment: 323538 INFO @ Fri, 16 Oct 2020 08:58:28: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:58:28: #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 08:58:28: #1 tags after filtering in treatment: 266920 INFO @ Fri, 16 Oct 2020 08:58:28: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 16 Oct 2020 08:58:28: #1 finished! INFO @ Fri, 16 Oct 2020 08:58:28: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:58:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:58:28: #2 number of paired peaks: 269 WARNING @ Fri, 16 Oct 2020 08:58:28: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Fri, 16 Oct 2020 08:58:28: start model_add_line... INFO @ Fri, 16 Oct 2020 08:58:28: start X-correlation... INFO @ Fri, 16 Oct 2020 08:58:28: end of X-cor INFO @ Fri, 16 Oct 2020 08:58:28: #2 finished! INFO @ Fri, 16 Oct 2020 08:58:28: #2 predicted fragment length is 218 bps INFO @ Fri, 16 Oct 2020 08:58:28: #2 alternative fragment length(s) may be 4,28,183,218,251,292,465,467,530,564,584 bps INFO @ Fri, 16 Oct 2020 08:58:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.05_model.r INFO @ Fri, 16 Oct 2020 08:58:28: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:58:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:58:29: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:58:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.05_peaks.xls INFO @ Fri, 16 Oct 2020 08:58:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:58:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.05_summits.bed INFO @ Fri, 16 Oct 2020 08:58:29: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (307 records, 4 fields): 3 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 08:58:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.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 08:58:53: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:58:53: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:58:57: #1 tag size is determined as 37 bps INFO @ Fri, 16 Oct 2020 08:58:57: #1 tag size = 37 INFO @ Fri, 16 Oct 2020 08:58:57: #1 total tags in treatment: 323538 INFO @ Fri, 16 Oct 2020 08:58:57: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:58:57: #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 08:58:57: #1 tags after filtering in treatment: 266920 INFO @ Fri, 16 Oct 2020 08:58:57: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 16 Oct 2020 08:58:57: #1 finished! INFO @ Fri, 16 Oct 2020 08:58:57: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:58:57: #2 number of paired peaks: 269 WARNING @ Fri, 16 Oct 2020 08:58:57: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Fri, 16 Oct 2020 08:58:57: start model_add_line... INFO @ Fri, 16 Oct 2020 08:58:57: start X-correlation... INFO @ Fri, 16 Oct 2020 08:58:57: end of X-cor INFO @ Fri, 16 Oct 2020 08:58:57: #2 finished! INFO @ Fri, 16 Oct 2020 08:58:57: #2 predicted fragment length is 218 bps INFO @ Fri, 16 Oct 2020 08:58:57: #2 alternative fragment length(s) may be 4,28,183,218,251,292,465,467,530,564,584 bps INFO @ Fri, 16 Oct 2020 08:58:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.10_model.r INFO @ Fri, 16 Oct 2020 08:58:57: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:58:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:58:58: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:58:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.10_peaks.xls INFO @ Fri, 16 Oct 2020 08:58:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:58:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.10_summits.bed INFO @ Fri, 16 Oct 2020 08:58:58: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (138 records, 4 fields): 2 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 08:59:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.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 08:59:23: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:59:23: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:59:27: #1 tag size is determined as 37 bps INFO @ Fri, 16 Oct 2020 08:59:27: #1 tag size = 37 INFO @ Fri, 16 Oct 2020 08:59:27: #1 total tags in treatment: 323538 INFO @ Fri, 16 Oct 2020 08:59:27: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:59:27: #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 08:59:27: #1 tags after filtering in treatment: 266920 INFO @ Fri, 16 Oct 2020 08:59:27: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 16 Oct 2020 08:59:27: #1 finished! INFO @ Fri, 16 Oct 2020 08:59:27: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:59:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:59:27: #2 number of paired peaks: 269 WARNING @ Fri, 16 Oct 2020 08:59:27: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Fri, 16 Oct 2020 08:59:27: start model_add_line... INFO @ Fri, 16 Oct 2020 08:59:27: start X-correlation... INFO @ Fri, 16 Oct 2020 08:59:27: end of X-cor INFO @ Fri, 16 Oct 2020 08:59:27: #2 finished! INFO @ Fri, 16 Oct 2020 08:59:27: #2 predicted fragment length is 218 bps INFO @ Fri, 16 Oct 2020 08:59:27: #2 alternative fragment length(s) may be 4,28,183,218,251,292,465,467,530,564,584 bps INFO @ Fri, 16 Oct 2020 08:59:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.20_model.r INFO @ Fri, 16 Oct 2020 08:59:27: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:59:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:59:28: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:59:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.20_peaks.xls INFO @ Fri, 16 Oct 2020 08:59:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:59:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496406/SRX7496406.20_summits.bed INFO @ Fri, 16 Oct 2020 08:59:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (32 records, 4 fields): 1 millis CompletedMACS2peakCalling