Job ID = 10224072 SRX = SRX8952629 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10151367 spots for SRR12458257/SRR12458257.sra Written 10151367 spots for SRR12458257/SRR12458257.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: 00:00:01 Multiseed full-index search: 00:03:06 10151367 reads; of these: 10151367 (100.00%) were paired; of these: 9520891 (93.79%) aligned concordantly 0 times 530256 (5.22%) aligned concordantly exactly 1 time 100220 (0.99%) aligned concordantly >1 times ---- 9520891 pairs aligned concordantly 0 times; of these: 1731697 (18.19%) aligned discordantly 1 time ---- 7789194 pairs aligned 0 times concordantly or discordantly; of these: 15578388 mates make up the pairs; of these: 10705924 (68.72%) aligned 0 times 4267806 (27.40%) aligned exactly 1 time 604658 (3.88%) aligned >1 times 47.27% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 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] 1751018 / 2337752 = 0.7490 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 09:26:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.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 09:26:17: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:26:17: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:26:21: 1000000 INFO @ Fri, 16 Oct 2020 09:26:25: 2000000 INFO @ Fri, 16 Oct 2020 09:26:29: 3000000 INFO @ Fri, 16 Oct 2020 09:26:32: 4000000 INFO @ Fri, 16 Oct 2020 09:26:36: 5000000 INFO @ Fri, 16 Oct 2020 09:26:40: 6000000 INFO @ Fri, 16 Oct 2020 09:26:41: #1 tag size is determined as 41 bps INFO @ Fri, 16 Oct 2020 09:26:41: #1 tag size = 41 INFO @ Fri, 16 Oct 2020 09:26:41: #1 total tags in treatment: 453778 INFO @ Fri, 16 Oct 2020 09:26:41: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:26:41: #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 09:26:41: #1 tags after filtering in treatment: 381460 INFO @ Fri, 16 Oct 2020 09:26:41: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 16 Oct 2020 09:26:41: #1 finished! INFO @ Fri, 16 Oct 2020 09:26:41: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:26:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:26:41: #2 number of paired peaks: 184 WARNING @ Fri, 16 Oct 2020 09:26:41: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Fri, 16 Oct 2020 09:26:41: start model_add_line... INFO @ Fri, 16 Oct 2020 09:26:41: start X-correlation... INFO @ Fri, 16 Oct 2020 09:26:41: end of X-cor INFO @ Fri, 16 Oct 2020 09:26:41: #2 finished! INFO @ Fri, 16 Oct 2020 09:26:41: #2 predicted fragment length is 305 bps INFO @ Fri, 16 Oct 2020 09:26:41: #2 alternative fragment length(s) may be 4,305 bps INFO @ Fri, 16 Oct 2020 09:26:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.05_model.r INFO @ Fri, 16 Oct 2020 09:26:41: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:26:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:26:42: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:26:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:26:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:26:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.05_summits.bed INFO @ Fri, 16 Oct 2020 09:26:43: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (83 records, 4 fields): 13 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 09:26:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.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 09:26:47: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:26:47: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:26:51: 1000000 INFO @ Fri, 16 Oct 2020 09:26:55: 2000000 INFO @ Fri, 16 Oct 2020 09:26:59: 3000000 INFO @ Fri, 16 Oct 2020 09:27:02: 4000000 INFO @ Fri, 16 Oct 2020 09:27:06: 5000000 INFO @ Fri, 16 Oct 2020 09:27:10: 6000000 INFO @ Fri, 16 Oct 2020 09:27:11: #1 tag size is determined as 41 bps INFO @ Fri, 16 Oct 2020 09:27:11: #1 tag size = 41 INFO @ Fri, 16 Oct 2020 09:27:11: #1 total tags in treatment: 453778 INFO @ Fri, 16 Oct 2020 09:27:11: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:27:11: #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 09:27:11: #1 tags after filtering in treatment: 381460 INFO @ Fri, 16 Oct 2020 09:27:11: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 16 Oct 2020 09:27:11: #1 finished! INFO @ Fri, 16 Oct 2020 09:27:11: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:27:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:27:11: #2 number of paired peaks: 184 WARNING @ Fri, 16 Oct 2020 09:27:11: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Fri, 16 Oct 2020 09:27:11: start model_add_line... INFO @ Fri, 16 Oct 2020 09:27:11: start X-correlation... INFO @ Fri, 16 Oct 2020 09:27:11: end of X-cor INFO @ Fri, 16 Oct 2020 09:27:11: #2 finished! INFO @ Fri, 16 Oct 2020 09:27:11: #2 predicted fragment length is 305 bps INFO @ Fri, 16 Oct 2020 09:27:11: #2 alternative fragment length(s) may be 4,305 bps INFO @ Fri, 16 Oct 2020 09:27:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.10_model.r INFO @ Fri, 16 Oct 2020 09:27:11: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:27:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:27:12: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:27:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:27:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:27:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.10_summits.bed INFO @ Fri, 16 Oct 2020 09:27:13: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (43 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 09:27:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.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 09:27:17: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:27:17: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:27:21: 1000000 INFO @ Fri, 16 Oct 2020 09:27:25: 2000000 INFO @ Fri, 16 Oct 2020 09:27:29: 3000000 INFO @ Fri, 16 Oct 2020 09:27:33: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:27:37: 5000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:27:41: 6000000 INFO @ Fri, 16 Oct 2020 09:27:41: #1 tag size is determined as 41 bps INFO @ Fri, 16 Oct 2020 09:27:41: #1 tag size = 41 INFO @ Fri, 16 Oct 2020 09:27:41: #1 total tags in treatment: 453778 INFO @ Fri, 16 Oct 2020 09:27:41: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:27:41: #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 09:27:41: #1 tags after filtering in treatment: 381460 INFO @ Fri, 16 Oct 2020 09:27:41: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 16 Oct 2020 09:27:41: #1 finished! INFO @ Fri, 16 Oct 2020 09:27:41: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:27:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:27:41: #2 number of paired peaks: 184 WARNING @ Fri, 16 Oct 2020 09:27:41: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Fri, 16 Oct 2020 09:27:41: start model_add_line... INFO @ Fri, 16 Oct 2020 09:27:41: start X-correlation... INFO @ Fri, 16 Oct 2020 09:27:41: end of X-cor INFO @ Fri, 16 Oct 2020 09:27:41: #2 finished! INFO @ Fri, 16 Oct 2020 09:27:41: #2 predicted fragment length is 305 bps INFO @ Fri, 16 Oct 2020 09:27:41: #2 alternative fragment length(s) may be 4,305 bps INFO @ Fri, 16 Oct 2020 09:27:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.20_model.r INFO @ Fri, 16 Oct 2020 09:27:41: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:27:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:27:43: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:27:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:27:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:27:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952629/SRX8952629.20_summits.bed INFO @ Fri, 16 Oct 2020 09:27:43: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (16 records, 4 fields): 2 millis CompletedMACS2peakCalling