Job ID = 14521136 SRX = SRX8245362 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8462832 spots for SRR11684573/SRR11684573.sra Written 8462832 spots for SRR11684573/SRR11684573.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: 00:04:34 8462832 reads; of these: 8462832 (100.00%) were paired; of these: 4183192 (49.43%) aligned concordantly 0 times 3543715 (41.87%) aligned concordantly exactly 1 time 735925 (8.70%) aligned concordantly >1 times ---- 4183192 pairs aligned concordantly 0 times; of these: 119704 (2.86%) aligned discordantly 1 time ---- 4063488 pairs aligned 0 times concordantly or discordantly; of these: 8126976 mates make up the pairs; of these: 4698539 (57.81%) aligned 0 times 2766770 (34.04%) aligned exactly 1 time 661667 (8.14%) aligned >1 times 72.24% overall alignment rate Time searching: 00:04:34 Overall time: 00:04:34 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_sort_core] merging from 8 files... [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] 177038 / 4398811 = 0.0402 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 20:38:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.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 20:38:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:38:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:38:54: 1000000 INFO @ Sat, 15 Jan 2022 20:39:00: 2000000 INFO @ Sat, 15 Jan 2022 20:39:05: 3000000 INFO @ Sat, 15 Jan 2022 20:39:10: 4000000 INFO @ Sat, 15 Jan 2022 20:39:15: 5000000 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 20:39:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.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 20:39:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:39:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:39:21: 6000000 INFO @ Sat, 15 Jan 2022 20:39:25: 1000000 INFO @ Sat, 15 Jan 2022 20:39:27: 7000000 INFO @ Sat, 15 Jan 2022 20:39:32: 2000000 INFO @ Sat, 15 Jan 2022 20:39:33: 8000000 INFO @ Sat, 15 Jan 2022 20:39:38: 3000000 INFO @ Sat, 15 Jan 2022 20:39:39: 9000000 INFO @ Sat, 15 Jan 2022 20:39:44: 4000000 INFO @ Sat, 15 Jan 2022 20:39:45: 10000000 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 20:39:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.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 20:39:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:39:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:39:50: 5000000 INFO @ Sat, 15 Jan 2022 20:39:51: 11000000 INFO @ Sat, 15 Jan 2022 20:39:55: 1000000 INFO @ Sat, 15 Jan 2022 20:39:57: 6000000 INFO @ Sat, 15 Jan 2022 20:39:57: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:39:57: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:39:57: #1 total tags in treatment: 4105231 INFO @ Sat, 15 Jan 2022 20:39:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:39:57: #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 20:39:57: #1 tags after filtering in treatment: 3010866 INFO @ Sat, 15 Jan 2022 20:39:57: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 20:39:57: #1 finished! INFO @ Sat, 15 Jan 2022 20:39:57: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:39:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:39:57: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 20:39:57: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 15 Jan 2022 20:39:57: start model_add_line... INFO @ Sat, 15 Jan 2022 20:39:57: start X-correlation... INFO @ Sat, 15 Jan 2022 20:39:57: end of X-cor INFO @ Sat, 15 Jan 2022 20:39:57: #2 finished! INFO @ Sat, 15 Jan 2022 20:39:57: #2 predicted fragment length is 271 bps INFO @ Sat, 15 Jan 2022 20:39:57: #2 alternative fragment length(s) may be 136,188,222,261,271,283,335 bps INFO @ Sat, 15 Jan 2022 20:39:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.05_model.r INFO @ Sat, 15 Jan 2022 20:39:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:39:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:40:02: 2000000 INFO @ Sat, 15 Jan 2022 20:40:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:40:03: 7000000 INFO @ Sat, 15 Jan 2022 20:40:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:40:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:40:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.05_summits.bed INFO @ Sat, 15 Jan 2022 20:40:05: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (49 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:40:08: 3000000 INFO @ Sat, 15 Jan 2022 20:40:10: 8000000 INFO @ Sat, 15 Jan 2022 20:40:14: 4000000 INFO @ Sat, 15 Jan 2022 20:40:16: 9000000 INFO @ Sat, 15 Jan 2022 20:40:21: 5000000 INFO @ Sat, 15 Jan 2022 20:40:23: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:40:27: 6000000 INFO @ Sat, 15 Jan 2022 20:40:29: 11000000 INFO @ Sat, 15 Jan 2022 20:40:34: 7000000 INFO @ Sat, 15 Jan 2022 20:40:35: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:40:35: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:40:35: #1 total tags in treatment: 4105231 INFO @ Sat, 15 Jan 2022 20:40:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:40:35: #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 20:40:35: #1 tags after filtering in treatment: 3010866 INFO @ Sat, 15 Jan 2022 20:40:35: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 20:40:35: #1 finished! INFO @ Sat, 15 Jan 2022 20:40:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:40:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:40:35: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 20:40:35: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 15 Jan 2022 20:40:35: start model_add_line... INFO @ Sat, 15 Jan 2022 20:40:35: start X-correlation... INFO @ Sat, 15 Jan 2022 20:40:35: end of X-cor INFO @ Sat, 15 Jan 2022 20:40:35: #2 finished! INFO @ Sat, 15 Jan 2022 20:40:35: #2 predicted fragment length is 271 bps INFO @ Sat, 15 Jan 2022 20:40:35: #2 alternative fragment length(s) may be 136,188,222,261,271,283,335 bps INFO @ Sat, 15 Jan 2022 20:40:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.10_model.r INFO @ Sat, 15 Jan 2022 20:40:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:40:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:40:40: 8000000 INFO @ Sat, 15 Jan 2022 20:40:41: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:40:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:40:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:40:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.10_summits.bed INFO @ Sat, 15 Jan 2022 20:40:43: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (18 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:40:46: 9000000 INFO @ Sat, 15 Jan 2022 20:40:52: 10000000 INFO @ Sat, 15 Jan 2022 20:40:57: 11000000 INFO @ Sat, 15 Jan 2022 20:41:02: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:41:02: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:41:02: #1 total tags in treatment: 4105231 INFO @ Sat, 15 Jan 2022 20:41:02: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:41:02: #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 20:41:03: #1 tags after filtering in treatment: 3010866 INFO @ Sat, 15 Jan 2022 20:41:03: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 20:41:03: #1 finished! INFO @ Sat, 15 Jan 2022 20:41:03: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:41:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:41:03: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 20:41:03: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 15 Jan 2022 20:41:03: start model_add_line... INFO @ Sat, 15 Jan 2022 20:41:03: start X-correlation... INFO @ Sat, 15 Jan 2022 20:41:03: end of X-cor INFO @ Sat, 15 Jan 2022 20:41:03: #2 finished! INFO @ Sat, 15 Jan 2022 20:41:03: #2 predicted fragment length is 271 bps INFO @ Sat, 15 Jan 2022 20:41:03: #2 alternative fragment length(s) may be 136,188,222,261,271,283,335 bps INFO @ Sat, 15 Jan 2022 20:41:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.20_model.r INFO @ Sat, 15 Jan 2022 20:41:03: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:41:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:41:09: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:41:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:41:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:41:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245362/SRX8245362.20_summits.bed INFO @ Sat, 15 Jan 2022 20:41:11: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 1 millis CompletedMACS2peakCalling