Job ID = 14520827 SRX = SRX8245534 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8902883 spots for SRR11684745/SRR11684745.sra Written 8902883 spots for SRR11684745/SRR11684745.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: 00:05:27 8902883 reads; of these: 8902883 (100.00%) were paired; of these: 4318916 (48.51%) aligned concordantly 0 times 3889990 (43.69%) aligned concordantly exactly 1 time 693977 (7.79%) aligned concordantly >1 times ---- 4318916 pairs aligned concordantly 0 times; of these: 32049 (0.74%) aligned discordantly 1 time ---- 4286867 pairs aligned 0 times concordantly or discordantly; of these: 8573734 mates make up the pairs; of these: 4769867 (55.63%) aligned 0 times 3200491 (37.33%) aligned exactly 1 time 603376 (7.04%) aligned >1 times 73.21% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 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] 96005 / 4615294 = 0.0208 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 20:13:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.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 20:13:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:13:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:13:55: 1000000 INFO @ Sat, 15 Jan 2022 20:13:59: 2000000 INFO @ Sat, 15 Jan 2022 20:14:04: 3000000 INFO @ Sat, 15 Jan 2022 20:14:08: 4000000 INFO @ Sat, 15 Jan 2022 20:14:13: 5000000 INFO @ Sat, 15 Jan 2022 20:14:17: 6000000 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 20:14:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.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 20:14:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:14:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:14:22: 7000000 INFO @ Sat, 15 Jan 2022 20:14:26: 1000000 INFO @ Sat, 15 Jan 2022 20:14:27: 8000000 INFO @ Sat, 15 Jan 2022 20:14:31: 2000000 INFO @ Sat, 15 Jan 2022 20:14:32: 9000000 INFO @ Sat, 15 Jan 2022 20:14:37: 3000000 INFO @ Sat, 15 Jan 2022 20:14:37: 10000000 INFO @ Sat, 15 Jan 2022 20:14:42: 4000000 INFO @ Sat, 15 Jan 2022 20:14:42: 11000000 INFO @ Sat, 15 Jan 2022 20:14:47: 12000000 INFO @ Sat, 15 Jan 2022 20:14:48: 5000000 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 20:14:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.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 20:14:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:14:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:14:52: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:14:52: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:14:52: #1 total tags in treatment: 4488065 INFO @ Sat, 15 Jan 2022 20:14:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:14:52: #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 20:14:52: #1 tags after filtering in treatment: 3205715 INFO @ Sat, 15 Jan 2022 20:14:52: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 20:14:52: #1 finished! INFO @ Sat, 15 Jan 2022 20:14:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:14:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:14:52: #2 number of paired peaks: 164 WARNING @ Sat, 15 Jan 2022 20:14:52: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Sat, 15 Jan 2022 20:14:52: start model_add_line... INFO @ Sat, 15 Jan 2022 20:14:52: start X-correlation... INFO @ Sat, 15 Jan 2022 20:14:52: end of X-cor INFO @ Sat, 15 Jan 2022 20:14:52: #2 finished! INFO @ Sat, 15 Jan 2022 20:14:52: #2 predicted fragment length is 209 bps INFO @ Sat, 15 Jan 2022 20:14:52: #2 alternative fragment length(s) may be 0,138,142,161,183,209,226,248,282,300,497,513,565 bps INFO @ Sat, 15 Jan 2022 20:14:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.05_model.r INFO @ Sat, 15 Jan 2022 20:14:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:14:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:14:53: 6000000 INFO @ Sat, 15 Jan 2022 20:14:55: 1000000 INFO @ Sat, 15 Jan 2022 20:14:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:14:59: 7000000 INFO @ Sat, 15 Jan 2022 20:15:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:15:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:15:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.05_summits.bed INFO @ Sat, 15 Jan 2022 20:15:00: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (93 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:15:01: 2000000 INFO @ Sat, 15 Jan 2022 20:15:04: 8000000 INFO @ Sat, 15 Jan 2022 20:15:06: 3000000 INFO @ Sat, 15 Jan 2022 20:15:10: 9000000 INFO @ Sat, 15 Jan 2022 20:15:11: 4000000 INFO @ Sat, 15 Jan 2022 20:15:16: 10000000 INFO @ Sat, 15 Jan 2022 20:15:16: 5000000 INFO @ Sat, 15 Jan 2022 20:15:21: 6000000 INFO @ Sat, 15 Jan 2022 20:15:21: 11000000 INFO @ Sat, 15 Jan 2022 20:15:26: 7000000 INFO @ Sat, 15 Jan 2022 20:15:27: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:15:31: 8000000 INFO @ Sat, 15 Jan 2022 20:15:32: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:15:32: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:15:32: #1 total tags in treatment: 4488065 INFO @ Sat, 15 Jan 2022 20:15:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:15:32: #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 20:15:32: #1 tags after filtering in treatment: 3205715 INFO @ Sat, 15 Jan 2022 20:15:32: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 20:15:32: #1 finished! INFO @ Sat, 15 Jan 2022 20:15:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:15:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:15:32: #2 number of paired peaks: 164 WARNING @ Sat, 15 Jan 2022 20:15:32: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Sat, 15 Jan 2022 20:15:32: start model_add_line... INFO @ Sat, 15 Jan 2022 20:15:32: start X-correlation... INFO @ Sat, 15 Jan 2022 20:15:32: end of X-cor INFO @ Sat, 15 Jan 2022 20:15:32: #2 finished! INFO @ Sat, 15 Jan 2022 20:15:32: #2 predicted fragment length is 209 bps INFO @ Sat, 15 Jan 2022 20:15:32: #2 alternative fragment length(s) may be 0,138,142,161,183,209,226,248,282,300,497,513,565 bps INFO @ Sat, 15 Jan 2022 20:15:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.10_model.r INFO @ Sat, 15 Jan 2022 20:15:32: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:15:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:15:36: 9000000 INFO @ Sat, 15 Jan 2022 20:15:38: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:15:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:15:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:15:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.10_summits.bed INFO @ Sat, 15 Jan 2022 20:15:40: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (25 records, 4 fields): 91 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:15:41: 10000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:15:46: 11000000 INFO @ Sat, 15 Jan 2022 20:15:51: 12000000 INFO @ Sat, 15 Jan 2022 20:15:55: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:15:55: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:15:55: #1 total tags in treatment: 4488065 INFO @ Sat, 15 Jan 2022 20:15:55: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:15:55: #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 20:15:55: #1 tags after filtering in treatment: 3205715 INFO @ Sat, 15 Jan 2022 20:15:55: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 20:15:55: #1 finished! INFO @ Sat, 15 Jan 2022 20:15:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:15:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:15:55: #2 number of paired peaks: 164 WARNING @ Sat, 15 Jan 2022 20:15:55: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Sat, 15 Jan 2022 20:15:55: start model_add_line... INFO @ Sat, 15 Jan 2022 20:15:55: start X-correlation... INFO @ Sat, 15 Jan 2022 20:15:55: end of X-cor INFO @ Sat, 15 Jan 2022 20:15:55: #2 finished! INFO @ Sat, 15 Jan 2022 20:15:55: #2 predicted fragment length is 209 bps INFO @ Sat, 15 Jan 2022 20:15:55: #2 alternative fragment length(s) may be 0,138,142,161,183,209,226,248,282,300,497,513,565 bps INFO @ Sat, 15 Jan 2022 20:15:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.20_model.r INFO @ Sat, 15 Jan 2022 20:15:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:15:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:16:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:16:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:16:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:16:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245534/SRX8245534.20_summits.bed INFO @ Sat, 15 Jan 2022 20:16:03: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling