Job ID = 14520899 SRX = SRX8245435 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14213280 spots for SRR11684646/SRR11684646.sra Written 14213280 spots for SRR11684646/SRR11684646.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: 00:45:34 14213280 reads; of these: 14213280 (100.00%) were paired; of these: 6044187 (42.52%) aligned concordantly 0 times 3736997 (26.29%) aligned concordantly exactly 1 time 4432096 (31.18%) aligned concordantly >1 times ---- 6044187 pairs aligned concordantly 0 times; of these: 34760 (0.58%) aligned discordantly 1 time ---- 6009427 pairs aligned 0 times concordantly or discordantly; of these: 12018854 mates make up the pairs; of these: 7461129 (62.08%) aligned 0 times 1997106 (16.62%) aligned exactly 1 time 2560619 (21.31%) aligned >1 times 73.75% overall alignment rate Time searching: 00:45:34 Overall time: 00:45:34 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 12 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] 705893 / 8202800 = 0.0861 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 21:02:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.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 21:02:52: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:02:52: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:03:02: 1000000 INFO @ Sat, 15 Jan 2022 21:03:12: 2000000 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 21:03:22: 3000000 INFO @ Sat, 15 Jan 2022 21:03:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.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 21:03:22: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:03:22: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:03:31: 4000000 INFO @ Sat, 15 Jan 2022 21:03:35: 1000000 INFO @ Sat, 15 Jan 2022 21:03:42: 5000000 INFO @ Sat, 15 Jan 2022 21:03:48: 2000000 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 21:03:52: 6000000 INFO @ Sat, 15 Jan 2022 21:03:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.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 21:03:52: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:03:52: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:04:01: 3000000 INFO @ Sat, 15 Jan 2022 21:04:01: 7000000 INFO @ Sat, 15 Jan 2022 21:04:01: 1000000 INFO @ Sat, 15 Jan 2022 21:04:10: 2000000 INFO @ Sat, 15 Jan 2022 21:04:12: 8000000 INFO @ Sat, 15 Jan 2022 21:04:14: 4000000 INFO @ Sat, 15 Jan 2022 21:04:18: 3000000 INFO @ Sat, 15 Jan 2022 21:04:23: 9000000 INFO @ Sat, 15 Jan 2022 21:04:27: 4000000 INFO @ Sat, 15 Jan 2022 21:04:27: 5000000 INFO @ Sat, 15 Jan 2022 21:04:34: 10000000 INFO @ Sat, 15 Jan 2022 21:04:36: 5000000 INFO @ Sat, 15 Jan 2022 21:04:40: 6000000 INFO @ Sat, 15 Jan 2022 21:04:44: 6000000 INFO @ Sat, 15 Jan 2022 21:04:45: 11000000 INFO @ Sat, 15 Jan 2022 21:04:52: 7000000 INFO @ Sat, 15 Jan 2022 21:04:54: 7000000 INFO @ Sat, 15 Jan 2022 21:04:56: 12000000 INFO @ Sat, 15 Jan 2022 21:05:01: 8000000 INFO @ Sat, 15 Jan 2022 21:05:07: 8000000 INFO @ Sat, 15 Jan 2022 21:05:09: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:05:10: 9000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:05:19: 10000000 INFO @ Sat, 15 Jan 2022 21:05:21: 9000000 INFO @ Sat, 15 Jan 2022 21:05:22: 14000000 INFO @ Sat, 15 Jan 2022 21:05:28: 11000000 INFO @ Sat, 15 Jan 2022 21:05:35: 10000000 INFO @ Sat, 15 Jan 2022 21:05:35: 15000000 INFO @ Sat, 15 Jan 2022 21:05:38: 12000000 INFO @ Sat, 15 Jan 2022 21:05:47: 13000000 INFO @ Sat, 15 Jan 2022 21:05:49: 11000000 INFO @ Sat, 15 Jan 2022 21:05:49: 16000000 INFO @ Sat, 15 Jan 2022 21:05:56: 14000000 INFO @ Sat, 15 Jan 2022 21:06:02: 17000000 INFO @ Sat, 15 Jan 2022 21:06:02: 12000000 INFO @ Sat, 15 Jan 2022 21:06:05: 15000000 INFO @ Sat, 15 Jan 2022 21:06:14: 16000000 INFO @ Sat, 15 Jan 2022 21:06:16: 18000000 INFO @ Sat, 15 Jan 2022 21:06:16: 13000000 INFO @ Sat, 15 Jan 2022 21:06:23: 17000000 INFO @ Sat, 15 Jan 2022 21:06:30: 19000000 INFO @ Sat, 15 Jan 2022 21:06:30: 14000000 INFO @ Sat, 15 Jan 2022 21:06:32: 18000000 INFO @ Sat, 15 Jan 2022 21:06:38: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:06:38: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:06:38: #1 total tags in treatment: 7463586 INFO @ Sat, 15 Jan 2022 21:06:38: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:06:38: #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 21:06:38: #1 tags after filtering in treatment: 1704618 INFO @ Sat, 15 Jan 2022 21:06:38: #1 Redundant rate of treatment: 0.77 INFO @ Sat, 15 Jan 2022 21:06:38: #1 finished! INFO @ Sat, 15 Jan 2022 21:06:38: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:06:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:06:38: #2 number of paired peaks: 137 WARNING @ Sat, 15 Jan 2022 21:06:38: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Sat, 15 Jan 2022 21:06:38: start model_add_line... INFO @ Sat, 15 Jan 2022 21:06:38: start X-correlation... INFO @ Sat, 15 Jan 2022 21:06:38: end of X-cor INFO @ Sat, 15 Jan 2022 21:06:38: #2 finished! INFO @ Sat, 15 Jan 2022 21:06:38: #2 predicted fragment length is 413 bps INFO @ Sat, 15 Jan 2022 21:06:38: #2 alternative fragment length(s) may be 4,396,413,446 bps INFO @ Sat, 15 Jan 2022 21:06:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.05_model.r INFO @ Sat, 15 Jan 2022 21:06:38: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:06:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:06:41: 19000000 INFO @ Sat, 15 Jan 2022 21:06:44: 15000000 INFO @ Sat, 15 Jan 2022 21:06:46: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:06:46: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:06:46: #1 total tags in treatment: 7463586 INFO @ Sat, 15 Jan 2022 21:06:46: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:06:46: #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 21:06:47: #1 tags after filtering in treatment: 1704618 INFO @ Sat, 15 Jan 2022 21:06:47: #1 Redundant rate of treatment: 0.77 INFO @ Sat, 15 Jan 2022 21:06:47: #1 finished! INFO @ Sat, 15 Jan 2022 21:06:47: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:06:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:06:47: #2 number of paired peaks: 137 WARNING @ Sat, 15 Jan 2022 21:06:47: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Sat, 15 Jan 2022 21:06:47: start model_add_line... INFO @ Sat, 15 Jan 2022 21:06:47: start X-correlation... INFO @ Sat, 15 Jan 2022 21:06:47: end of X-cor INFO @ Sat, 15 Jan 2022 21:06:47: #2 finished! INFO @ Sat, 15 Jan 2022 21:06:47: #2 predicted fragment length is 413 bps INFO @ Sat, 15 Jan 2022 21:06:47: #2 alternative fragment length(s) may be 4,396,413,446 bps INFO @ Sat, 15 Jan 2022 21:06:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.20_model.r INFO @ Sat, 15 Jan 2022 21:06:47: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:06:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:06:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:06:57: 16000000 INFO @ Sat, 15 Jan 2022 21:06:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:06:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:06:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.05_summits.bed INFO @ Sat, 15 Jan 2022 21:06:58: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (148 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:07:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:07:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:07:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:07:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.20_summits.bed INFO @ Sat, 15 Jan 2022 21:07:05: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (97 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:07:11: 17000000 INFO @ Sat, 15 Jan 2022 21:07:24: 18000000 INFO @ Sat, 15 Jan 2022 21:07:37: 19000000 INFO @ Sat, 15 Jan 2022 21:07:44: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:07:44: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:07:44: #1 total tags in treatment: 7463586 INFO @ Sat, 15 Jan 2022 21:07:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:07:44: #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 21:07:44: #1 tags after filtering in treatment: 1704618 INFO @ Sat, 15 Jan 2022 21:07:44: #1 Redundant rate of treatment: 0.77 INFO @ Sat, 15 Jan 2022 21:07:44: #1 finished! INFO @ Sat, 15 Jan 2022 21:07:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:07:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:07:45: #2 number of paired peaks: 137 WARNING @ Sat, 15 Jan 2022 21:07:45: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Sat, 15 Jan 2022 21:07:45: start model_add_line... INFO @ Sat, 15 Jan 2022 21:07:45: start X-correlation... INFO @ Sat, 15 Jan 2022 21:07:45: end of X-cor INFO @ Sat, 15 Jan 2022 21:07:45: #2 finished! INFO @ Sat, 15 Jan 2022 21:07:45: #2 predicted fragment length is 413 bps INFO @ Sat, 15 Jan 2022 21:07:45: #2 alternative fragment length(s) may be 4,396,413,446 bps INFO @ Sat, 15 Jan 2022 21:07:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.10_model.r INFO @ Sat, 15 Jan 2022 21:07:45: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:07:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:08:02: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:08:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:08:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:08:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245435/SRX8245435.10_summits.bed INFO @ Sat, 15 Jan 2022 21:08:04: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (110 records, 4 fields): 3 millis CompletedMACS2peakCalling