Job ID = 14521198 SRX = SRX8245376 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8109132 spots for SRR11684587/SRR11684587.sra Written 8109132 spots for SRR11684587/SRR11684587.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: 00:11:10 8109132 reads; of these: 8109132 (100.00%) were paired; of these: 4214826 (51.98%) aligned concordantly 0 times 2280108 (28.12%) aligned concordantly exactly 1 time 1614198 (19.91%) aligned concordantly >1 times ---- 4214826 pairs aligned concordantly 0 times; of these: 39571 (0.94%) aligned discordantly 1 time ---- 4175255 pairs aligned 0 times concordantly or discordantly; of these: 8350510 mates make up the pairs; of these: 5649846 (67.66%) aligned 0 times 1531369 (18.34%) aligned exactly 1 time 1169295 (14.00%) aligned >1 times 65.16% overall alignment rate Time searching: 00:11:10 Overall time: 00:11:10 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] 183110 / 3933249 = 0.0466 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 20:51:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.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 20:51:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:51:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:51:23: 1000000 INFO @ Sat, 15 Jan 2022 20:51:27: 2000000 INFO @ Sat, 15 Jan 2022 20:51:31: 3000000 INFO @ Sat, 15 Jan 2022 20:51:36: 4000000 INFO @ Sat, 15 Jan 2022 20:51:40: 5000000 INFO @ Sat, 15 Jan 2022 20:51:44: 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 20:51:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.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 20:51:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:51:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:51:49: 7000000 INFO @ Sat, 15 Jan 2022 20:51:53: 1000000 INFO @ Sat, 15 Jan 2022 20:51:53: 8000000 INFO @ Sat, 15 Jan 2022 20:51:58: 2000000 INFO @ Sat, 15 Jan 2022 20:51:58: 9000000 INFO @ Sat, 15 Jan 2022 20:52:02: 3000000 INFO @ Sat, 15 Jan 2022 20:52:02: 10000000 INFO @ Sat, 15 Jan 2022 20:52:03: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:52:03: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:52:03: #1 total tags in treatment: 3711679 INFO @ Sat, 15 Jan 2022 20:52:03: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:52:03: #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 20:52:03: #1 tags after filtering in treatment: 1526533 INFO @ Sat, 15 Jan 2022 20:52:03: #1 Redundant rate of treatment: 0.59 INFO @ Sat, 15 Jan 2022 20:52:03: #1 finished! INFO @ Sat, 15 Jan 2022 20:52:03: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:52:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:52:03: #2 number of paired peaks: 113 WARNING @ Sat, 15 Jan 2022 20:52:03: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Sat, 15 Jan 2022 20:52:03: start model_add_line... INFO @ Sat, 15 Jan 2022 20:52:03: start X-correlation... INFO @ Sat, 15 Jan 2022 20:52:04: end of X-cor INFO @ Sat, 15 Jan 2022 20:52:04: #2 finished! INFO @ Sat, 15 Jan 2022 20:52:04: #2 predicted fragment length is 545 bps INFO @ Sat, 15 Jan 2022 20:52:04: #2 alternative fragment length(s) may be 3,505,513,520,545,561,575 bps INFO @ Sat, 15 Jan 2022 20:52:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.05_model.r INFO @ Sat, 15 Jan 2022 20:52:04: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:52:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:52:07: 4000000 INFO @ Sat, 15 Jan 2022 20:52:11: 5000000 INFO @ Sat, 15 Jan 2022 20:52:15: 6000000 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 20:52:17: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:52:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.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 20:52:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:52:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:52:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:52:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:52:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.05_summits.bed INFO @ Sat, 15 Jan 2022 20:52:19: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (138 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:52:20: 7000000 INFO @ Sat, 15 Jan 2022 20:52:23: 1000000 INFO @ Sat, 15 Jan 2022 20:52:25: 8000000 INFO @ Sat, 15 Jan 2022 20:52:28: 2000000 INFO @ Sat, 15 Jan 2022 20:52:30: 9000000 INFO @ Sat, 15 Jan 2022 20:52:32: 3000000 INFO @ Sat, 15 Jan 2022 20:52:34: 10000000 INFO @ Sat, 15 Jan 2022 20:52:35: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:52:35: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:52:35: #1 total tags in treatment: 3711679 INFO @ Sat, 15 Jan 2022 20:52:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:52:35: #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 20:52:35: #1 tags after filtering in treatment: 1526533 INFO @ Sat, 15 Jan 2022 20:52:35: #1 Redundant rate of treatment: 0.59 INFO @ Sat, 15 Jan 2022 20:52:35: #1 finished! INFO @ Sat, 15 Jan 2022 20:52:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:52:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:52:35: #2 number of paired peaks: 113 WARNING @ Sat, 15 Jan 2022 20:52:35: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Sat, 15 Jan 2022 20:52:35: start model_add_line... INFO @ Sat, 15 Jan 2022 20:52:35: start X-correlation... INFO @ Sat, 15 Jan 2022 20:52:35: end of X-cor INFO @ Sat, 15 Jan 2022 20:52:35: #2 finished! INFO @ Sat, 15 Jan 2022 20:52:35: #2 predicted fragment length is 545 bps INFO @ Sat, 15 Jan 2022 20:52:35: #2 alternative fragment length(s) may be 3,505,513,520,545,561,575 bps INFO @ Sat, 15 Jan 2022 20:52:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.10_model.r INFO @ Sat, 15 Jan 2022 20:52:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:52:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:52:37: 4000000 INFO @ Sat, 15 Jan 2022 20:52:41: 5000000 INFO @ Sat, 15 Jan 2022 20:52:46: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:52:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:52:50: 7000000 INFO @ Sat, 15 Jan 2022 20:52:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:52:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:52:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.10_summits.bed INFO @ Sat, 15 Jan 2022 20:52:50: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (102 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:52:54: 8000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:52:59: 9000000 INFO @ Sat, 15 Jan 2022 20:53:03: 10000000 INFO @ Sat, 15 Jan 2022 20:53:04: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:53:04: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:53:04: #1 total tags in treatment: 3711679 INFO @ Sat, 15 Jan 2022 20:53:04: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:53:04: #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 20:53:04: #1 tags after filtering in treatment: 1526533 INFO @ Sat, 15 Jan 2022 20:53:04: #1 Redundant rate of treatment: 0.59 INFO @ Sat, 15 Jan 2022 20:53:04: #1 finished! INFO @ Sat, 15 Jan 2022 20:53:04: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:53:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:53:04: #2 number of paired peaks: 113 WARNING @ Sat, 15 Jan 2022 20:53:04: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Sat, 15 Jan 2022 20:53:04: start model_add_line... INFO @ Sat, 15 Jan 2022 20:53:04: start X-correlation... INFO @ Sat, 15 Jan 2022 20:53:04: end of X-cor INFO @ Sat, 15 Jan 2022 20:53:04: #2 finished! INFO @ Sat, 15 Jan 2022 20:53:04: #2 predicted fragment length is 545 bps INFO @ Sat, 15 Jan 2022 20:53:04: #2 alternative fragment length(s) may be 3,505,513,520,545,561,575 bps INFO @ Sat, 15 Jan 2022 20:53:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.20_model.r INFO @ Sat, 15 Jan 2022 20:53:04: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:53:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:53:18: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:53:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:53:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:53:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245376/SRX8245376.20_summits.bed INFO @ Sat, 15 Jan 2022 20:53:19: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (101 records, 4 fields): 1 millis CompletedMACS2peakCalling