Job ID = 7105056 SRX = SRX6911529 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5279921 spots for SRR10191140/SRR10191140.sra Written 5279921 spots for SRR10191140/SRR10191140.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: 00:06:41 5279921 reads; of these: 5279921 (100.00%) were paired; of these: 2985188 (56.54%) aligned concordantly 0 times 1379353 (26.12%) aligned concordantly exactly 1 time 915380 (17.34%) aligned concordantly >1 times ---- 2985188 pairs aligned concordantly 0 times; of these: 1126755 (37.74%) aligned discordantly 1 time ---- 1858433 pairs aligned 0 times concordantly or discordantly; of these: 3716866 mates make up the pairs; of these: 1430530 (38.49%) aligned 0 times 542854 (14.61%) aligned exactly 1 time 1743482 (46.91%) aligned >1 times 86.45% overall alignment rate Time searching: 00:06:41 Overall time: 00:06:41 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] 1041111 / 3420445 = 0.3044 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 @ Wed, 22 Jul 2020 12:44:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.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 @ Wed, 22 Jul 2020 12:44:54: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:44:54: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:45:02: 1000000 INFO @ Wed, 22 Jul 2020 12:45:11: 2000000 INFO @ Wed, 22 Jul 2020 12:45:19: 3000000 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 @ Wed, 22 Jul 2020 12:45:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.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 @ Wed, 22 Jul 2020 12:45:24: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:45:24: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:45:28: 4000000 INFO @ Wed, 22 Jul 2020 12:45:33: 1000000 INFO @ Wed, 22 Jul 2020 12:45:37: 5000000 INFO @ Wed, 22 Jul 2020 12:45:43: 2000000 INFO @ Wed, 22 Jul 2020 12:45:46: 6000000 INFO @ Wed, 22 Jul 2020 12:45:52: 3000000 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 @ Wed, 22 Jul 2020 12:45:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.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 @ Wed, 22 Jul 2020 12:45:54: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:45:54: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:45:55: 7000000 INFO @ Wed, 22 Jul 2020 12:45:55: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:45:55: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:45:55: #1 total tags in treatment: 1570179 INFO @ Wed, 22 Jul 2020 12:45:55: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:45:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:45:55: #1 tags after filtering in treatment: 914225 INFO @ Wed, 22 Jul 2020 12:45:55: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Jul 2020 12:45:55: #1 finished! INFO @ Wed, 22 Jul 2020 12:45:55: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:45:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:45:55: #2 number of paired peaks: 164 WARNING @ Wed, 22 Jul 2020 12:45:55: 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 @ Wed, 22 Jul 2020 12:45:55: start model_add_line... INFO @ Wed, 22 Jul 2020 12:45:55: start X-correlation... INFO @ Wed, 22 Jul 2020 12:45:55: end of X-cor INFO @ Wed, 22 Jul 2020 12:45:55: #2 finished! INFO @ Wed, 22 Jul 2020 12:45:55: #2 predicted fragment length is 287 bps INFO @ Wed, 22 Jul 2020 12:45:55: #2 alternative fragment length(s) may be 2,11,50,112,170,228,287,314,587 bps INFO @ Wed, 22 Jul 2020 12:45:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.05_model.r INFO @ Wed, 22 Jul 2020 12:45:55: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:45:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:45:58: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:45:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.05_peaks.xls INFO @ Wed, 22 Jul 2020 12:45:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:45:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.05_summits.bed INFO @ Wed, 22 Jul 2020 12:45:59: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (173 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 12:46:01: 4000000 INFO @ Wed, 22 Jul 2020 12:46:03: 1000000 INFO @ Wed, 22 Jul 2020 12:46:10: 5000000 INFO @ Wed, 22 Jul 2020 12:46:12: 2000000 INFO @ Wed, 22 Jul 2020 12:46:20: 6000000 INFO @ Wed, 22 Jul 2020 12:46:20: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 12:46:29: 7000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 12:46:29: 4000000 INFO @ Wed, 22 Jul 2020 12:46:29: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:46:29: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:46:29: #1 total tags in treatment: 1570179 INFO @ Wed, 22 Jul 2020 12:46:29: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:46:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:46:29: #1 tags after filtering in treatment: 914225 INFO @ Wed, 22 Jul 2020 12:46:29: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Jul 2020 12:46:29: #1 finished! INFO @ Wed, 22 Jul 2020 12:46:29: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:46:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:46:29: #2 number of paired peaks: 164 WARNING @ Wed, 22 Jul 2020 12:46:29: 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 @ Wed, 22 Jul 2020 12:46:29: start model_add_line... INFO @ Wed, 22 Jul 2020 12:46:29: start X-correlation... INFO @ Wed, 22 Jul 2020 12:46:29: end of X-cor INFO @ Wed, 22 Jul 2020 12:46:29: #2 finished! INFO @ Wed, 22 Jul 2020 12:46:29: #2 predicted fragment length is 287 bps INFO @ Wed, 22 Jul 2020 12:46:29: #2 alternative fragment length(s) may be 2,11,50,112,170,228,287,314,587 bps INFO @ Wed, 22 Jul 2020 12:46:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.10_model.r INFO @ Wed, 22 Jul 2020 12:46:29: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:46:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:46:32: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:46:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.10_peaks.xls INFO @ Wed, 22 Jul 2020 12:46:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:46:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.10_summits.bed INFO @ Wed, 22 Jul 2020 12:46:33: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (64 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 12:46:36: 5000000 INFO @ Wed, 22 Jul 2020 12:46:43: 6000000 INFO @ Wed, 22 Jul 2020 12:46:50: 7000000 INFO @ Wed, 22 Jul 2020 12:46:50: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:46:50: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:46:50: #1 total tags in treatment: 1570179 INFO @ Wed, 22 Jul 2020 12:46:50: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:46:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:46:50: #1 tags after filtering in treatment: 914225 INFO @ Wed, 22 Jul 2020 12:46:50: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Jul 2020 12:46:50: #1 finished! INFO @ Wed, 22 Jul 2020 12:46:50: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:46:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:46:50: #2 number of paired peaks: 164 WARNING @ Wed, 22 Jul 2020 12:46:50: 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 @ Wed, 22 Jul 2020 12:46:50: start model_add_line... INFO @ Wed, 22 Jul 2020 12:46:50: start X-correlation... INFO @ Wed, 22 Jul 2020 12:46:50: end of X-cor INFO @ Wed, 22 Jul 2020 12:46:50: #2 finished! INFO @ Wed, 22 Jul 2020 12:46:50: #2 predicted fragment length is 287 bps INFO @ Wed, 22 Jul 2020 12:46:50: #2 alternative fragment length(s) may be 2,11,50,112,170,228,287,314,587 bps INFO @ Wed, 22 Jul 2020 12:46:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.20_model.r INFO @ Wed, 22 Jul 2020 12:46:50: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:46:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:46:53: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:46:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.20_peaks.xls INFO @ Wed, 22 Jul 2020 12:46:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:46:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911529/SRX6911529.20_summits.bed INFO @ Wed, 22 Jul 2020 12:46:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (10 records, 4 fields): 1 millis CompletedMACS2peakCalling