Job ID = 7108091 SRX = SRX7438932 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18313653 spots for SRR10764998/SRR10764998.sra Written 18313653 spots for SRR10764998/SRR10764998.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: 00:08:03 18313653 reads; of these: 18313653 (100.00%) were paired; of these: 5107192 (27.89%) aligned concordantly 0 times 10723807 (58.56%) aligned concordantly exactly 1 time 2482654 (13.56%) aligned concordantly >1 times ---- 5107192 pairs aligned concordantly 0 times; of these: 671963 (13.16%) aligned discordantly 1 time ---- 4435229 pairs aligned 0 times concordantly or discordantly; of these: 8870458 mates make up the pairs; of these: 8286035 (93.41%) aligned 0 times 236601 (2.67%) aligned exactly 1 time 347822 (3.92%) aligned >1 times 77.38% overall alignment rate Time searching: 00:08:03 Overall time: 00:08:03 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] 12195983 / 13807204 = 0.8833 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 13:37:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.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 13:37:33: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:37:33: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:37:37: 1000000 INFO @ Wed, 22 Jul 2020 13:37:41: 2000000 INFO @ Wed, 22 Jul 2020 13:37:45: 3000000 INFO @ Wed, 22 Jul 2020 13:37:49: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 13:37:49: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 13:37:49: #1 total tags in treatment: 1476663 INFO @ Wed, 22 Jul 2020 13:37:49: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:37:49: #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 13:37:49: #1 tags after filtering in treatment: 1171349 INFO @ Wed, 22 Jul 2020 13:37:49: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Jul 2020 13:37:49: #1 finished! INFO @ Wed, 22 Jul 2020 13:37:49: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:37:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:37:49: #2 number of paired peaks: 206 WARNING @ Wed, 22 Jul 2020 13:37:49: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Wed, 22 Jul 2020 13:37:49: start model_add_line... INFO @ Wed, 22 Jul 2020 13:37:49: start X-correlation... INFO @ Wed, 22 Jul 2020 13:37:49: end of X-cor INFO @ Wed, 22 Jul 2020 13:37:49: #2 finished! INFO @ Wed, 22 Jul 2020 13:37:49: #2 predicted fragment length is 188 bps INFO @ Wed, 22 Jul 2020 13:37:49: #2 alternative fragment length(s) may be 1,26,49,91,135,156,188,210,224,258,330,361,413,435,469,534,542,592 bps INFO @ Wed, 22 Jul 2020 13:37:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.05_model.r INFO @ Wed, 22 Jul 2020 13:37:49: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:37:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:37:52: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:37:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.05_peaks.xls INFO @ Wed, 22 Jul 2020 13:37:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:37:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.05_summits.bed INFO @ Wed, 22 Jul 2020 13:37:53: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (169 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 13:38:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.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 13:38:02: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:38:02: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:38:06: 1000000 INFO @ Wed, 22 Jul 2020 13:38:10: 2000000 INFO @ Wed, 22 Jul 2020 13:38:14: 3000000 INFO @ Wed, 22 Jul 2020 13:38:18: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 13:38:18: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 13:38:18: #1 total tags in treatment: 1476663 INFO @ Wed, 22 Jul 2020 13:38:18: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:38:18: #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 13:38:18: #1 tags after filtering in treatment: 1171349 INFO @ Wed, 22 Jul 2020 13:38:18: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Jul 2020 13:38:18: #1 finished! INFO @ Wed, 22 Jul 2020 13:38:18: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:38:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:38:18: #2 number of paired peaks: 206 WARNING @ Wed, 22 Jul 2020 13:38:18: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Wed, 22 Jul 2020 13:38:18: start model_add_line... INFO @ Wed, 22 Jul 2020 13:38:18: start X-correlation... INFO @ Wed, 22 Jul 2020 13:38:18: end of X-cor INFO @ Wed, 22 Jul 2020 13:38:18: #2 finished! INFO @ Wed, 22 Jul 2020 13:38:18: #2 predicted fragment length is 188 bps INFO @ Wed, 22 Jul 2020 13:38:18: #2 alternative fragment length(s) may be 1,26,49,91,135,156,188,210,224,258,330,361,413,435,469,534,542,592 bps INFO @ Wed, 22 Jul 2020 13:38:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.10_model.r INFO @ Wed, 22 Jul 2020 13:38:18: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:38:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:38:21: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:38:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.10_peaks.xls INFO @ Wed, 22 Jul 2020 13:38:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:38:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.10_summits.bed INFO @ Wed, 22 Jul 2020 13:38:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (52 records, 4 fields): 11 millis CompletedMACS2peakCalling 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 13:38:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.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 13:38:31: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:38:31: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:38:36: 1000000 INFO @ Wed, 22 Jul 2020 13:38:40: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 13:38:44: 3000000 INFO @ Wed, 22 Jul 2020 13:38:48: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 13:38:48: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 13:38:48: #1 total tags in treatment: 1476663 INFO @ Wed, 22 Jul 2020 13:38:48: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:38:48: #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 13:38:48: #1 tags after filtering in treatment: 1171349 INFO @ Wed, 22 Jul 2020 13:38:48: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Jul 2020 13:38:48: #1 finished! INFO @ Wed, 22 Jul 2020 13:38:48: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:38:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:38:48: #2 number of paired peaks: 206 WARNING @ Wed, 22 Jul 2020 13:38:48: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Wed, 22 Jul 2020 13:38:48: start model_add_line... INFO @ Wed, 22 Jul 2020 13:38:48: start X-correlation... INFO @ Wed, 22 Jul 2020 13:38:48: end of X-cor INFO @ Wed, 22 Jul 2020 13:38:48: #2 finished! INFO @ Wed, 22 Jul 2020 13:38:48: #2 predicted fragment length is 188 bps INFO @ Wed, 22 Jul 2020 13:38:48: #2 alternative fragment length(s) may be 1,26,49,91,135,156,188,210,224,258,330,361,413,435,469,534,542,592 bps INFO @ Wed, 22 Jul 2020 13:38:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.20_model.r INFO @ Wed, 22 Jul 2020 13:38:48: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:38:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 13:38:51: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:38:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.20_peaks.xls INFO @ Wed, 22 Jul 2020 13:38:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:38:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7438932/SRX7438932.20_summits.bed INFO @ Wed, 22 Jul 2020 13:38:52: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis CompletedMACS2peakCalling