Job ID = 7107452 SRX = SRX6911551 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8737292 spots for SRR10191178/SRR10191178.sra Written 8737292 spots for SRR10191178/SRR10191178.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: 00:07:05 8737292 reads; of these: 8737292 (100.00%) were paired; of these: 3612524 (41.35%) aligned concordantly 0 times 4304821 (49.27%) aligned concordantly exactly 1 time 819947 (9.38%) aligned concordantly >1 times ---- 3612524 pairs aligned concordantly 0 times; of these: 276157 (7.64%) aligned discordantly 1 time ---- 3336367 pairs aligned 0 times concordantly or discordantly; of these: 6672734 mates make up the pairs; of these: 6296521 (94.36%) aligned 0 times 185373 (2.78%) aligned exactly 1 time 190840 (2.86%) aligned >1 times 63.97% overall alignment rate Time searching: 00:07:05 Overall time: 00:07:05 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] 4283513 / 5399774 = 0.7933 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 13:16:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.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 13:16:45: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:16:45: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:16:51: 1000000 INFO @ Wed, 22 Jul 2020 13:16:58: 2000000 INFO @ Wed, 22 Jul 2020 13:17:03: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:17:03: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:17:03: #1 total tags in treatment: 1024799 INFO @ Wed, 22 Jul 2020 13:17:03: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:17:03: #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 13:17:03: #1 tags after filtering in treatment: 689065 INFO @ Wed, 22 Jul 2020 13:17:03: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Jul 2020 13:17:03: #1 finished! INFO @ Wed, 22 Jul 2020 13:17:03: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:17:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:17:03: #2 number of paired peaks: 345 WARNING @ Wed, 22 Jul 2020 13:17:03: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Wed, 22 Jul 2020 13:17:03: start model_add_line... INFO @ Wed, 22 Jul 2020 13:17:03: start X-correlation... INFO @ Wed, 22 Jul 2020 13:17:03: end of X-cor INFO @ Wed, 22 Jul 2020 13:17:03: #2 finished! INFO @ Wed, 22 Jul 2020 13:17:03: #2 predicted fragment length is 249 bps INFO @ Wed, 22 Jul 2020 13:17:03: #2 alternative fragment length(s) may be 3,213,249,271 bps INFO @ Wed, 22 Jul 2020 13:17:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.05_model.r INFO @ Wed, 22 Jul 2020 13:17:03: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:17:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:17:06: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:17:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.05_peaks.xls INFO @ Wed, 22 Jul 2020 13:17:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:17:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.05_summits.bed INFO @ Wed, 22 Jul 2020 13:17:06: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (197 records, 4 fields): 19 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 13:17:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.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 13:17:15: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:17:15: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:17:21: 1000000 INFO @ Wed, 22 Jul 2020 13:17:28: 2000000 INFO @ Wed, 22 Jul 2020 13:17:32: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:17:32: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:17:32: #1 total tags in treatment: 1024799 INFO @ Wed, 22 Jul 2020 13:17:32: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:17:32: #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 13:17:32: #1 tags after filtering in treatment: 689065 INFO @ Wed, 22 Jul 2020 13:17:32: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Jul 2020 13:17:32: #1 finished! INFO @ Wed, 22 Jul 2020 13:17:32: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:17:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:17:33: #2 number of paired peaks: 345 WARNING @ Wed, 22 Jul 2020 13:17:33: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Wed, 22 Jul 2020 13:17:33: start model_add_line... INFO @ Wed, 22 Jul 2020 13:17:33: start X-correlation... INFO @ Wed, 22 Jul 2020 13:17:33: end of X-cor INFO @ Wed, 22 Jul 2020 13:17:33: #2 finished! INFO @ Wed, 22 Jul 2020 13:17:33: #2 predicted fragment length is 249 bps INFO @ Wed, 22 Jul 2020 13:17:33: #2 alternative fragment length(s) may be 3,213,249,271 bps INFO @ Wed, 22 Jul 2020 13:17:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.10_model.r INFO @ Wed, 22 Jul 2020 13:17:33: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:17:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:17:35: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:17:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.10_peaks.xls INFO @ Wed, 22 Jul 2020 13:17:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:17:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.10_summits.bed INFO @ Wed, 22 Jul 2020 13:17:36: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (117 records, 4 fields): 15 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 13:17:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.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 13:17:45: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:17:45: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:17:52: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 13:17:59: 2000000 INFO @ Wed, 22 Jul 2020 13:18:03: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:18:03: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:18:03: #1 total tags in treatment: 1024799 INFO @ Wed, 22 Jul 2020 13:18:03: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:18:03: #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 13:18:03: #1 tags after filtering in treatment: 689065 INFO @ Wed, 22 Jul 2020 13:18:03: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Jul 2020 13:18:03: #1 finished! INFO @ Wed, 22 Jul 2020 13:18:03: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:18:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:18:03: #2 number of paired peaks: 345 WARNING @ Wed, 22 Jul 2020 13:18:03: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Wed, 22 Jul 2020 13:18:03: start model_add_line... INFO @ Wed, 22 Jul 2020 13:18:03: start X-correlation... INFO @ Wed, 22 Jul 2020 13:18:03: end of X-cor INFO @ Wed, 22 Jul 2020 13:18:03: #2 finished! INFO @ Wed, 22 Jul 2020 13:18:03: #2 predicted fragment length is 249 bps INFO @ Wed, 22 Jul 2020 13:18:03: #2 alternative fragment length(s) may be 3,213,249,271 bps INFO @ Wed, 22 Jul 2020 13:18:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.20_model.r INFO @ Wed, 22 Jul 2020 13:18:03: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:18:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:18:06: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:18:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.20_peaks.xls INFO @ Wed, 22 Jul 2020 13:18:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:18:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911551/SRX6911551.20_summits.bed INFO @ Wed, 22 Jul 2020 13:18:07: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (37 records, 4 fields): 33 millis CompletedMACS2peakCalling