Job ID = 7100966 SRX = SRX6911517 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12915057 spots for SRR10191160/SRR10191160.sra Written 12915057 spots for SRR10191160/SRR10191160.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: 00:08:55 12915057 reads; of these: 12915057 (100.00%) were paired; of these: 7853490 (60.81%) aligned concordantly 0 times 3821121 (29.59%) aligned concordantly exactly 1 time 1240446 (9.60%) aligned concordantly >1 times ---- 7853490 pairs aligned concordantly 0 times; of these: 364310 (4.64%) aligned discordantly 1 time ---- 7489180 pairs aligned 0 times concordantly or discordantly; of these: 14978360 mates make up the pairs; of these: 14608102 (97.53%) aligned 0 times 111987 (0.75%) aligned exactly 1 time 258271 (1.72%) aligned >1 times 43.45% overall alignment rate Time searching: 00:08:55 Overall time: 00:08:55 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] 1816828 / 5425109 = 0.3349 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 12:27:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.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 12:27:34: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:27:34: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:27:40: 1000000 INFO @ Wed, 22 Jul 2020 12:27:47: 2000000 INFO @ Wed, 22 Jul 2020 12:27:53: 3000000 INFO @ Wed, 22 Jul 2020 12:27:59: 4000000 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 12:28:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.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 12:28:04: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:28:04: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:28:05: 5000000 INFO @ Wed, 22 Jul 2020 12:28:11: 1000000 INFO @ Wed, 22 Jul 2020 12:28:12: 6000000 INFO @ Wed, 22 Jul 2020 12:28:18: 2000000 INFO @ Wed, 22 Jul 2020 12:28:18: 7000000 INFO @ Wed, 22 Jul 2020 12:28:23: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:28:23: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:28:23: #1 total tags in treatment: 3333806 INFO @ Wed, 22 Jul 2020 12:28:23: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:28:23: #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 12:28:23: #1 tags after filtering in treatment: 2071974 INFO @ Wed, 22 Jul 2020 12:28:23: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Jul 2020 12:28:23: #1 finished! INFO @ Wed, 22 Jul 2020 12:28:23: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:28:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:28:23: #2 number of paired peaks: 241 WARNING @ Wed, 22 Jul 2020 12:28:23: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Wed, 22 Jul 2020 12:28:23: start model_add_line... INFO @ Wed, 22 Jul 2020 12:28:23: start X-correlation... INFO @ Wed, 22 Jul 2020 12:28:23: end of X-cor INFO @ Wed, 22 Jul 2020 12:28:23: #2 finished! INFO @ Wed, 22 Jul 2020 12:28:23: #2 predicted fragment length is 521 bps INFO @ Wed, 22 Jul 2020 12:28:23: #2 alternative fragment length(s) may be 3,417,463,487,501,521,547,585 bps INFO @ Wed, 22 Jul 2020 12:28:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.05_model.r INFO @ Wed, 22 Jul 2020 12:28:23: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:28:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:28:26: 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 12:28:32: 4000000 INFO @ Wed, 22 Jul 2020 12:28:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.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 12:28:34: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:28:34: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:28:39: 5000000 INFO @ Wed, 22 Jul 2020 12:28:40: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:28:40: 1000000 INFO @ Wed, 22 Jul 2020 12:28:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.05_peaks.xls INFO @ Wed, 22 Jul 2020 12:28:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:28:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.05_summits.bed INFO @ Wed, 22 Jul 2020 12:28:42: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (286 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 12:28:45: 6000000 INFO @ Wed, 22 Jul 2020 12:28:47: 2000000 INFO @ Wed, 22 Jul 2020 12:28:52: 7000000 INFO @ Wed, 22 Jul 2020 12:28:54: 3000000 INFO @ Wed, 22 Jul 2020 12:28:56: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:28:56: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:28:56: #1 total tags in treatment: 3333806 INFO @ Wed, 22 Jul 2020 12:28:56: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:28:56: #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 12:28:56: #1 tags after filtering in treatment: 2071974 INFO @ Wed, 22 Jul 2020 12:28:56: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Jul 2020 12:28:56: #1 finished! INFO @ Wed, 22 Jul 2020 12:28:56: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:28:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:28:56: #2 number of paired peaks: 241 WARNING @ Wed, 22 Jul 2020 12:28:56: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Wed, 22 Jul 2020 12:28:56: start model_add_line... INFO @ Wed, 22 Jul 2020 12:28:56: start X-correlation... INFO @ Wed, 22 Jul 2020 12:28:56: end of X-cor INFO @ Wed, 22 Jul 2020 12:28:56: #2 finished! INFO @ Wed, 22 Jul 2020 12:28:56: #2 predicted fragment length is 521 bps INFO @ Wed, 22 Jul 2020 12:28:56: #2 alternative fragment length(s) may be 3,417,463,487,501,521,547,585 bps INFO @ Wed, 22 Jul 2020 12:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.10_model.r INFO @ Wed, 22 Jul 2020 12:28:56: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:29:00: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 12:29:07: 5000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 12:29:13: 6000000 INFO @ Wed, 22 Jul 2020 12:29:14: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:29:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.10_peaks.xls INFO @ Wed, 22 Jul 2020 12:29:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:29:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.10_summits.bed INFO @ Wed, 22 Jul 2020 12:29:16: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (214 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 12:29:19: 7000000 INFO @ Wed, 22 Jul 2020 12:29:23: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:29:23: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:29:23: #1 total tags in treatment: 3333806 INFO @ Wed, 22 Jul 2020 12:29:23: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:29:23: #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 12:29:23: #1 tags after filtering in treatment: 2071974 INFO @ Wed, 22 Jul 2020 12:29:23: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Jul 2020 12:29:23: #1 finished! INFO @ Wed, 22 Jul 2020 12:29:23: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:29:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:29:23: #2 number of paired peaks: 241 WARNING @ Wed, 22 Jul 2020 12:29:23: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Wed, 22 Jul 2020 12:29:23: start model_add_line... INFO @ Wed, 22 Jul 2020 12:29:23: start X-correlation... INFO @ Wed, 22 Jul 2020 12:29:23: end of X-cor INFO @ Wed, 22 Jul 2020 12:29:23: #2 finished! INFO @ Wed, 22 Jul 2020 12:29:23: #2 predicted fragment length is 521 bps INFO @ Wed, 22 Jul 2020 12:29:23: #2 alternative fragment length(s) may be 3,417,463,487,501,521,547,585 bps INFO @ Wed, 22 Jul 2020 12:29:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.20_model.r INFO @ Wed, 22 Jul 2020 12:29:23: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:29:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:29:41: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:29:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.20_peaks.xls INFO @ Wed, 22 Jul 2020 12:29:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:29:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911517/SRX6911517.20_summits.bed INFO @ Wed, 22 Jul 2020 12:29:43: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (77 records, 4 fields): 1 millis CompletedMACS2peakCalling