Job ID = 10224056 SRX = SRX8952613 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12321128 spots for SRR12458273/SRR12458273.sra Written 12321128 spots for SRR12458273/SRR12458273.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: 00:44:53 12321128 reads; of these: 12321128 (100.00%) were paired; of these: 10244154 (83.14%) aligned concordantly 0 times 1044727 (8.48%) aligned concordantly exactly 1 time 1032247 (8.38%) aligned concordantly >1 times ---- 10244154 pairs aligned concordantly 0 times; of these: 2 (0.00%) aligned discordantly 1 time ---- 10244152 pairs aligned 0 times concordantly or discordantly; of these: 20488304 mates make up the pairs; of these: 7993311 (39.01%) aligned 0 times 2065543 (10.08%) aligned exactly 1 time 10429450 (50.90%) aligned >1 times 67.56% overall alignment rate Time searching: 00:44:53 Overall time: 00:44:53 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] 1121580 / 2075022 = 0.5405 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 @ Fri, 16 Oct 2020 10:04:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.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 @ Fri, 16 Oct 2020 10:04:21: #1 read tag files... INFO @ Fri, 16 Oct 2020 10:04:21: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 10:04:25: 1000000 INFO @ Fri, 16 Oct 2020 10:04:30: 2000000 INFO @ Fri, 16 Oct 2020 10:04:33: 3000000 INFO @ Fri, 16 Oct 2020 10:04:38: 4000000 INFO @ Fri, 16 Oct 2020 10:04:42: 5000000 INFO @ Fri, 16 Oct 2020 10:04:46: 6000000 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 @ Fri, 16 Oct 2020 10:04:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.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 @ Fri, 16 Oct 2020 10:04:49: #1 read tag files... INFO @ Fri, 16 Oct 2020 10:04:49: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 10:04:50: 7000000 INFO @ Fri, 16 Oct 2020 10:04:54: 8000000 INFO @ Fri, 16 Oct 2020 10:04:54: 1000000 INFO @ Fri, 16 Oct 2020 10:04:58: 9000000 INFO @ Fri, 16 Oct 2020 10:04:59: 2000000 INFO @ Fri, 16 Oct 2020 10:05:02: 10000000 INFO @ Fri, 16 Oct 2020 10:05:03: 3000000 INFO @ Fri, 16 Oct 2020 10:05:07: 11000000 INFO @ Fri, 16 Oct 2020 10:05:08: 4000000 INFO @ Fri, 16 Oct 2020 10:05:11: 12000000 INFO @ Fri, 16 Oct 2020 10:05:13: 5000000 INFO @ Fri, 16 Oct 2020 10:05:15: 13000000 INFO @ Fri, 16 Oct 2020 10:05:16: 6000000 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 @ Fri, 16 Oct 2020 10:05:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.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 @ Fri, 16 Oct 2020 10:05:19: #1 read tag files... INFO @ Fri, 16 Oct 2020 10:05:19: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 10:05:20: 14000000 INFO @ Fri, 16 Oct 2020 10:05:21: 7000000 INFO @ Fri, 16 Oct 2020 10:05:21: #1 tag size is determined as 11 bps INFO @ Fri, 16 Oct 2020 10:05:21: #1 tag size = 11 INFO @ Fri, 16 Oct 2020 10:05:21: #1 total tags in treatment: 955394 INFO @ Fri, 16 Oct 2020 10:05:21: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 10:05:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 10:05:21: #1 tags after filtering in treatment: 689586 INFO @ Fri, 16 Oct 2020 10:05:21: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 16 Oct 2020 10:05:21: #1 finished! INFO @ Fri, 16 Oct 2020 10:05:21: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 10:05:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 10:05:21: #2 number of paired peaks: 337 WARNING @ Fri, 16 Oct 2020 10:05:21: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Fri, 16 Oct 2020 10:05:21: start model_add_line... INFO @ Fri, 16 Oct 2020 10:05:21: start X-correlation... INFO @ Fri, 16 Oct 2020 10:05:21: end of X-cor INFO @ Fri, 16 Oct 2020 10:05:21: #2 finished! INFO @ Fri, 16 Oct 2020 10:05:21: #2 predicted fragment length is 217 bps INFO @ Fri, 16 Oct 2020 10:05:21: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 16 Oct 2020 10:05:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.05_model.r INFO @ Fri, 16 Oct 2020 10:05:21: #3 Call peaks... INFO @ Fri, 16 Oct 2020 10:05:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 10:05:24: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 10:05:24: 1000000 INFO @ Fri, 16 Oct 2020 10:05:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.05_peaks.xls INFO @ Fri, 16 Oct 2020 10:05:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 10:05:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.05_summits.bed INFO @ Fri, 16 Oct 2020 10:05:25: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (527 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 10:05:25: 8000000 INFO @ Fri, 16 Oct 2020 10:05:29: 9000000 INFO @ Fri, 16 Oct 2020 10:05:29: 2000000 INFO @ Fri, 16 Oct 2020 10:05:33: 3000000 INFO @ Fri, 16 Oct 2020 10:05:33: 10000000 INFO @ Fri, 16 Oct 2020 10:05:38: 4000000 INFO @ Fri, 16 Oct 2020 10:05:38: 11000000 INFO @ Fri, 16 Oct 2020 10:05:42: 5000000 INFO @ Fri, 16 Oct 2020 10:05:42: 12000000 INFO @ Fri, 16 Oct 2020 10:05:46: 6000000 INFO @ Fri, 16 Oct 2020 10:05:46: 13000000 INFO @ Fri, 16 Oct 2020 10:05:50: 7000000 INFO @ Fri, 16 Oct 2020 10:05:51: 14000000 INFO @ Fri, 16 Oct 2020 10:05:52: #1 tag size is determined as 11 bps INFO @ Fri, 16 Oct 2020 10:05:52: #1 tag size = 11 INFO @ Fri, 16 Oct 2020 10:05:52: #1 total tags in treatment: 955394 INFO @ Fri, 16 Oct 2020 10:05:52: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 10:05:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 10:05:52: #1 tags after filtering in treatment: 689586 INFO @ Fri, 16 Oct 2020 10:05:52: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 16 Oct 2020 10:05:52: #1 finished! INFO @ Fri, 16 Oct 2020 10:05:52: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 10:05:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 10:05:52: #2 number of paired peaks: 337 WARNING @ Fri, 16 Oct 2020 10:05:52: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Fri, 16 Oct 2020 10:05:52: start model_add_line... INFO @ Fri, 16 Oct 2020 10:05:52: start X-correlation... INFO @ Fri, 16 Oct 2020 10:05:52: end of X-cor INFO @ Fri, 16 Oct 2020 10:05:52: #2 finished! INFO @ Fri, 16 Oct 2020 10:05:52: #2 predicted fragment length is 217 bps INFO @ Fri, 16 Oct 2020 10:05:52: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 16 Oct 2020 10:05:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.10_model.r INFO @ Fri, 16 Oct 2020 10:05:52: #3 Call peaks... INFO @ Fri, 16 Oct 2020 10:05:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 10:05:55: 8000000 INFO @ Fri, 16 Oct 2020 10:05:55: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 10:05:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.10_peaks.xls INFO @ Fri, 16 Oct 2020 10:05:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 10:05:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.10_summits.bed INFO @ Fri, 16 Oct 2020 10:05:56: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (335 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 10:05:58: 9000000 INFO @ Fri, 16 Oct 2020 10:06:02: 10000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 10:06:07: 11000000 INFO @ Fri, 16 Oct 2020 10:06:11: 12000000 INFO @ Fri, 16 Oct 2020 10:06:15: 13000000 INFO @ Fri, 16 Oct 2020 10:06:19: 14000000 INFO @ Fri, 16 Oct 2020 10:06:20: #1 tag size is determined as 11 bps INFO @ Fri, 16 Oct 2020 10:06:20: #1 tag size = 11 INFO @ Fri, 16 Oct 2020 10:06:20: #1 total tags in treatment: 955394 INFO @ Fri, 16 Oct 2020 10:06:20: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 10:06:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 10:06:20: #1 tags after filtering in treatment: 689586 INFO @ Fri, 16 Oct 2020 10:06:20: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 16 Oct 2020 10:06:20: #1 finished! INFO @ Fri, 16 Oct 2020 10:06:20: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 10:06:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 10:06:20: #2 number of paired peaks: 337 WARNING @ Fri, 16 Oct 2020 10:06:20: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Fri, 16 Oct 2020 10:06:20: start model_add_line... INFO @ Fri, 16 Oct 2020 10:06:20: start X-correlation... INFO @ Fri, 16 Oct 2020 10:06:20: end of X-cor INFO @ Fri, 16 Oct 2020 10:06:20: #2 finished! INFO @ Fri, 16 Oct 2020 10:06:20: #2 predicted fragment length is 217 bps INFO @ Fri, 16 Oct 2020 10:06:20: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 16 Oct 2020 10:06:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.20_model.r INFO @ Fri, 16 Oct 2020 10:06:20: #3 Call peaks... INFO @ Fri, 16 Oct 2020 10:06:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 10:06:23: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 10:06:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.20_peaks.xls INFO @ Fri, 16 Oct 2020 10:06:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 10:06:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952613/SRX8952613.20_summits.bed INFO @ Fri, 16 Oct 2020 10:06:24: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (179 records, 4 fields): 2 millis CompletedMACS2peakCalling