Job ID = 7113423 SRX = SRX8462167 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T05:36:55 prefetch.2.10.7: 1) Downloading 'SRR11915626'... 2020-07-22T05:36:55 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:39:48 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:39:49 prefetch.2.10.7: 'SRR11915626' is valid 2020-07-22T05:39:49 prefetch.2.10.7: 1) 'SRR11915626' was downloaded successfully 2020-07-22T05:39:49 prefetch.2.10.7: 'SRR11915626' has 0 unresolved dependencies Read 7854929 spots for SRR11915626/SRR11915626.sra Written 7854929 spots for SRR11915626/SRR11915626.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: 00:03:46 7854929 reads; of these: 7854929 (100.00%) were paired; of these: 4525435 (57.61%) aligned concordantly 0 times 2785789 (35.47%) aligned concordantly exactly 1 time 543705 (6.92%) aligned concordantly >1 times ---- 4525435 pairs aligned concordantly 0 times; of these: 25789 (0.57%) aligned discordantly 1 time ---- 4499646 pairs aligned 0 times concordantly or discordantly; of these: 8999292 mates make up the pairs; of these: 8918923 (99.11%) aligned 0 times 56277 (0.63%) aligned exactly 1 time 24092 (0.27%) aligned >1 times 43.23% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 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] 2871441 / 3355023 = 0.8559 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 14:46:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.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 14:46:13: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:46:13: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:46:20: 1000000 INFO @ Wed, 22 Jul 2020 14:46:20: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 14:46:20: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 14:46:20: #1 total tags in treatment: 474002 INFO @ Wed, 22 Jul 2020 14:46:20: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:46:20: #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 14:46:20: #1 tags after filtering in treatment: 367512 INFO @ Wed, 22 Jul 2020 14:46:20: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 22 Jul 2020 14:46:20: #1 finished! INFO @ Wed, 22 Jul 2020 14:46:20: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:46:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:46:20: #2 number of paired peaks: 160 WARNING @ Wed, 22 Jul 2020 14:46:20: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Wed, 22 Jul 2020 14:46:20: start model_add_line... INFO @ Wed, 22 Jul 2020 14:46:20: start X-correlation... INFO @ Wed, 22 Jul 2020 14:46:20: end of X-cor INFO @ Wed, 22 Jul 2020 14:46:20: #2 finished! INFO @ Wed, 22 Jul 2020 14:46:20: #2 predicted fragment length is 207 bps INFO @ Wed, 22 Jul 2020 14:46:20: #2 alternative fragment length(s) may be 4,155,185,207,248,267 bps INFO @ Wed, 22 Jul 2020 14:46:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.05_model.r INFO @ Wed, 22 Jul 2020 14:46:20: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:46:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:46:21: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:46:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.05_peaks.xls INFO @ Wed, 22 Jul 2020 14:46:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:46:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.05_summits.bed INFO @ Wed, 22 Jul 2020 14:46:21: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (75 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 14:46:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.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 14:46:43: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:46:43: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:46:50: 1000000 INFO @ Wed, 22 Jul 2020 14:46:51: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 14:46:51: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 14:46:51: #1 total tags in treatment: 474002 INFO @ Wed, 22 Jul 2020 14:46:51: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:46:51: #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 14:46:51: #1 tags after filtering in treatment: 367512 INFO @ Wed, 22 Jul 2020 14:46:51: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 22 Jul 2020 14:46:51: #1 finished! INFO @ Wed, 22 Jul 2020 14:46:51: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:46:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:46:51: #2 number of paired peaks: 160 WARNING @ Wed, 22 Jul 2020 14:46:51: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Wed, 22 Jul 2020 14:46:51: start model_add_line... INFO @ Wed, 22 Jul 2020 14:46:51: start X-correlation... INFO @ Wed, 22 Jul 2020 14:46:51: end of X-cor INFO @ Wed, 22 Jul 2020 14:46:51: #2 finished! INFO @ Wed, 22 Jul 2020 14:46:51: #2 predicted fragment length is 207 bps INFO @ Wed, 22 Jul 2020 14:46:51: #2 alternative fragment length(s) may be 4,155,185,207,248,267 bps INFO @ Wed, 22 Jul 2020 14:46:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.10_model.r INFO @ Wed, 22 Jul 2020 14:46:51: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:46:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:46:52: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:46:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.10_peaks.xls INFO @ Wed, 22 Jul 2020 14:46:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:46:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.10_summits.bed INFO @ Wed, 22 Jul 2020 14:46:52: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (9 records, 4 fields): 1 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 14:47:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.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 14:47:13: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:47:13: #1 read treatment tags... 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 14:47:21: 1000000 INFO @ Wed, 22 Jul 2020 14:47:21: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 14:47:21: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 14:47:21: #1 total tags in treatment: 474002 INFO @ Wed, 22 Jul 2020 14:47:21: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:47:21: #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 14:47:21: #1 tags after filtering in treatment: 367512 INFO @ Wed, 22 Jul 2020 14:47:21: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 22 Jul 2020 14:47:21: #1 finished! INFO @ Wed, 22 Jul 2020 14:47:21: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:47:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:47:21: #2 number of paired peaks: 160 WARNING @ Wed, 22 Jul 2020 14:47:21: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Wed, 22 Jul 2020 14:47:21: start model_add_line... INFO @ Wed, 22 Jul 2020 14:47:21: start X-correlation... INFO @ Wed, 22 Jul 2020 14:47:21: end of X-cor INFO @ Wed, 22 Jul 2020 14:47:21: #2 finished! INFO @ Wed, 22 Jul 2020 14:47:21: #2 predicted fragment length is 207 bps INFO @ Wed, 22 Jul 2020 14:47:21: #2 alternative fragment length(s) may be 4,155,185,207,248,267 bps INFO @ Wed, 22 Jul 2020 14:47:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.20_model.r INFO @ Wed, 22 Jul 2020 14:47:21: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:47:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:47:22: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:47:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.20_peaks.xls INFO @ Wed, 22 Jul 2020 14:47:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:47:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8462167/SRX8462167.20_summits.bed INFO @ Wed, 22 Jul 2020 14:47:22: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling