Job ID = 10224100 SRX = SRX8952655 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3127904 spots for SRR12458231/SRR12458231.sra Written 3127904 spots for SRR12458231/SRR12458231.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: 00:00:58 3127904 reads; of these: 3127904 (100.00%) were paired; of these: 2292475 (73.29%) aligned concordantly 0 times 674842 (21.57%) aligned concordantly exactly 1 time 160587 (5.13%) aligned concordantly >1 times ---- 2292475 pairs aligned concordantly 0 times; of these: 209021 (9.12%) aligned discordantly 1 time ---- 2083454 pairs aligned 0 times concordantly or discordantly; of these: 4166908 mates make up the pairs; of these: 3241674 (77.80%) aligned 0 times 790188 (18.96%) aligned exactly 1 time 135046 (3.24%) aligned >1 times 48.18% overall alignment rate Time searching: 00:00:58 Overall time: 00:00:58 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] 176387 / 1016675 = 0.1735 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 09:27:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.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 09:27:15: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:27:15: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:27:21: 1000000 INFO @ Fri, 16 Oct 2020 09:27:28: 2000000 INFO @ Fri, 16 Oct 2020 09:27:32: #1 tag size is determined as 41 bps INFO @ Fri, 16 Oct 2020 09:27:32: #1 tag size = 41 INFO @ Fri, 16 Oct 2020 09:27:32: #1 total tags in treatment: 767022 INFO @ Fri, 16 Oct 2020 09:27:32: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:27:32: #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 09:27:32: #1 tags after filtering in treatment: 673351 INFO @ Fri, 16 Oct 2020 09:27:32: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 16 Oct 2020 09:27:32: #1 finished! INFO @ Fri, 16 Oct 2020 09:27:32: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:27:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:27:32: #2 number of paired peaks: 173 WARNING @ Fri, 16 Oct 2020 09:27:32: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Fri, 16 Oct 2020 09:27:32: start model_add_line... INFO @ Fri, 16 Oct 2020 09:27:32: start X-correlation... INFO @ Fri, 16 Oct 2020 09:27:32: end of X-cor INFO @ Fri, 16 Oct 2020 09:27:32: #2 finished! INFO @ Fri, 16 Oct 2020 09:27:32: #2 predicted fragment length is 283 bps INFO @ Fri, 16 Oct 2020 09:27:32: #2 alternative fragment length(s) may be 1,19,73,125,148,265,283,322,507,593 bps INFO @ Fri, 16 Oct 2020 09:27:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.05_model.r INFO @ Fri, 16 Oct 2020 09:27:32: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:27:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:27:34: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:27:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:27:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:27:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.05_summits.bed INFO @ Fri, 16 Oct 2020 09:27:34: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (48 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 @ Fri, 16 Oct 2020 09:27:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.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 09:27:45: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:27:45: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:27:51: 1000000 INFO @ Fri, 16 Oct 2020 09:27:56: 2000000 INFO @ Fri, 16 Oct 2020 09:28:00: #1 tag size is determined as 41 bps INFO @ Fri, 16 Oct 2020 09:28:00: #1 tag size = 41 INFO @ Fri, 16 Oct 2020 09:28:00: #1 total tags in treatment: 767022 INFO @ Fri, 16 Oct 2020 09:28:00: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:28:00: #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 09:28:00: #1 tags after filtering in treatment: 673351 INFO @ Fri, 16 Oct 2020 09:28:00: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 16 Oct 2020 09:28:00: #1 finished! INFO @ Fri, 16 Oct 2020 09:28:00: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:28:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:28:00: #2 number of paired peaks: 173 WARNING @ Fri, 16 Oct 2020 09:28:00: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Fri, 16 Oct 2020 09:28:00: start model_add_line... INFO @ Fri, 16 Oct 2020 09:28:00: start X-correlation... INFO @ Fri, 16 Oct 2020 09:28:00: end of X-cor INFO @ Fri, 16 Oct 2020 09:28:00: #2 finished! INFO @ Fri, 16 Oct 2020 09:28:00: #2 predicted fragment length is 283 bps INFO @ Fri, 16 Oct 2020 09:28:00: #2 alternative fragment length(s) may be 1,19,73,125,148,265,283,322,507,593 bps INFO @ Fri, 16 Oct 2020 09:28:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.10_model.r INFO @ Fri, 16 Oct 2020 09:28:00: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:28:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:28:02: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:28:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:28:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:28:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.10_summits.bed INFO @ Fri, 16 Oct 2020 09:28:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (16 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 @ Fri, 16 Oct 2020 09:28:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.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 09:28:15: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:28:15: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:28:20: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:28:26: 2000000 INFO @ Fri, 16 Oct 2020 09:28:29: #1 tag size is determined as 41 bps INFO @ Fri, 16 Oct 2020 09:28:29: #1 tag size = 41 INFO @ Fri, 16 Oct 2020 09:28:29: #1 total tags in treatment: 767022 INFO @ Fri, 16 Oct 2020 09:28:29: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:28:29: #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 09:28:29: #1 tags after filtering in treatment: 673351 INFO @ Fri, 16 Oct 2020 09:28:29: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 16 Oct 2020 09:28:29: #1 finished! INFO @ Fri, 16 Oct 2020 09:28:29: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:28:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:28:29: #2 number of paired peaks: 173 WARNING @ Fri, 16 Oct 2020 09:28:29: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Fri, 16 Oct 2020 09:28:29: start model_add_line... INFO @ Fri, 16 Oct 2020 09:28:29: start X-correlation... INFO @ Fri, 16 Oct 2020 09:28:29: end of X-cor INFO @ Fri, 16 Oct 2020 09:28:29: #2 finished! INFO @ Fri, 16 Oct 2020 09:28:29: #2 predicted fragment length is 283 bps INFO @ Fri, 16 Oct 2020 09:28:29: #2 alternative fragment length(s) may be 1,19,73,125,148,265,283,322,507,593 bps INFO @ Fri, 16 Oct 2020 09:28:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.20_model.r INFO @ Fri, 16 Oct 2020 09:28:29: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:28:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:28:31: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.20_summits.bed INFO @ Fri, 16 Oct 2020 09:28:32: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling