Job ID = 10224069 SRX = SRX8952626 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3963049 spots for SRR12458260/SRR12458260.sra Written 3963049 spots for SRR12458260/SRR12458260.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: 00:06:27 3963049 reads; of these: 3963049 (100.00%) were paired; of these: 1936144 (48.85%) aligned concordantly 0 times 1394566 (35.19%) aligned concordantly exactly 1 time 632339 (15.96%) aligned concordantly >1 times ---- 1936144 pairs aligned concordantly 0 times; of these: 1469 (0.08%) aligned discordantly 1 time ---- 1934675 pairs aligned 0 times concordantly or discordantly; of these: 3869350 mates make up the pairs; of these: 1411309 (36.47%) aligned 0 times 1111135 (28.72%) aligned exactly 1 time 1346906 (34.81%) aligned >1 times 82.19% overall alignment rate Time searching: 00:06:27 Overall time: 00:06:27 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] 83091 / 2026701 = 0.0410 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 09:26:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.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 09:26:03: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:26:03: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:26:07: 1000000 INFO @ Fri, 16 Oct 2020 09:26:11: 2000000 INFO @ Fri, 16 Oct 2020 09:26:15: 3000000 INFO @ Fri, 16 Oct 2020 09:26:19: 4000000 INFO @ Fri, 16 Oct 2020 09:26:23: 5000000 INFO @ Fri, 16 Oct 2020 09:26:27: 6000000 INFO @ Fri, 16 Oct 2020 09:26:28: #1 tag size is determined as 23 bps INFO @ Fri, 16 Oct 2020 09:26:28: #1 tag size = 23 INFO @ Fri, 16 Oct 2020 09:26:28: #1 total tags in treatment: 1943817 INFO @ Fri, 16 Oct 2020 09:26:28: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:26:28: #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 09:26:28: #1 tags after filtering in treatment: 1324796 INFO @ Fri, 16 Oct 2020 09:26:28: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 16 Oct 2020 09:26:28: #1 finished! INFO @ Fri, 16 Oct 2020 09:26:28: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:26:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:26:29: #2 number of paired peaks: 229 WARNING @ Fri, 16 Oct 2020 09:26:29: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Fri, 16 Oct 2020 09:26:29: start model_add_line... INFO @ Fri, 16 Oct 2020 09:26:29: start X-correlation... INFO @ Fri, 16 Oct 2020 09:26:29: end of X-cor INFO @ Fri, 16 Oct 2020 09:26:29: #2 finished! INFO @ Fri, 16 Oct 2020 09:26:29: #2 predicted fragment length is 210 bps INFO @ Fri, 16 Oct 2020 09:26:29: #2 alternative fragment length(s) may be 2,152,187,210 bps INFO @ Fri, 16 Oct 2020 09:26:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.05_model.r INFO @ Fri, 16 Oct 2020 09:26:29: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:26:29: #3 Pre-compute pvalue-qvalue table... 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 09:26:33: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:26:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.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 09:26:33: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:26:33: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:26:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:26:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:26:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.05_summits.bed INFO @ Fri, 16 Oct 2020 09:26:34: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (282 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:26:38: 1000000 INFO @ Fri, 16 Oct 2020 09:26:43: 2000000 INFO @ Fri, 16 Oct 2020 09:26:48: 3000000 INFO @ Fri, 16 Oct 2020 09:26:53: 4000000 INFO @ Fri, 16 Oct 2020 09:26:58: 5000000 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 09:27:03: 6000000 INFO @ Fri, 16 Oct 2020 09:27:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.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 09:27:03: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:27:03: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:27:04: #1 tag size is determined as 23 bps INFO @ Fri, 16 Oct 2020 09:27:04: #1 tag size = 23 INFO @ Fri, 16 Oct 2020 09:27:04: #1 total tags in treatment: 1943817 INFO @ Fri, 16 Oct 2020 09:27:04: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:27:04: #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 09:27:04: #1 tags after filtering in treatment: 1324796 INFO @ Fri, 16 Oct 2020 09:27:04: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 16 Oct 2020 09:27:04: #1 finished! INFO @ Fri, 16 Oct 2020 09:27:04: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:27:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:27:04: #2 number of paired peaks: 229 WARNING @ Fri, 16 Oct 2020 09:27:04: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Fri, 16 Oct 2020 09:27:04: start model_add_line... INFO @ Fri, 16 Oct 2020 09:27:04: start X-correlation... INFO @ Fri, 16 Oct 2020 09:27:04: end of X-cor INFO @ Fri, 16 Oct 2020 09:27:04: #2 finished! INFO @ Fri, 16 Oct 2020 09:27:04: #2 predicted fragment length is 210 bps INFO @ Fri, 16 Oct 2020 09:27:04: #2 alternative fragment length(s) may be 2,152,187,210 bps INFO @ Fri, 16 Oct 2020 09:27:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.10_model.r INFO @ Fri, 16 Oct 2020 09:27:05: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:27:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:27:08: 1000000 INFO @ Fri, 16 Oct 2020 09:27:09: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:27:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:27:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:27:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.10_summits.bed INFO @ Fri, 16 Oct 2020 09:27:10: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (150 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:27:13: 2000000 INFO @ Fri, 16 Oct 2020 09:27:18: 3000000 INFO @ Fri, 16 Oct 2020 09:27:23: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:27:27: 5000000 INFO @ Fri, 16 Oct 2020 09:27:32: 6000000 INFO @ Fri, 16 Oct 2020 09:27:34: #1 tag size is determined as 23 bps INFO @ Fri, 16 Oct 2020 09:27:34: #1 tag size = 23 INFO @ Fri, 16 Oct 2020 09:27:34: #1 total tags in treatment: 1943817 INFO @ Fri, 16 Oct 2020 09:27:34: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:27:34: #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 09:27:34: #1 tags after filtering in treatment: 1324796 INFO @ Fri, 16 Oct 2020 09:27:34: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 16 Oct 2020 09:27:34: #1 finished! INFO @ Fri, 16 Oct 2020 09:27:34: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:27:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:27:34: #2 number of paired peaks: 229 WARNING @ Fri, 16 Oct 2020 09:27:34: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Fri, 16 Oct 2020 09:27:34: start model_add_line... INFO @ Fri, 16 Oct 2020 09:27:34: start X-correlation... INFO @ Fri, 16 Oct 2020 09:27:34: end of X-cor INFO @ Fri, 16 Oct 2020 09:27:34: #2 finished! INFO @ Fri, 16 Oct 2020 09:27:34: #2 predicted fragment length is 210 bps INFO @ Fri, 16 Oct 2020 09:27:34: #2 alternative fragment length(s) may be 2,152,187,210 bps INFO @ Fri, 16 Oct 2020 09:27:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.20_model.r INFO @ Fri, 16 Oct 2020 09:27:34: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:27:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:27:38: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:27:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:27:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:27:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952626/SRX8952626.20_summits.bed INFO @ Fri, 16 Oct 2020 09:27:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 1 millis CompletedMACS2peakCalling