Job ID = 14520130 SRX = SRX9390798 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4258113 spots for SRR12926693/SRR12926693.sra Written 4258113 spots for SRR12926693/SRR12926693.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: 00:03:12 4258113 reads; of these: 4258113 (100.00%) were paired; of these: 3660273 (85.96%) aligned concordantly 0 times 402416 (9.45%) aligned concordantly exactly 1 time 195424 (4.59%) aligned concordantly >1 times ---- 3660273 pairs aligned concordantly 0 times; of these: 245345 (6.70%) aligned discordantly 1 time ---- 3414928 pairs aligned 0 times concordantly or discordantly; of these: 6829856 mates make up the pairs; of these: 3290346 (48.18%) aligned 0 times 1514810 (22.18%) aligned exactly 1 time 2024700 (29.64%) aligned >1 times 61.36% overall alignment rate Time searching: 00:03:12 Overall time: 00:03:12 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] 149619 / 836119 = 0.1789 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 18:28:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.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 @ Sat, 15 Jan 2022 18:28:02: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:28:02: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:28:06: 1000000 INFO @ Sat, 15 Jan 2022 18:28:10: 2000000 INFO @ Sat, 15 Jan 2022 18:28:14: 3000000 INFO @ Sat, 15 Jan 2022 18:28:18: 4000000 INFO @ Sat, 15 Jan 2022 18:28:22: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 18:28:22: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 18:28:22: #1 total tags in treatment: 481918 INFO @ Sat, 15 Jan 2022 18:28:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:28:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 18:28:22: #1 tags after filtering in treatment: 381309 INFO @ Sat, 15 Jan 2022 18:28:22: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 18:28:22: #1 finished! INFO @ Sat, 15 Jan 2022 18:28:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:28:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:28:22: #2 number of paired peaks: 130 WARNING @ Sat, 15 Jan 2022 18:28:22: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Sat, 15 Jan 2022 18:28:22: start model_add_line... INFO @ Sat, 15 Jan 2022 18:28:22: start X-correlation... INFO @ Sat, 15 Jan 2022 18:28:22: end of X-cor INFO @ Sat, 15 Jan 2022 18:28:22: #2 finished! INFO @ Sat, 15 Jan 2022 18:28:22: #2 predicted fragment length is 146 bps INFO @ Sat, 15 Jan 2022 18:28:22: #2 alternative fragment length(s) may be 130,146 bps INFO @ Sat, 15 Jan 2022 18:28:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.05_model.r INFO @ Sat, 15 Jan 2022 18:28:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:28:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:28:23: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:28:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.05_peaks.xls INFO @ Sat, 15 Jan 2022 18:28:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:28:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.05_summits.bed INFO @ Sat, 15 Jan 2022 18:28:23: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (496 records, 4 fields): 2 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 18:28:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.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 @ Sat, 15 Jan 2022 18:28:32: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:28:32: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:28:36: 1000000 INFO @ Sat, 15 Jan 2022 18:28:40: 2000000 INFO @ Sat, 15 Jan 2022 18:28:44: 3000000 INFO @ Sat, 15 Jan 2022 18:28:48: 4000000 INFO @ Sat, 15 Jan 2022 18:28:52: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 18:28:52: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 18:28:52: #1 total tags in treatment: 481918 INFO @ Sat, 15 Jan 2022 18:28:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:28:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 18:28:52: #1 tags after filtering in treatment: 381309 INFO @ Sat, 15 Jan 2022 18:28:52: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 18:28:52: #1 finished! INFO @ Sat, 15 Jan 2022 18:28:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:28:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:28:52: #2 number of paired peaks: 130 WARNING @ Sat, 15 Jan 2022 18:28:52: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Sat, 15 Jan 2022 18:28:52: start model_add_line... INFO @ Sat, 15 Jan 2022 18:28:52: start X-correlation... INFO @ Sat, 15 Jan 2022 18:28:52: end of X-cor INFO @ Sat, 15 Jan 2022 18:28:52: #2 finished! INFO @ Sat, 15 Jan 2022 18:28:52: #2 predicted fragment length is 146 bps INFO @ Sat, 15 Jan 2022 18:28:52: #2 alternative fragment length(s) may be 130,146 bps INFO @ Sat, 15 Jan 2022 18:28:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.10_model.r INFO @ Sat, 15 Jan 2022 18:28:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:28:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:28:53: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:28:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.10_peaks.xls INFO @ Sat, 15 Jan 2022 18:28:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:28:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.10_summits.bed INFO @ Sat, 15 Jan 2022 18:28:53: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (138 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 18:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.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 @ Sat, 15 Jan 2022 18:29:02: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:29:02: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:29:07: 1000000 INFO @ Sat, 15 Jan 2022 18:29:12: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 18:29:17: 3000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 18:29:22: 4000000 INFO @ Sat, 15 Jan 2022 18:29:27: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 18:29:27: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 18:29:27: #1 total tags in treatment: 481918 INFO @ Sat, 15 Jan 2022 18:29:27: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:29:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 18:29:27: #1 tags after filtering in treatment: 381309 INFO @ Sat, 15 Jan 2022 18:29:27: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 18:29:27: #1 finished! INFO @ Sat, 15 Jan 2022 18:29:27: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:29:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:29:27: #2 number of paired peaks: 130 WARNING @ Sat, 15 Jan 2022 18:29:27: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Sat, 15 Jan 2022 18:29:27: start model_add_line... INFO @ Sat, 15 Jan 2022 18:29:27: start X-correlation... INFO @ Sat, 15 Jan 2022 18:29:27: end of X-cor INFO @ Sat, 15 Jan 2022 18:29:27: #2 finished! INFO @ Sat, 15 Jan 2022 18:29:27: #2 predicted fragment length is 146 bps INFO @ Sat, 15 Jan 2022 18:29:27: #2 alternative fragment length(s) may be 130,146 bps INFO @ Sat, 15 Jan 2022 18:29:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.20_model.r INFO @ Sat, 15 Jan 2022 18:29:27: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:29:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:29:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:29:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.20_peaks.xls INFO @ Sat, 15 Jan 2022 18:29:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:29:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9390798/SRX9390798.20_summits.bed INFO @ Sat, 15 Jan 2022 18:29:29: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (13 records, 4 fields): 2 millis CompletedMACS2peakCalling