Job ID = 14520401 SRX = SRX11781129 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:02:21 prefetch.2.10.7: 1) Downloading 'SRR15481072'... 2022-01-15T10:02:21 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:02:34 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:02:35 prefetch.2.10.7: 'SRR15481072' is valid 2022-01-15T10:02:35 prefetch.2.10.7: 1) 'SRR15481072' was downloaded successfully 2022-01-15T10:02:35 prefetch.2.10.7: 'SRR15481072' has 0 unresolved dependencies Read 6545974 spots for SRR15481072/SRR15481072.sra Written 6545974 spots for SRR15481072/SRR15481072.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: 00:02:54 6545974 reads; of these: 6545974 (100.00%) were paired; of these: 3952946 (60.39%) aligned concordantly 0 times 2311972 (35.32%) aligned concordantly exactly 1 time 281056 (4.29%) aligned concordantly >1 times ---- 3952946 pairs aligned concordantly 0 times; of these: 42894 (1.09%) aligned discordantly 1 time ---- 3910052 pairs aligned 0 times concordantly or discordantly; of these: 7820104 mates make up the pairs; of these: 4231609 (54.11%) aligned 0 times 3159524 (40.40%) aligned exactly 1 time 428971 (5.49%) aligned >1 times 67.68% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:54 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] 235159 / 2635028 = 0.0892 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 19:08:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.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 19:08:16: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:08:16: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:08:21: 1000000 INFO @ Sat, 15 Jan 2022 19:08:27: 2000000 INFO @ Sat, 15 Jan 2022 19:08:33: 3000000 INFO @ Sat, 15 Jan 2022 19:08:38: 4000000 INFO @ Sat, 15 Jan 2022 19:08:44: 5000000 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 19:08:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.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 19:08:46: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:08:46: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:08:50: 6000000 INFO @ Sat, 15 Jan 2022 19:08:52: 1000000 INFO @ Sat, 15 Jan 2022 19:08:56: 7000000 INFO @ Sat, 15 Jan 2022 19:08:57: 2000000 INFO @ Sat, 15 Jan 2022 19:09:03: 8000000 INFO @ Sat, 15 Jan 2022 19:09:03: 3000000 INFO @ Sat, 15 Jan 2022 19:09:05: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:09:05: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:09:05: #1 total tags in treatment: 2359731 INFO @ Sat, 15 Jan 2022 19:09:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:09:05: #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 19:09:05: #1 tags after filtering in treatment: 1887931 INFO @ Sat, 15 Jan 2022 19:09:05: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 15 Jan 2022 19:09:05: #1 finished! INFO @ Sat, 15 Jan 2022 19:09:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:09:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:09:05: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 19:09:05: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 15 Jan 2022 19:09:05: start model_add_line... INFO @ Sat, 15 Jan 2022 19:09:05: start X-correlation... INFO @ Sat, 15 Jan 2022 19:09:05: end of X-cor INFO @ Sat, 15 Jan 2022 19:09:05: #2 finished! INFO @ Sat, 15 Jan 2022 19:09:05: #2 predicted fragment length is 295 bps INFO @ Sat, 15 Jan 2022 19:09:05: #2 alternative fragment length(s) may be 0,251,269,281,295 bps INFO @ Sat, 15 Jan 2022 19:09:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.05_model.r INFO @ Sat, 15 Jan 2022 19:09:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:09:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:09:08: 4000000 INFO @ Sat, 15 Jan 2022 19:09:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:09:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:09:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:09:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.05_summits.bed INFO @ Sat, 15 Jan 2022 19:09:11: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (26 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:09:14: 5000000 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 19:09:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.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 19:09:16: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:09:16: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:09:19: 6000000 INFO @ Sat, 15 Jan 2022 19:09:22: 1000000 INFO @ Sat, 15 Jan 2022 19:09:25: 7000000 INFO @ Sat, 15 Jan 2022 19:09:28: 2000000 INFO @ Sat, 15 Jan 2022 19:09:31: 8000000 INFO @ Sat, 15 Jan 2022 19:09:33: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:09:33: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:09:33: #1 total tags in treatment: 2359731 INFO @ Sat, 15 Jan 2022 19:09:33: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:09:33: #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 19:09:33: #1 tags after filtering in treatment: 1887931 INFO @ Sat, 15 Jan 2022 19:09:33: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 15 Jan 2022 19:09:33: #1 finished! INFO @ Sat, 15 Jan 2022 19:09:33: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:09:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:09:33: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 19:09:33: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 15 Jan 2022 19:09:33: start model_add_line... INFO @ Sat, 15 Jan 2022 19:09:33: start X-correlation... INFO @ Sat, 15 Jan 2022 19:09:33: end of X-cor INFO @ Sat, 15 Jan 2022 19:09:33: #2 finished! INFO @ Sat, 15 Jan 2022 19:09:33: #2 predicted fragment length is 295 bps INFO @ Sat, 15 Jan 2022 19:09:33: #2 alternative fragment length(s) may be 0,251,269,281,295 bps INFO @ Sat, 15 Jan 2022 19:09:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.10_model.r INFO @ Sat, 15 Jan 2022 19:09:33: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:09:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:09:34: 3000000 INFO @ Sat, 15 Jan 2022 19:09:38: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:09:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:09:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:09:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.10_summits.bed INFO @ Sat, 15 Jan 2022 19:09:39: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (14 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:09:40: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:09:46: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:09:51: 6000000 INFO @ Sat, 15 Jan 2022 19:09:57: 7000000 INFO @ Sat, 15 Jan 2022 19:10:02: 8000000 INFO @ Sat, 15 Jan 2022 19:10:04: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:10:04: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:10:04: #1 total tags in treatment: 2359731 INFO @ Sat, 15 Jan 2022 19:10:04: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:10:04: #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 19:10:04: #1 tags after filtering in treatment: 1887931 INFO @ Sat, 15 Jan 2022 19:10:04: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 15 Jan 2022 19:10:04: #1 finished! INFO @ Sat, 15 Jan 2022 19:10:04: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:10:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:10:05: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 19:10:05: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 15 Jan 2022 19:10:05: start model_add_line... INFO @ Sat, 15 Jan 2022 19:10:05: start X-correlation... INFO @ Sat, 15 Jan 2022 19:10:05: end of X-cor INFO @ Sat, 15 Jan 2022 19:10:05: #2 finished! INFO @ Sat, 15 Jan 2022 19:10:05: #2 predicted fragment length is 295 bps INFO @ Sat, 15 Jan 2022 19:10:05: #2 alternative fragment length(s) may be 0,251,269,281,295 bps INFO @ Sat, 15 Jan 2022 19:10:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.20_model.r INFO @ Sat, 15 Jan 2022 19:10:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:10:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:10:09: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:10:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:10:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:10:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781129/SRX11781129.20_summits.bed INFO @ Sat, 15 Jan 2022 19:10:10: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis CompletedMACS2peakCalling