Job ID = 14521283 SRX = SRX8952615 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24722718 spots for SRR12458271/SRR12458271.sra Written 24722718 spots for SRR12458271/SRR12458271.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: 01:17:13 24722718 reads; of these: 24722718 (100.00%) were paired; of these: 16619508 (67.22%) aligned concordantly 0 times 3100601 (12.54%) aligned concordantly exactly 1 time 5002609 (20.23%) aligned concordantly >1 times ---- 16619508 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 16619508 pairs aligned 0 times concordantly or discordantly; of these: 33239016 mates make up the pairs; of these: 7392971 (22.24%) aligned 0 times 11890058 (35.77%) aligned exactly 1 time 13955987 (41.99%) aligned >1 times 85.05% overall alignment rate Time searching: 01:17:13 Overall time: 01:17:13 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_sort_core] merging from 16 files... [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] 6816987 / 8098410 = 0.8418 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 22:14:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.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 22:14:36: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:14:36: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:14:41: 1000000 INFO @ Sat, 15 Jan 2022 22:14:46: 2000000 INFO @ Sat, 15 Jan 2022 22:14:50: 3000000 INFO @ Sat, 15 Jan 2022 22:14:55: 4000000 INFO @ Sat, 15 Jan 2022 22:15:00: 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 22:15:04: 6000000 INFO @ Sat, 15 Jan 2022 22:15:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.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 22:15:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:15:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:15:09: 7000000 INFO @ Sat, 15 Jan 2022 22:15:11: 1000000 INFO @ Sat, 15 Jan 2022 22:15:15: 8000000 INFO @ Sat, 15 Jan 2022 22:15:16: 2000000 INFO @ Sat, 15 Jan 2022 22:15:21: 9000000 INFO @ Sat, 15 Jan 2022 22:15:21: 3000000 INFO @ Sat, 15 Jan 2022 22:15:26: 10000000 INFO @ Sat, 15 Jan 2022 22:15:27: 4000000 INFO @ Sat, 15 Jan 2022 22:15:31: 11000000 INFO @ Sat, 15 Jan 2022 22:15:32: 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 22:15:36: 12000000 INFO @ Sat, 15 Jan 2022 22:15:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.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 22:15:36: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:15:36: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:15:37: 6000000 INFO @ Sat, 15 Jan 2022 22:15:41: 13000000 INFO @ Sat, 15 Jan 2022 22:15:41: 1000000 INFO @ Sat, 15 Jan 2022 22:15:43: 7000000 INFO @ Sat, 15 Jan 2022 22:15:46: 14000000 INFO @ Sat, 15 Jan 2022 22:15:46: 2000000 INFO @ Sat, 15 Jan 2022 22:15:49: 8000000 INFO @ Sat, 15 Jan 2022 22:15:51: 3000000 INFO @ Sat, 15 Jan 2022 22:15:51: 15000000 INFO @ Sat, 15 Jan 2022 22:15:55: 9000000 INFO @ Sat, 15 Jan 2022 22:15:57: 4000000 INFO @ Sat, 15 Jan 2022 22:15:57: 16000000 INFO @ Sat, 15 Jan 2022 22:16:00: 10000000 INFO @ Sat, 15 Jan 2022 22:16:02: 17000000 INFO @ Sat, 15 Jan 2022 22:16:02: 5000000 INFO @ Sat, 15 Jan 2022 22:16:05: 11000000 INFO @ Sat, 15 Jan 2022 22:16:07: 18000000 INFO @ Sat, 15 Jan 2022 22:16:07: 6000000 INFO @ Sat, 15 Jan 2022 22:16:11: 12000000 INFO @ Sat, 15 Jan 2022 22:16:12: 19000000 INFO @ Sat, 15 Jan 2022 22:16:12: 7000000 INFO @ Sat, 15 Jan 2022 22:16:16: 13000000 INFO @ Sat, 15 Jan 2022 22:16:17: 20000000 INFO @ Sat, 15 Jan 2022 22:16:18: 8000000 INFO @ Sat, 15 Jan 2022 22:16:21: 14000000 INFO @ Sat, 15 Jan 2022 22:16:22: 21000000 INFO @ Sat, 15 Jan 2022 22:16:24: 9000000 INFO @ Sat, 15 Jan 2022 22:16:26: 15000000 INFO @ Sat, 15 Jan 2022 22:16:27: 22000000 INFO @ Sat, 15 Jan 2022 22:16:30: 10000000 INFO @ Sat, 15 Jan 2022 22:16:30: 16000000 INFO @ Sat, 15 Jan 2022 22:16:32: 23000000 INFO @ Sat, 15 Jan 2022 22:16:35: 17000000 INFO @ Sat, 15 Jan 2022 22:16:35: 11000000 INFO @ Sat, 15 Jan 2022 22:16:37: 24000000 INFO @ Sat, 15 Jan 2022 22:16:40: 12000000 INFO @ Sat, 15 Jan 2022 22:16:40: 18000000 INFO @ Sat, 15 Jan 2022 22:16:42: 25000000 INFO @ Sat, 15 Jan 2022 22:16:46: 13000000 INFO @ Sat, 15 Jan 2022 22:16:46: 19000000 INFO @ Sat, 15 Jan 2022 22:16:47: 26000000 INFO @ Sat, 15 Jan 2022 22:16:50: 14000000 INFO @ Sat, 15 Jan 2022 22:16:52: 20000000 INFO @ Sat, 15 Jan 2022 22:16:52: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:16:55: 15000000 INFO @ Sat, 15 Jan 2022 22:16:57: 21000000 INFO @ Sat, 15 Jan 2022 22:16:57: 28000000 INFO @ Sat, 15 Jan 2022 22:16:59: #1 tag size is determined as 10 bps INFO @ Sat, 15 Jan 2022 22:16:59: #1 tag size = 10 INFO @ Sat, 15 Jan 2022 22:16:59: #1 total tags in treatment: 1286223 INFO @ Sat, 15 Jan 2022 22:16:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:16:59: #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 22:16:59: #1 tags after filtering in treatment: 760037 INFO @ Sat, 15 Jan 2022 22:16:59: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 15 Jan 2022 22:16:59: #1 finished! INFO @ Sat, 15 Jan 2022 22:16:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:16:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:16:59: #2 number of paired peaks: 298 WARNING @ Sat, 15 Jan 2022 22:16:59: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Sat, 15 Jan 2022 22:16:59: start model_add_line... INFO @ Sat, 15 Jan 2022 22:16:59: start X-correlation... INFO @ Sat, 15 Jan 2022 22:16:59: end of X-cor INFO @ Sat, 15 Jan 2022 22:16:59: #2 finished! INFO @ Sat, 15 Jan 2022 22:16:59: #2 predicted fragment length is 132 bps INFO @ Sat, 15 Jan 2022 22:16:59: #2 alternative fragment length(s) may be 4,88,109,132 bps INFO @ Sat, 15 Jan 2022 22:16:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.05_model.r INFO @ Sat, 15 Jan 2022 22:16:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:16:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:17:00: 16000000 INFO @ Sat, 15 Jan 2022 22:17:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:17:02: 22000000 INFO @ Sat, 15 Jan 2022 22:17:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.05_peaks.xls INFO @ Sat, 15 Jan 2022 22:17:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:17:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.05_summits.bed INFO @ Sat, 15 Jan 2022 22:17:02: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (455 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:17:05: 17000000 INFO @ Sat, 15 Jan 2022 22:17:06: 23000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 22:17:10: 18000000 INFO @ Sat, 15 Jan 2022 22:17:11: 24000000 INFO @ Sat, 15 Jan 2022 22:17:16: 19000000 INFO @ Sat, 15 Jan 2022 22:17:16: 25000000 INFO @ Sat, 15 Jan 2022 22:17:21: 26000000 INFO @ Sat, 15 Jan 2022 22:17:21: 20000000 INFO @ Sat, 15 Jan 2022 22:17:26: 27000000 INFO @ Sat, 15 Jan 2022 22:17:26: 21000000 INFO @ Sat, 15 Jan 2022 22:17:30: 28000000 INFO @ Sat, 15 Jan 2022 22:17:31: 22000000 INFO @ Sat, 15 Jan 2022 22:17:32: #1 tag size is determined as 10 bps INFO @ Sat, 15 Jan 2022 22:17:32: #1 tag size = 10 INFO @ Sat, 15 Jan 2022 22:17:32: #1 total tags in treatment: 1286223 INFO @ Sat, 15 Jan 2022 22:17:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:17:32: #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 22:17:32: #1 tags after filtering in treatment: 760037 INFO @ Sat, 15 Jan 2022 22:17:32: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 15 Jan 2022 22:17:32: #1 finished! INFO @ Sat, 15 Jan 2022 22:17:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:17:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:17:32: #2 number of paired peaks: 298 WARNING @ Sat, 15 Jan 2022 22:17:32: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Sat, 15 Jan 2022 22:17:32: start model_add_line... INFO @ Sat, 15 Jan 2022 22:17:32: start X-correlation... INFO @ Sat, 15 Jan 2022 22:17:32: end of X-cor INFO @ Sat, 15 Jan 2022 22:17:32: #2 finished! INFO @ Sat, 15 Jan 2022 22:17:32: #2 predicted fragment length is 132 bps INFO @ Sat, 15 Jan 2022 22:17:32: #2 alternative fragment length(s) may be 4,88,109,132 bps INFO @ Sat, 15 Jan 2022 22:17:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.10_model.r INFO @ Sat, 15 Jan 2022 22:17:32: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:17:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:17:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:17:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.10_peaks.xls INFO @ Sat, 15 Jan 2022 22:17:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:17:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.10_summits.bed INFO @ Sat, 15 Jan 2022 22:17:35: Done! INFO @ Sat, 15 Jan 2022 22:17:36: 23000000 pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (290 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:17:40: 24000000 INFO @ Sat, 15 Jan 2022 22:17:45: 25000000 INFO @ Sat, 15 Jan 2022 22:17:49: 26000000 INFO @ Sat, 15 Jan 2022 22:17:54: 27000000 INFO @ Sat, 15 Jan 2022 22:17:59: 28000000 INFO @ Sat, 15 Jan 2022 22:18:00: #1 tag size is determined as 10 bps INFO @ Sat, 15 Jan 2022 22:18:00: #1 tag size = 10 INFO @ Sat, 15 Jan 2022 22:18:00: #1 total tags in treatment: 1286223 INFO @ Sat, 15 Jan 2022 22:18:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:18:00: #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 22:18:00: #1 tags after filtering in treatment: 760037 INFO @ Sat, 15 Jan 2022 22:18:00: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 15 Jan 2022 22:18:00: #1 finished! INFO @ Sat, 15 Jan 2022 22:18:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:18:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:18:00: #2 number of paired peaks: 298 WARNING @ Sat, 15 Jan 2022 22:18:00: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Sat, 15 Jan 2022 22:18:00: start model_add_line... INFO @ Sat, 15 Jan 2022 22:18:00: start X-correlation... INFO @ Sat, 15 Jan 2022 22:18:00: end of X-cor INFO @ Sat, 15 Jan 2022 22:18:00: #2 finished! INFO @ Sat, 15 Jan 2022 22:18:00: #2 predicted fragment length is 132 bps INFO @ Sat, 15 Jan 2022 22:18:00: #2 alternative fragment length(s) may be 4,88,109,132 bps INFO @ Sat, 15 Jan 2022 22:18:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.20_model.r INFO @ Sat, 15 Jan 2022 22:18:00: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:18:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:18:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:18:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.20_peaks.xls INFO @ Sat, 15 Jan 2022 22:18:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:18:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.20_summits.bed INFO @ Sat, 15 Jan 2022 22:18:03: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 2 millis CompletedMACS2peakCalling