Job ID = 10224058 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: 01:16:34 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: 01:16:34 Overall time: 01:16:34 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 10:42:14: # 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 @ Fri, 16 Oct 2020 10:42:14: #1 read tag files... INFO @ Fri, 16 Oct 2020 10:42:14: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 10:42:18: 1000000 INFO @ Fri, 16 Oct 2020 10:42:23: 2000000 INFO @ Fri, 16 Oct 2020 10:42:28: 3000000 INFO @ Fri, 16 Oct 2020 10:42:33: 4000000 INFO @ Fri, 16 Oct 2020 10:42:37: 5000000 INFO @ Fri, 16 Oct 2020 10:42:42: 6000000 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 10:42:44: # 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 @ Fri, 16 Oct 2020 10:42:44: #1 read tag files... INFO @ Fri, 16 Oct 2020 10:42:44: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 10:42:47: 7000000 INFO @ Fri, 16 Oct 2020 10:42:48: 1000000 INFO @ Fri, 16 Oct 2020 10:42:53: 8000000 INFO @ Fri, 16 Oct 2020 10:42:54: 2000000 INFO @ Fri, 16 Oct 2020 10:42:59: 9000000 INFO @ Fri, 16 Oct 2020 10:42:59: 3000000 INFO @ Fri, 16 Oct 2020 10:43:04: 4000000 INFO @ Fri, 16 Oct 2020 10:43:04: 10000000 INFO @ Fri, 16 Oct 2020 10:43:09: 5000000 INFO @ Fri, 16 Oct 2020 10:43:09: 11000000 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 10:43:13: 6000000 INFO @ Fri, 16 Oct 2020 10:43:14: # 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 @ Fri, 16 Oct 2020 10:43:14: #1 read tag files... INFO @ Fri, 16 Oct 2020 10:43:14: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 10:43:14: 12000000 INFO @ Fri, 16 Oct 2020 10:43:18: 7000000 INFO @ Fri, 16 Oct 2020 10:43:19: 1000000 INFO @ Fri, 16 Oct 2020 10:43:20: 13000000 INFO @ Fri, 16 Oct 2020 10:43:24: 8000000 INFO @ Fri, 16 Oct 2020 10:43:25: 2000000 INFO @ Fri, 16 Oct 2020 10:43:25: 14000000 INFO @ Fri, 16 Oct 2020 10:43:29: 9000000 INFO @ Fri, 16 Oct 2020 10:43:30: 3000000 INFO @ Fri, 16 Oct 2020 10:43:31: 15000000 INFO @ Fri, 16 Oct 2020 10:43:34: 10000000 INFO @ Fri, 16 Oct 2020 10:43:36: 4000000 INFO @ Fri, 16 Oct 2020 10:43:36: 16000000 INFO @ Fri, 16 Oct 2020 10:43:39: 11000000 INFO @ Fri, 16 Oct 2020 10:43:41: 5000000 INFO @ Fri, 16 Oct 2020 10:43:41: 17000000 INFO @ Fri, 16 Oct 2020 10:43:43: 12000000 INFO @ Fri, 16 Oct 2020 10:43:46: 18000000 INFO @ Fri, 16 Oct 2020 10:43:46: 6000000 INFO @ Fri, 16 Oct 2020 10:43:48: 13000000 INFO @ Fri, 16 Oct 2020 10:43:51: 19000000 INFO @ Fri, 16 Oct 2020 10:43:52: 7000000 INFO @ Fri, 16 Oct 2020 10:43:53: 14000000 INFO @ Fri, 16 Oct 2020 10:43:57: 20000000 INFO @ Fri, 16 Oct 2020 10:43:58: 15000000 INFO @ Fri, 16 Oct 2020 10:43:58: 8000000 INFO @ Fri, 16 Oct 2020 10:44:02: 21000000 INFO @ Fri, 16 Oct 2020 10:44:03: 16000000 INFO @ Fri, 16 Oct 2020 10:44:04: 9000000 INFO @ Fri, 16 Oct 2020 10:44:07: 22000000 INFO @ Fri, 16 Oct 2020 10:44:08: 17000000 INFO @ Fri, 16 Oct 2020 10:44:10: 10000000 INFO @ Fri, 16 Oct 2020 10:44:12: 18000000 INFO @ Fri, 16 Oct 2020 10:44:13: 23000000 INFO @ Fri, 16 Oct 2020 10:44:16: 11000000 INFO @ Fri, 16 Oct 2020 10:44:17: 19000000 INFO @ Fri, 16 Oct 2020 10:44:18: 24000000 INFO @ Fri, 16 Oct 2020 10:44:21: 12000000 INFO @ Fri, 16 Oct 2020 10:44:23: 20000000 INFO @ Fri, 16 Oct 2020 10:44:23: 25000000 INFO @ Fri, 16 Oct 2020 10:44:27: 13000000 INFO @ Fri, 16 Oct 2020 10:44:27: 21000000 INFO @ Fri, 16 Oct 2020 10:44:28: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 10:44:32: 22000000 INFO @ Fri, 16 Oct 2020 10:44:32: 14000000 INFO @ Fri, 16 Oct 2020 10:44:33: 27000000 INFO @ Fri, 16 Oct 2020 10:44:37: 23000000 INFO @ Fri, 16 Oct 2020 10:44:38: 15000000 INFO @ Fri, 16 Oct 2020 10:44:38: 28000000 INFO @ Fri, 16 Oct 2020 10:44:40: #1 tag size is determined as 10 bps INFO @ Fri, 16 Oct 2020 10:44:40: #1 tag size = 10 INFO @ Fri, 16 Oct 2020 10:44:40: #1 total tags in treatment: 1286223 INFO @ Fri, 16 Oct 2020 10:44:40: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 10:44:40: #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 10:44:40: #1 tags after filtering in treatment: 760037 INFO @ Fri, 16 Oct 2020 10:44:40: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 16 Oct 2020 10:44:40: #1 finished! INFO @ Fri, 16 Oct 2020 10:44:40: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 10:44:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 10:44:40: #2 number of paired peaks: 298 WARNING @ Fri, 16 Oct 2020 10:44:40: 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 @ Fri, 16 Oct 2020 10:44:40: start model_add_line... INFO @ Fri, 16 Oct 2020 10:44:40: start X-correlation... INFO @ Fri, 16 Oct 2020 10:44:40: end of X-cor INFO @ Fri, 16 Oct 2020 10:44:40: #2 finished! INFO @ Fri, 16 Oct 2020 10:44:40: #2 predicted fragment length is 132 bps INFO @ Fri, 16 Oct 2020 10:44:40: #2 alternative fragment length(s) may be 4,88,109,132 bps INFO @ Fri, 16 Oct 2020 10:44:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.05_model.r INFO @ Fri, 16 Oct 2020 10:44:40: #3 Call peaks... INFO @ Fri, 16 Oct 2020 10:44:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 10:44:42: 24000000 INFO @ Fri, 16 Oct 2020 10:44:43: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 10:44:43: 16000000 INFO @ Fri, 16 Oct 2020 10:44:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.05_peaks.xls INFO @ Fri, 16 Oct 2020 10:44:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 10:44:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.05_summits.bed INFO @ Fri, 16 Oct 2020 10:44:43: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (455 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 10:44:46: 25000000 INFO @ Fri, 16 Oct 2020 10:44:49: 17000000 INFO @ Fri, 16 Oct 2020 10:44:51: 26000000 INFO @ Fri, 16 Oct 2020 10:44:54: 18000000 INFO @ Fri, 16 Oct 2020 10:44:56: 27000000 INFO @ Fri, 16 Oct 2020 10:45:00: 19000000 INFO @ Fri, 16 Oct 2020 10:45:01: 28000000 INFO @ Fri, 16 Oct 2020 10:45:03: #1 tag size is determined as 10 bps INFO @ Fri, 16 Oct 2020 10:45:03: #1 tag size = 10 INFO @ Fri, 16 Oct 2020 10:45:03: #1 total tags in treatment: 1286223 INFO @ Fri, 16 Oct 2020 10:45:03: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 10:45:03: #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 10:45:03: #1 tags after filtering in treatment: 760037 INFO @ Fri, 16 Oct 2020 10:45:03: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 16 Oct 2020 10:45:03: #1 finished! INFO @ Fri, 16 Oct 2020 10:45:03: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 10:45:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 10:45:03: #2 number of paired peaks: 298 WARNING @ Fri, 16 Oct 2020 10:45:03: 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 @ Fri, 16 Oct 2020 10:45:03: start model_add_line... INFO @ Fri, 16 Oct 2020 10:45:03: start X-correlation... INFO @ Fri, 16 Oct 2020 10:45:03: end of X-cor INFO @ Fri, 16 Oct 2020 10:45:03: #2 finished! INFO @ Fri, 16 Oct 2020 10:45:03: #2 predicted fragment length is 132 bps INFO @ Fri, 16 Oct 2020 10:45:03: #2 alternative fragment length(s) may be 4,88,109,132 bps INFO @ Fri, 16 Oct 2020 10:45:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.10_model.r INFO @ Fri, 16 Oct 2020 10:45:03: #3 Call peaks... INFO @ Fri, 16 Oct 2020 10:45:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 10:45:05: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 10:45:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.10_peaks.xls INFO @ Fri, 16 Oct 2020 10:45:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 10:45:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.10_summits.bed INFO @ Fri, 16 Oct 2020 10:45:06: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (290 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 10:45:06: 20000000 INFO @ Fri, 16 Oct 2020 10:45:11: 21000000 INFO @ Fri, 16 Oct 2020 10:45:16: 22000000 INFO @ Fri, 16 Oct 2020 10:45:22: 23000000 INFO @ Fri, 16 Oct 2020 10:45:27: 24000000 INFO @ Fri, 16 Oct 2020 10:45:32: 25000000 INFO @ Fri, 16 Oct 2020 10:45:37: 26000000 INFO @ Fri, 16 Oct 2020 10:45:42: 27000000 INFO @ Fri, 16 Oct 2020 10:45:47: 28000000 INFO @ Fri, 16 Oct 2020 10:45:49: #1 tag size is determined as 10 bps INFO @ Fri, 16 Oct 2020 10:45:49: #1 tag size = 10 INFO @ Fri, 16 Oct 2020 10:45:49: #1 total tags in treatment: 1286223 INFO @ Fri, 16 Oct 2020 10:45:49: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 10:45:49: #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 10:45:49: #1 tags after filtering in treatment: 760037 INFO @ Fri, 16 Oct 2020 10:45:49: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 16 Oct 2020 10:45:49: #1 finished! INFO @ Fri, 16 Oct 2020 10:45:49: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 10:45:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 10:45:49: #2 number of paired peaks: 298 WARNING @ Fri, 16 Oct 2020 10:45:49: 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 @ Fri, 16 Oct 2020 10:45:49: start model_add_line... INFO @ Fri, 16 Oct 2020 10:45:49: start X-correlation... INFO @ Fri, 16 Oct 2020 10:45:49: end of X-cor INFO @ Fri, 16 Oct 2020 10:45:49: #2 finished! INFO @ Fri, 16 Oct 2020 10:45:49: #2 predicted fragment length is 132 bps INFO @ Fri, 16 Oct 2020 10:45:49: #2 alternative fragment length(s) may be 4,88,109,132 bps INFO @ Fri, 16 Oct 2020 10:45:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.20_model.r INFO @ Fri, 16 Oct 2020 10:45:49: #3 Call peaks... INFO @ Fri, 16 Oct 2020 10:45:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 10:45:52: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 10:45:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.20_peaks.xls INFO @ Fri, 16 Oct 2020 10:45:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 10:45:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952615/SRX8952615.20_summits.bed INFO @ Fri, 16 Oct 2020 10:45:52: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 1 millis CompletedMACS2peakCalling