Job ID = 14522041 SRX = SRX9773808 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 46191459 spots for SRR13347749/SRR13347749.sra Written 46191459 spots for SRR13347749/SRR13347749.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: 00:23:27 46191459 reads; of these: 46191459 (100.00%) were paired; of these: 10942326 (23.69%) aligned concordantly 0 times 23118844 (50.05%) aligned concordantly exactly 1 time 12130289 (26.26%) aligned concordantly >1 times ---- 10942326 pairs aligned concordantly 0 times; of these: 3647888 (33.34%) aligned discordantly 1 time ---- 7294438 pairs aligned 0 times concordantly or discordantly; of these: 14588876 mates make up the pairs; of these: 2836366 (19.44%) aligned 0 times 3445070 (23.61%) aligned exactly 1 time 8307440 (56.94%) aligned >1 times 96.93% overall alignment rate Time searching: 00:23:27 Overall time: 00:23:27 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_sort_core] merging from 32 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] 31585798 / 38885053 = 0.8123 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 22:40:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.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 22:40:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:40:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:40:46: 1000000 INFO @ Sat, 15 Jan 2022 22:40:51: 2000000 INFO @ Sat, 15 Jan 2022 22:40:56: 3000000 INFO @ Sat, 15 Jan 2022 22:41:00: 4000000 INFO @ Sat, 15 Jan 2022 22:41:04: 5000000 INFO @ Sat, 15 Jan 2022 22:41:09: 6000000 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 22:41:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.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 22:41:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:41:11: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:41:13: 7000000 INFO @ Sat, 15 Jan 2022 22:41:17: 1000000 INFO @ Sat, 15 Jan 2022 22:41:19: 8000000 INFO @ Sat, 15 Jan 2022 22:41:22: 2000000 INFO @ Sat, 15 Jan 2022 22:41:23: 9000000 INFO @ Sat, 15 Jan 2022 22:41:27: 3000000 INFO @ Sat, 15 Jan 2022 22:41:28: 10000000 INFO @ Sat, 15 Jan 2022 22:41:32: 4000000 INFO @ Sat, 15 Jan 2022 22:41:34: 11000000 INFO @ Sat, 15 Jan 2022 22:41:37: 5000000 INFO @ Sat, 15 Jan 2022 22:41:39: 12000000 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 22:41:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.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 22:41:41: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:41:41: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:41:43: 6000000 INFO @ Sat, 15 Jan 2022 22:41:44: 13000000 INFO @ Sat, 15 Jan 2022 22:41:47: 1000000 INFO @ Sat, 15 Jan 2022 22:41:48: 7000000 INFO @ Sat, 15 Jan 2022 22:41:49: 14000000 INFO @ Sat, 15 Jan 2022 22:41:52: 2000000 INFO @ Sat, 15 Jan 2022 22:41:53: 8000000 INFO @ Sat, 15 Jan 2022 22:41:54: 15000000 INFO @ Sat, 15 Jan 2022 22:41:57: 3000000 INFO @ Sat, 15 Jan 2022 22:41:58: 9000000 INFO @ Sat, 15 Jan 2022 22:41:59: 16000000 INFO @ Sat, 15 Jan 2022 22:42:03: 4000000 INFO @ Sat, 15 Jan 2022 22:42:03: 10000000 INFO @ Sat, 15 Jan 2022 22:42:03: 17000000 INFO @ Sat, 15 Jan 2022 22:42:08: 5000000 INFO @ Sat, 15 Jan 2022 22:42:08: 11000000 INFO @ Sat, 15 Jan 2022 22:42:08: 18000000 INFO @ Sat, 15 Jan 2022 22:42:13: 6000000 INFO @ Sat, 15 Jan 2022 22:42:13: 19000000 INFO @ Sat, 15 Jan 2022 22:42:13: 12000000 INFO @ Sat, 15 Jan 2022 22:42:19: 13000000 INFO @ Sat, 15 Jan 2022 22:42:19: 7000000 INFO @ Sat, 15 Jan 2022 22:42:19: 20000000 INFO @ Sat, 15 Jan 2022 22:42:24: 14000000 INFO @ Sat, 15 Jan 2022 22:42:24: 8000000 INFO @ Sat, 15 Jan 2022 22:42:24: 21000000 INFO @ Sat, 15 Jan 2022 22:42:28: 15000000 INFO @ Sat, 15 Jan 2022 22:42:29: 9000000 INFO @ Sat, 15 Jan 2022 22:42:29: 22000000 INFO @ Sat, 15 Jan 2022 22:42:33: 16000000 INFO @ Sat, 15 Jan 2022 22:42:34: 10000000 INFO @ Sat, 15 Jan 2022 22:42:34: 23000000 INFO @ Sat, 15 Jan 2022 22:42:38: 17000000 INFO @ Sat, 15 Jan 2022 22:42:39: 11000000 INFO @ Sat, 15 Jan 2022 22:42:39: 24000000 INFO @ Sat, 15 Jan 2022 22:42:43: 18000000 INFO @ Sat, 15 Jan 2022 22:42:44: 12000000 INFO @ Sat, 15 Jan 2022 22:42:45: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:42:48: 19000000 INFO @ Sat, 15 Jan 2022 22:42:49: 13000000 INFO @ Sat, 15 Jan 2022 22:42:50: 26000000 INFO @ Sat, 15 Jan 2022 22:42:52: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 22:42:52: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 22:42:52: #1 total tags in treatment: 6070379 INFO @ Sat, 15 Jan 2022 22:42:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:42:52: #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 22:42:52: #1 tags after filtering in treatment: 2856489 INFO @ Sat, 15 Jan 2022 22:42:52: #1 Redundant rate of treatment: 0.53 INFO @ Sat, 15 Jan 2022 22:42:52: #1 finished! INFO @ Sat, 15 Jan 2022 22:42:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:42:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:42:52: #2 number of paired peaks: 144 WARNING @ Sat, 15 Jan 2022 22:42:52: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Sat, 15 Jan 2022 22:42:52: start model_add_line... INFO @ Sat, 15 Jan 2022 22:42:52: start X-correlation... INFO @ Sat, 15 Jan 2022 22:42:52: end of X-cor INFO @ Sat, 15 Jan 2022 22:42:52: #2 finished! INFO @ Sat, 15 Jan 2022 22:42:52: #2 predicted fragment length is 276 bps INFO @ Sat, 15 Jan 2022 22:42:52: #2 alternative fragment length(s) may be 2,276 bps INFO @ Sat, 15 Jan 2022 22:42:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.05_model.r INFO @ Sat, 15 Jan 2022 22:42:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:42:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:42:53: 20000000 INFO @ Sat, 15 Jan 2022 22:42:54: 14000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 22:42:58: 21000000 INFO @ Sat, 15 Jan 2022 22:42:59: 15000000 INFO @ Sat, 15 Jan 2022 22:43:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:43:03: 22000000 INFO @ Sat, 15 Jan 2022 22:43:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.05_peaks.xls INFO @ Sat, 15 Jan 2022 22:43:04: 16000000 INFO @ Sat, 15 Jan 2022 22:43:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:43:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.05_summits.bed INFO @ Sat, 15 Jan 2022 22:43:04: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (2824 records, 4 fields): 129 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:43:08: 23000000 INFO @ Sat, 15 Jan 2022 22:43:09: 17000000 INFO @ Sat, 15 Jan 2022 22:43:13: 24000000 INFO @ Sat, 15 Jan 2022 22:43:13: 18000000 INFO @ Sat, 15 Jan 2022 22:43:18: 25000000 INFO @ Sat, 15 Jan 2022 22:43:18: 19000000 INFO @ Sat, 15 Jan 2022 22:43:23: 26000000 INFO @ Sat, 15 Jan 2022 22:43:23: 20000000 INFO @ Sat, 15 Jan 2022 22:43:25: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 22:43:25: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 22:43:25: #1 total tags in treatment: 6070379 INFO @ Sat, 15 Jan 2022 22:43:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:43:25: #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 22:43:25: #1 tags after filtering in treatment: 2856489 INFO @ Sat, 15 Jan 2022 22:43:25: #1 Redundant rate of treatment: 0.53 INFO @ Sat, 15 Jan 2022 22:43:25: #1 finished! INFO @ Sat, 15 Jan 2022 22:43:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:43:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:43:25: #2 number of paired peaks: 144 WARNING @ Sat, 15 Jan 2022 22:43:25: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Sat, 15 Jan 2022 22:43:25: start model_add_line... INFO @ Sat, 15 Jan 2022 22:43:25: start X-correlation... INFO @ Sat, 15 Jan 2022 22:43:25: end of X-cor INFO @ Sat, 15 Jan 2022 22:43:25: #2 finished! INFO @ Sat, 15 Jan 2022 22:43:25: #2 predicted fragment length is 276 bps INFO @ Sat, 15 Jan 2022 22:43:25: #2 alternative fragment length(s) may be 2,276 bps INFO @ Sat, 15 Jan 2022 22:43:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.10_model.r INFO @ Sat, 15 Jan 2022 22:43:25: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:43:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:43:28: 21000000 INFO @ Sat, 15 Jan 2022 22:43:33: 22000000 INFO @ Sat, 15 Jan 2022 22:43:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:43:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.10_peaks.xls INFO @ Sat, 15 Jan 2022 22:43:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:43:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.10_summits.bed INFO @ Sat, 15 Jan 2022 22:43:36: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1574 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:43:38: 23000000 INFO @ Sat, 15 Jan 2022 22:43:42: 24000000 INFO @ Sat, 15 Jan 2022 22:43:47: 25000000 INFO @ Sat, 15 Jan 2022 22:43:52: 26000000 INFO @ Sat, 15 Jan 2022 22:43:54: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 22:43:54: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 22:43:54: #1 total tags in treatment: 6070379 INFO @ Sat, 15 Jan 2022 22:43:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:43:54: #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 22:43:54: #1 tags after filtering in treatment: 2856489 INFO @ Sat, 15 Jan 2022 22:43:54: #1 Redundant rate of treatment: 0.53 INFO @ Sat, 15 Jan 2022 22:43:54: #1 finished! INFO @ Sat, 15 Jan 2022 22:43:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:43:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:43:54: #2 number of paired peaks: 144 WARNING @ Sat, 15 Jan 2022 22:43:54: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Sat, 15 Jan 2022 22:43:54: start model_add_line... INFO @ Sat, 15 Jan 2022 22:43:54: start X-correlation... INFO @ Sat, 15 Jan 2022 22:43:54: end of X-cor INFO @ Sat, 15 Jan 2022 22:43:54: #2 finished! INFO @ Sat, 15 Jan 2022 22:43:54: #2 predicted fragment length is 276 bps INFO @ Sat, 15 Jan 2022 22:43:54: #2 alternative fragment length(s) may be 2,276 bps INFO @ Sat, 15 Jan 2022 22:43:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.20_model.r INFO @ Sat, 15 Jan 2022 22:43:54: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:43:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:44:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:44:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.20_peaks.xls INFO @ Sat, 15 Jan 2022 22:44:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:44:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9773808/SRX9773808.20_summits.bed INFO @ Sat, 15 Jan 2022 22:44:05: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (578 records, 4 fields): 2 millis CompletedMACS2peakCalling