Job ID = 14519833 SRX = SRX8829408 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23829358 spots for SRR12329188/SRR12329188.sra Written 23829358 spots for SRR12329188/SRR12329188.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: 00:13:27 23829358 reads; of these: 23829358 (100.00%) were paired; of these: 2688930 (11.28%) aligned concordantly 0 times 15287741 (64.16%) aligned concordantly exactly 1 time 5852687 (24.56%) aligned concordantly >1 times ---- 2688930 pairs aligned concordantly 0 times; of these: 238285 (8.86%) aligned discordantly 1 time ---- 2450645 pairs aligned 0 times concordantly or discordantly; of these: 4901290 mates make up the pairs; of these: 3139399 (64.05%) aligned 0 times 1076871 (21.97%) aligned exactly 1 time 685020 (13.98%) aligned >1 times 93.41% overall alignment rate Time searching: 00:13:27 Overall time: 00:13:27 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 20 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] 20007970 / 21323457 = 0.9383 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 18:12:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.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 18:12:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:12:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:12:41: 1000000 INFO @ Sat, 15 Jan 2022 18:12:45: 2000000 INFO @ Sat, 15 Jan 2022 18:12:49: 3000000 INFO @ Sat, 15 Jan 2022 18:12:53: 4000000 INFO @ Sat, 15 Jan 2022 18:12:55: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:12:55: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:12:55: #1 total tags in treatment: 1321251 INFO @ Sat, 15 Jan 2022 18:12:55: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:12:55: #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 18:12:55: #1 tags after filtering in treatment: 904085 INFO @ Sat, 15 Jan 2022 18:12:55: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 15 Jan 2022 18:12:55: #1 finished! INFO @ Sat, 15 Jan 2022 18:12:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:12:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:12:55: #2 number of paired peaks: 394 WARNING @ Sat, 15 Jan 2022 18:12:55: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Sat, 15 Jan 2022 18:12:55: start model_add_line... INFO @ Sat, 15 Jan 2022 18:12:55: start X-correlation... INFO @ Sat, 15 Jan 2022 18:12:55: end of X-cor INFO @ Sat, 15 Jan 2022 18:12:55: #2 finished! INFO @ Sat, 15 Jan 2022 18:12:55: #2 predicted fragment length is 145 bps INFO @ Sat, 15 Jan 2022 18:12:55: #2 alternative fragment length(s) may be 2,127,145,478,546,563,598 bps INFO @ Sat, 15 Jan 2022 18:12:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.05_model.r INFO @ Sat, 15 Jan 2022 18:12:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:12:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:12:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:12:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.05_peaks.xls INFO @ Sat, 15 Jan 2022 18:12:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:12:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.05_summits.bed INFO @ Sat, 15 Jan 2022 18:12:59: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (543 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 18:13:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.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 18:13:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:13:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:13:11: 1000000 INFO @ Sat, 15 Jan 2022 18:13:15: 2000000 INFO @ Sat, 15 Jan 2022 18:13:19: 3000000 INFO @ Sat, 15 Jan 2022 18:13:23: 4000000 INFO @ Sat, 15 Jan 2022 18:13:25: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:13:25: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:13:25: #1 total tags in treatment: 1321251 INFO @ Sat, 15 Jan 2022 18:13:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:13:25: #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 18:13:25: #1 tags after filtering in treatment: 904085 INFO @ Sat, 15 Jan 2022 18:13:25: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 15 Jan 2022 18:13:25: #1 finished! INFO @ Sat, 15 Jan 2022 18:13:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:13:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:13:25: #2 number of paired peaks: 394 WARNING @ Sat, 15 Jan 2022 18:13:25: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Sat, 15 Jan 2022 18:13:25: start model_add_line... INFO @ Sat, 15 Jan 2022 18:13:25: start X-correlation... INFO @ Sat, 15 Jan 2022 18:13:25: end of X-cor INFO @ Sat, 15 Jan 2022 18:13:25: #2 finished! INFO @ Sat, 15 Jan 2022 18:13:25: #2 predicted fragment length is 145 bps INFO @ Sat, 15 Jan 2022 18:13:25: #2 alternative fragment length(s) may be 2,127,145,478,546,563,598 bps INFO @ Sat, 15 Jan 2022 18:13:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.10_model.r INFO @ Sat, 15 Jan 2022 18:13:25: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:13:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:13:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:13:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.10_peaks.xls INFO @ Sat, 15 Jan 2022 18:13:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:13:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.10_summits.bed INFO @ Sat, 15 Jan 2022 18:13:29: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (274 records, 4 fields): 2 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 18:13:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.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 18:13:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:13:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:13:41: 1000000 INFO @ Sat, 15 Jan 2022 18:13:45: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 18:13:50: 3000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 18:13:54: 4000000 INFO @ Sat, 15 Jan 2022 18:13:56: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:13:56: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:13:56: #1 total tags in treatment: 1321251 INFO @ Sat, 15 Jan 2022 18:13:56: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:13:56: #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 18:13:56: #1 tags after filtering in treatment: 904085 INFO @ Sat, 15 Jan 2022 18:13:56: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 15 Jan 2022 18:13:56: #1 finished! INFO @ Sat, 15 Jan 2022 18:13:56: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:13:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:13:56: #2 number of paired peaks: 394 WARNING @ Sat, 15 Jan 2022 18:13:56: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Sat, 15 Jan 2022 18:13:56: start model_add_line... INFO @ Sat, 15 Jan 2022 18:13:56: start X-correlation... INFO @ Sat, 15 Jan 2022 18:13:56: end of X-cor INFO @ Sat, 15 Jan 2022 18:13:56: #2 finished! INFO @ Sat, 15 Jan 2022 18:13:56: #2 predicted fragment length is 145 bps INFO @ Sat, 15 Jan 2022 18:13:56: #2 alternative fragment length(s) may be 2,127,145,478,546,563,598 bps INFO @ Sat, 15 Jan 2022 18:13:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.20_model.r INFO @ Sat, 15 Jan 2022 18:13:56: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:13:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:13:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:14:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.20_peaks.xls INFO @ Sat, 15 Jan 2022 18:14:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:14:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8829408/SRX8829408.20_summits.bed INFO @ Sat, 15 Jan 2022 18:14:00: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (87 records, 4 fields): 1 millis CompletedMACS2peakCalling