Job ID = 14519785 SRX = SRX9390805 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2844213 spots for SRR12926700/SRR12926700.sra Written 2844213 spots for SRR12926700/SRR12926700.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: 00:02:08 2844213 reads; of these: 2844213 (100.00%) were paired; of these: 2525700 (88.80%) aligned concordantly 0 times 210713 (7.41%) aligned concordantly exactly 1 time 107800 (3.79%) aligned concordantly >1 times ---- 2525700 pairs aligned concordantly 0 times; of these: 176764 (7.00%) aligned discordantly 1 time ---- 2348936 pairs aligned 0 times concordantly or discordantly; of these: 4697872 mates make up the pairs; of these: 2272250 (48.37%) aligned 0 times 1066397 (22.70%) aligned exactly 1 time 1359225 (28.93%) aligned >1 times 60.05% overall alignment rate Time searching: 00:02:08 Overall time: 00:02:08 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] 79756 / 490436 = 0.1626 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 17:48:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.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 17:48:25: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:48:25: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:48:30: 1000000 INFO @ Sat, 15 Jan 2022 17:48:35: 2000000 INFO @ Sat, 15 Jan 2022 17:48:39: 3000000 INFO @ Sat, 15 Jan 2022 17:48:40: #1 tag size is determined as 26 bps INFO @ Sat, 15 Jan 2022 17:48:40: #1 tag size = 26 INFO @ Sat, 15 Jan 2022 17:48:40: #1 total tags in treatment: 261717 INFO @ Sat, 15 Jan 2022 17:48:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:48:40: #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 17:48:40: #1 tags after filtering in treatment: 212433 INFO @ Sat, 15 Jan 2022 17:48:40: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 17:48:40: #1 finished! INFO @ Sat, 15 Jan 2022 17:48:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:48:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:48:40: #2 number of paired peaks: 239 WARNING @ Sat, 15 Jan 2022 17:48:40: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Sat, 15 Jan 2022 17:48:40: start model_add_line... INFO @ Sat, 15 Jan 2022 17:48:40: start X-correlation... INFO @ Sat, 15 Jan 2022 17:48:40: end of X-cor INFO @ Sat, 15 Jan 2022 17:48:40: #2 finished! INFO @ Sat, 15 Jan 2022 17:48:40: #2 predicted fragment length is 129 bps INFO @ Sat, 15 Jan 2022 17:48:40: #2 alternative fragment length(s) may be 129,574 bps INFO @ Sat, 15 Jan 2022 17:48:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.05_model.r INFO @ Sat, 15 Jan 2022 17:48:40: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:48:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:48:41: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:48:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:48:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:48:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.05_summits.bed INFO @ Sat, 15 Jan 2022 17:48:41: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (427 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 17:48:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.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 17:48:55: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:48:55: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:48:59: 1000000 INFO @ Sat, 15 Jan 2022 17:49:03: 2000000 INFO @ Sat, 15 Jan 2022 17:49:08: 3000000 INFO @ Sat, 15 Jan 2022 17:49:09: #1 tag size is determined as 26 bps INFO @ Sat, 15 Jan 2022 17:49:09: #1 tag size = 26 INFO @ Sat, 15 Jan 2022 17:49:09: #1 total tags in treatment: 261717 INFO @ Sat, 15 Jan 2022 17:49:09: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:49:09: #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 17:49:09: #1 tags after filtering in treatment: 212433 INFO @ Sat, 15 Jan 2022 17:49:09: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 17:49:09: #1 finished! INFO @ Sat, 15 Jan 2022 17:49:09: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:49:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:49:09: #2 number of paired peaks: 239 WARNING @ Sat, 15 Jan 2022 17:49:09: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Sat, 15 Jan 2022 17:49:09: start model_add_line... INFO @ Sat, 15 Jan 2022 17:49:09: start X-correlation... INFO @ Sat, 15 Jan 2022 17:49:09: end of X-cor INFO @ Sat, 15 Jan 2022 17:49:09: #2 finished! INFO @ Sat, 15 Jan 2022 17:49:09: #2 predicted fragment length is 129 bps INFO @ Sat, 15 Jan 2022 17:49:09: #2 alternative fragment length(s) may be 129,574 bps INFO @ Sat, 15 Jan 2022 17:49:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.10_model.r INFO @ Sat, 15 Jan 2022 17:49:09: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:49:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:49:09: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:49:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:49:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:49:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.10_summits.bed INFO @ Sat, 15 Jan 2022 17:49:10: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (117 records, 4 fields): 100 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 17:49:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.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 17:49:25: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:49:25: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:49:29: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:49:34: 2000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:49:38: 3000000 INFO @ Sat, 15 Jan 2022 17:49:39: #1 tag size is determined as 26 bps INFO @ Sat, 15 Jan 2022 17:49:39: #1 tag size = 26 INFO @ Sat, 15 Jan 2022 17:49:39: #1 total tags in treatment: 261717 INFO @ Sat, 15 Jan 2022 17:49:39: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:49:39: #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 17:49:39: #1 tags after filtering in treatment: 212433 INFO @ Sat, 15 Jan 2022 17:49:39: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 17:49:39: #1 finished! INFO @ Sat, 15 Jan 2022 17:49:39: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:49:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:49:39: #2 number of paired peaks: 239 WARNING @ Sat, 15 Jan 2022 17:49:39: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Sat, 15 Jan 2022 17:49:39: start model_add_line... INFO @ Sat, 15 Jan 2022 17:49:39: start X-correlation... INFO @ Sat, 15 Jan 2022 17:49:39: end of X-cor INFO @ Sat, 15 Jan 2022 17:49:39: #2 finished! INFO @ Sat, 15 Jan 2022 17:49:39: #2 predicted fragment length is 129 bps INFO @ Sat, 15 Jan 2022 17:49:39: #2 alternative fragment length(s) may be 129,574 bps INFO @ Sat, 15 Jan 2022 17:49:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.20_model.r INFO @ Sat, 15 Jan 2022 17:49:39: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:49:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:49:40: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:49:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:49:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:49:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9390805/SRX9390805.20_summits.bed INFO @ Sat, 15 Jan 2022 17:49:40: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 333 millis CompletedMACS2peakCalling