Job ID = 14521308 SRX = SRX8952627 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4493082 spots for SRR12458259/SRR12458259.sra Written 4493082 spots for SRR12458259/SRR12458259.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: 00:01:43 4493082 reads; of these: 4493082 (100.00%) were paired; of these: 3073391 (68.40%) aligned concordantly 0 times 1185342 (26.38%) aligned concordantly exactly 1 time 234349 (5.22%) aligned concordantly >1 times ---- 3073391 pairs aligned concordantly 0 times; of these: 560497 (18.24%) aligned discordantly 1 time ---- 2512894 pairs aligned 0 times concordantly or discordantly; of these: 5025788 mates make up the pairs; of these: 3617265 (71.97%) aligned 0 times 1109689 (22.08%) aligned exactly 1 time 298834 (5.95%) aligned >1 times 59.75% overall alignment rate Time searching: 00:01:43 Overall time: 00:01:43 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] 298945 / 1686033 = 0.1773 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 20:51:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.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 20:51:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:51:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:51:50: 1000000 INFO @ Sat, 15 Jan 2022 20:51:55: 2000000 INFO @ Sat, 15 Jan 2022 20:52:01: 3000000 INFO @ Sat, 15 Jan 2022 20:52:06: 4000000 INFO @ Sat, 15 Jan 2022 20:52:11: #1 tag size is determined as 39 bps INFO @ Sat, 15 Jan 2022 20:52:11: #1 tag size = 39 INFO @ Sat, 15 Jan 2022 20:52:11: #1 total tags in treatment: 1260411 INFO @ Sat, 15 Jan 2022 20:52:11: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:52:11: #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 20:52:11: #1 tags after filtering in treatment: 1087336 INFO @ Sat, 15 Jan 2022 20:52:11: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Jan 2022 20:52:11: #1 finished! INFO @ Sat, 15 Jan 2022 20:52:11: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:52:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:52:11: #2 number of paired peaks: 162 WARNING @ Sat, 15 Jan 2022 20:52:11: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Sat, 15 Jan 2022 20:52:11: start model_add_line... INFO @ Sat, 15 Jan 2022 20:52:11: start X-correlation... INFO @ Sat, 15 Jan 2022 20:52:11: end of X-cor INFO @ Sat, 15 Jan 2022 20:52:11: #2 finished! INFO @ Sat, 15 Jan 2022 20:52:11: #2 predicted fragment length is 235 bps INFO @ Sat, 15 Jan 2022 20:52:11: #2 alternative fragment length(s) may be 235 bps INFO @ Sat, 15 Jan 2022 20:52:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.05_model.r INFO @ Sat, 15 Jan 2022 20:52:11: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:52:11: #3 Pre-compute pvalue-qvalue table... 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 20:52:14: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:52:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:52:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:52:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.05_summits.bed INFO @ Sat, 15 Jan 2022 20:52:15: Done! INFO @ Sat, 15 Jan 2022 20:52:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.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 20:52:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:52:15: #1 read treatment tags... pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (512 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:52:19: 1000000 INFO @ Sat, 15 Jan 2022 20:52:24: 2000000 INFO @ Sat, 15 Jan 2022 20:52:28: 3000000 INFO @ Sat, 15 Jan 2022 20:52:33: 4000000 INFO @ Sat, 15 Jan 2022 20:52:36: #1 tag size is determined as 39 bps INFO @ Sat, 15 Jan 2022 20:52:36: #1 tag size = 39 INFO @ Sat, 15 Jan 2022 20:52:36: #1 total tags in treatment: 1260411 INFO @ Sat, 15 Jan 2022 20:52:36: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:52:36: #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 20:52:36: #1 tags after filtering in treatment: 1087336 INFO @ Sat, 15 Jan 2022 20:52:36: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Jan 2022 20:52:36: #1 finished! INFO @ Sat, 15 Jan 2022 20:52:36: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:52:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:52:36: #2 number of paired peaks: 162 WARNING @ Sat, 15 Jan 2022 20:52:36: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Sat, 15 Jan 2022 20:52:36: start model_add_line... INFO @ Sat, 15 Jan 2022 20:52:36: start X-correlation... INFO @ Sat, 15 Jan 2022 20:52:36: end of X-cor INFO @ Sat, 15 Jan 2022 20:52:36: #2 finished! INFO @ Sat, 15 Jan 2022 20:52:36: #2 predicted fragment length is 235 bps INFO @ Sat, 15 Jan 2022 20:52:36: #2 alternative fragment length(s) may be 235 bps INFO @ Sat, 15 Jan 2022 20:52:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.10_model.r INFO @ Sat, 15 Jan 2022 20:52:36: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:52:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:52:39: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:52:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:52:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:52:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.10_summits.bed INFO @ Sat, 15 Jan 2022 20:52:40: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (308 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 20:52:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.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 20:52:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:52:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:52:49: 1000000 INFO @ Sat, 15 Jan 2022 20:52:53: 2000000 INFO @ Sat, 15 Jan 2022 20:52:58: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:53:02: 4000000 INFO @ Sat, 15 Jan 2022 20:53:05: #1 tag size is determined as 39 bps INFO @ Sat, 15 Jan 2022 20:53:05: #1 tag size = 39 INFO @ Sat, 15 Jan 2022 20:53:05: #1 total tags in treatment: 1260411 INFO @ Sat, 15 Jan 2022 20:53:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:53:05: #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 20:53:05: #1 tags after filtering in treatment: 1087336 INFO @ Sat, 15 Jan 2022 20:53:05: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Jan 2022 20:53:05: #1 finished! INFO @ Sat, 15 Jan 2022 20:53:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:53:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:53:05: #2 number of paired peaks: 162 WARNING @ Sat, 15 Jan 2022 20:53:05: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Sat, 15 Jan 2022 20:53:05: start model_add_line... INFO @ Sat, 15 Jan 2022 20:53:05: start X-correlation... INFO @ Sat, 15 Jan 2022 20:53:05: end of X-cor INFO @ Sat, 15 Jan 2022 20:53:05: #2 finished! INFO @ Sat, 15 Jan 2022 20:53:05: #2 predicted fragment length is 235 bps INFO @ Sat, 15 Jan 2022 20:53:05: #2 alternative fragment length(s) may be 235 bps INFO @ Sat, 15 Jan 2022 20:53:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.20_model.r INFO @ Sat, 15 Jan 2022 20:53:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:53:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:53:08: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:53:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:53:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:53:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952627/SRX8952627.20_summits.bed INFO @ Sat, 15 Jan 2022 20:53:09: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 2 millis CompletedMACS2peakCalling