Job ID = 14520865 SRX = SRX8245544 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7894431 spots for SRR11684755/SRR11684755.sra Written 7894431 spots for SRR11684755/SRR11684755.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: 00:03:06 7894431 reads; of these: 7894431 (100.00%) were paired; of these: 6303009 (79.84%) aligned concordantly 0 times 1420846 (18.00%) aligned concordantly exactly 1 time 170576 (2.16%) aligned concordantly >1 times ---- 6303009 pairs aligned concordantly 0 times; of these: 1787 (0.03%) aligned discordantly 1 time ---- 6301222 pairs aligned 0 times concordantly or discordantly; of these: 12602444 mates make up the pairs; of these: 11080016 (87.92%) aligned 0 times 1338874 (10.62%) aligned exactly 1 time 183554 (1.46%) aligned >1 times 29.82% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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] 180923 / 1592893 = 0.1136 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 20:06:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.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 20:06:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:06:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:07:03: 1000000 INFO @ Sat, 15 Jan 2022 20:07:12: 2000000 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 20:07:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.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 20:07:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:07:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:07:26: 3000000 INFO @ Sat, 15 Jan 2022 20:07:34: 1000000 INFO @ Sat, 15 Jan 2022 20:07:34: 4000000 INFO @ Sat, 15 Jan 2022 20:07:37: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:07:37: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:07:37: #1 total tags in treatment: 1410560 INFO @ Sat, 15 Jan 2022 20:07:37: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:07:37: #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 20:07:37: #1 tags after filtering in treatment: 1001794 INFO @ Sat, 15 Jan 2022 20:07:37: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 20:07:37: #1 finished! INFO @ Sat, 15 Jan 2022 20:07:37: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:07:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:07:37: #2 number of paired peaks: 193 WARNING @ Sat, 15 Jan 2022 20:07:37: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 15 Jan 2022 20:07:37: start model_add_line... INFO @ Sat, 15 Jan 2022 20:07:37: start X-correlation... INFO @ Sat, 15 Jan 2022 20:07:37: end of X-cor INFO @ Sat, 15 Jan 2022 20:07:37: #2 finished! INFO @ Sat, 15 Jan 2022 20:07:37: #2 predicted fragment length is 152 bps INFO @ Sat, 15 Jan 2022 20:07:37: #2 alternative fragment length(s) may be 2,152,169,580,597 bps INFO @ Sat, 15 Jan 2022 20:07:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.05_model.r INFO @ Sat, 15 Jan 2022 20:07:37: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:07:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:07:41: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:07:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:07:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:07:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.05_summits.bed INFO @ Sat, 15 Jan 2022 20:07:42: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (69 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:07:43: 2000000 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 20:07:52: 3000000 INFO @ Sat, 15 Jan 2022 20:07:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.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 20:07:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:07:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:08:04: 4000000 INFO @ Sat, 15 Jan 2022 20:08:07: 1000000 INFO @ Sat, 15 Jan 2022 20:08:09: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:08:09: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:08:09: #1 total tags in treatment: 1410560 INFO @ Sat, 15 Jan 2022 20:08:09: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:08:09: #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 20:08:09: #1 tags after filtering in treatment: 1001794 INFO @ Sat, 15 Jan 2022 20:08:09: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 20:08:09: #1 finished! INFO @ Sat, 15 Jan 2022 20:08:09: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:08:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:08:09: #2 number of paired peaks: 193 WARNING @ Sat, 15 Jan 2022 20:08:09: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 15 Jan 2022 20:08:09: start model_add_line... INFO @ Sat, 15 Jan 2022 20:08:09: start X-correlation... INFO @ Sat, 15 Jan 2022 20:08:09: end of X-cor INFO @ Sat, 15 Jan 2022 20:08:09: #2 finished! INFO @ Sat, 15 Jan 2022 20:08:09: #2 predicted fragment length is 152 bps INFO @ Sat, 15 Jan 2022 20:08:09: #2 alternative fragment length(s) may be 2,152,169,580,597 bps INFO @ Sat, 15 Jan 2022 20:08:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.10_model.r INFO @ Sat, 15 Jan 2022 20:08:09: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:08:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:08:14: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:08:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:08:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:08:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.10_summits.bed INFO @ Sat, 15 Jan 2022 20:08:16: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (21 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:08:18: 2000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:08:28: 3000000 INFO @ Sat, 15 Jan 2022 20:08:39: 4000000 INFO @ Sat, 15 Jan 2022 20:08:42: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:08:42: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:08:42: #1 total tags in treatment: 1410560 INFO @ Sat, 15 Jan 2022 20:08:42: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:08:42: #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 20:08:42: #1 tags after filtering in treatment: 1001794 INFO @ Sat, 15 Jan 2022 20:08:42: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 20:08:42: #1 finished! INFO @ Sat, 15 Jan 2022 20:08:42: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:08:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:08:42: #2 number of paired peaks: 193 WARNING @ Sat, 15 Jan 2022 20:08:42: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 15 Jan 2022 20:08:42: start model_add_line... INFO @ Sat, 15 Jan 2022 20:08:43: start X-correlation... INFO @ Sat, 15 Jan 2022 20:08:43: end of X-cor INFO @ Sat, 15 Jan 2022 20:08:43: #2 finished! INFO @ Sat, 15 Jan 2022 20:08:43: #2 predicted fragment length is 152 bps INFO @ Sat, 15 Jan 2022 20:08:43: #2 alternative fragment length(s) may be 2,152,169,580,597 bps INFO @ Sat, 15 Jan 2022 20:08:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.20_model.r INFO @ Sat, 15 Jan 2022 20:08:43: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:08:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:08:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:08:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:08:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:08:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245544/SRX8245544.20_summits.bed INFO @ Sat, 15 Jan 2022 20:08:50: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (5 records, 4 fields): 2 millis CompletedMACS2peakCalling