Job ID = 12531704 SRX = SRX5521488 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2386179 spots for SRR8728299/SRR8728299.sra Written 2386179 spots for SRR8728299/SRR8728299.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: 00:02:14 2386179 reads; of these: 2386179 (100.00%) were paired; of these: 713179 (29.89%) aligned concordantly 0 times 1074413 (45.03%) aligned concordantly exactly 1 time 598587 (25.09%) aligned concordantly >1 times ---- 713179 pairs aligned concordantly 0 times; of these: 150668 (21.13%) aligned discordantly 1 time ---- 562511 pairs aligned 0 times concordantly or discordantly; of these: 1125022 mates make up the pairs; of these: 922938 (82.04%) aligned 0 times 33696 (3.00%) aligned exactly 1 time 168388 (14.97%) aligned >1 times 80.66% overall alignment rate Time searching: 00:02:14 Overall time: 00:02:14 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] 253989 / 1811140 = 0.1402 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:18:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.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, 17 Apr 2021 09:18:43: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:18:43: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:18:50: 1000000 INFO @ Sat, 17 Apr 2021 09:18:56: 2000000 INFO @ Sat, 17 Apr 2021 09:19:03: 3000000 INFO @ Sat, 17 Apr 2021 09:19:05: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 09:19:05: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 09:19:05: #1 total tags in treatment: 1428874 INFO @ Sat, 17 Apr 2021 09:19:05: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:19:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:19:05: #1 tags after filtering in treatment: 912343 INFO @ Sat, 17 Apr 2021 09:19:05: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 17 Apr 2021 09:19:05: #1 finished! INFO @ Sat, 17 Apr 2021 09:19:05: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:19:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:19:05: #2 number of paired peaks: 334 WARNING @ Sat, 17 Apr 2021 09:19:05: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Sat, 17 Apr 2021 09:19:05: start model_add_line... INFO @ Sat, 17 Apr 2021 09:19:05: start X-correlation... INFO @ Sat, 17 Apr 2021 09:19:05: end of X-cor INFO @ Sat, 17 Apr 2021 09:19:05: #2 finished! INFO @ Sat, 17 Apr 2021 09:19:05: #2 predicted fragment length is 89 bps INFO @ Sat, 17 Apr 2021 09:19:05: #2 alternative fragment length(s) may be 4,89,108 bps INFO @ Sat, 17 Apr 2021 09:19:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.05_model.r WARNING @ Sat, 17 Apr 2021 09:19:05: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:19:05: #2 You may need to consider one of the other alternative d(s): 4,89,108 WARNING @ Sat, 17 Apr 2021 09:19:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:19:05: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:19:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:19:08: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:19:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.05_peaks.xls INFO @ Sat, 17 Apr 2021 09:19:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:19:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.05_summits.bed INFO @ Sat, 17 Apr 2021 09:19:09: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (1077 records, 4 fields): 7 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:19:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.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, 17 Apr 2021 09:19:13: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:19:13: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:19:20: 1000000 INFO @ Sat, 17 Apr 2021 09:19:26: 2000000 INFO @ Sat, 17 Apr 2021 09:19:33: 3000000 INFO @ Sat, 17 Apr 2021 09:19:35: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 09:19:35: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 09:19:35: #1 total tags in treatment: 1428874 INFO @ Sat, 17 Apr 2021 09:19:35: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:19:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:19:35: #1 tags after filtering in treatment: 912343 INFO @ Sat, 17 Apr 2021 09:19:35: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 17 Apr 2021 09:19:35: #1 finished! INFO @ Sat, 17 Apr 2021 09:19:35: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:19:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:19:35: #2 number of paired peaks: 334 WARNING @ Sat, 17 Apr 2021 09:19:35: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Sat, 17 Apr 2021 09:19:35: start model_add_line... INFO @ Sat, 17 Apr 2021 09:19:35: start X-correlation... INFO @ Sat, 17 Apr 2021 09:19:35: end of X-cor INFO @ Sat, 17 Apr 2021 09:19:35: #2 finished! INFO @ Sat, 17 Apr 2021 09:19:35: #2 predicted fragment length is 89 bps INFO @ Sat, 17 Apr 2021 09:19:35: #2 alternative fragment length(s) may be 4,89,108 bps INFO @ Sat, 17 Apr 2021 09:19:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.10_model.r WARNING @ Sat, 17 Apr 2021 09:19:35: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:19:35: #2 You may need to consider one of the other alternative d(s): 4,89,108 WARNING @ Sat, 17 Apr 2021 09:19:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:19:35: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:19:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:19:38: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:19:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.10_peaks.xls INFO @ Sat, 17 Apr 2021 09:19:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:19:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.10_summits.bed INFO @ Sat, 17 Apr 2021 09:19:39: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (647 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:19:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.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, 17 Apr 2021 09:19:43: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:19:43: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:19:50: 1000000 INFO @ Sat, 17 Apr 2021 09:19:56: 2000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:20:03: 3000000 INFO @ Sat, 17 Apr 2021 09:20:05: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 09:20:05: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 09:20:05: #1 total tags in treatment: 1428874 INFO @ Sat, 17 Apr 2021 09:20:05: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:20:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:20:05: #1 tags after filtering in treatment: 912343 INFO @ Sat, 17 Apr 2021 09:20:05: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 17 Apr 2021 09:20:05: #1 finished! INFO @ Sat, 17 Apr 2021 09:20:05: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:20:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:20:05: #2 number of paired peaks: 334 WARNING @ Sat, 17 Apr 2021 09:20:05: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Sat, 17 Apr 2021 09:20:05: start model_add_line... INFO @ Sat, 17 Apr 2021 09:20:05: start X-correlation... INFO @ Sat, 17 Apr 2021 09:20:05: end of X-cor INFO @ Sat, 17 Apr 2021 09:20:05: #2 finished! INFO @ Sat, 17 Apr 2021 09:20:05: #2 predicted fragment length is 89 bps INFO @ Sat, 17 Apr 2021 09:20:05: #2 alternative fragment length(s) may be 4,89,108 bps INFO @ Sat, 17 Apr 2021 09:20:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.20_model.r WARNING @ Sat, 17 Apr 2021 09:20:05: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:20:05: #2 You may need to consider one of the other alternative d(s): 4,89,108 WARNING @ Sat, 17 Apr 2021 09:20:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:20:05: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:20:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:20:08: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:20:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.20_peaks.xls INFO @ Sat, 17 Apr 2021 09:20:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:20:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521488/SRX5521488.20_summits.bed INFO @ Sat, 17 Apr 2021 09:20:09: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (205 records, 4 fields): 4 millis CompletedMACS2peakCalling