Job ID = 12531709 SRX = SRX5521490 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2280626 spots for SRR8728301/SRR8728301.sra Written 2280626 spots for SRR8728301/SRR8728301.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: 00:01:58 2280626 reads; of these: 2280626 (100.00%) were paired; of these: 691016 (30.30%) aligned concordantly 0 times 1008868 (44.24%) aligned concordantly exactly 1 time 580742 (25.46%) aligned concordantly >1 times ---- 691016 pairs aligned concordantly 0 times; of these: 139492 (20.19%) aligned discordantly 1 time ---- 551524 pairs aligned 0 times concordantly or discordantly; of these: 1103048 mates make up the pairs; of these: 912125 (82.69%) aligned 0 times 31443 (2.85%) aligned exactly 1 time 159480 (14.46%) aligned >1 times 80.00% overall alignment rate Time searching: 00:01:59 Overall time: 00:01:59 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] 251349 / 1716622 = 0.1464 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 09:19:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.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 09:19:32: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:19:32: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:19:38: 1000000 INFO @ Sat, 17 Apr 2021 09:19:44: 2000000 INFO @ Sat, 17 Apr 2021 09:19:50: 3000000 INFO @ Sat, 17 Apr 2021 09:19:50: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 09:19:50: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 09:19:50: #1 total tags in treatment: 1348601 INFO @ Sat, 17 Apr 2021 09:19:50: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:19:50: #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 09:19:50: #1 tags after filtering in treatment: 837029 INFO @ Sat, 17 Apr 2021 09:19:50: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 17 Apr 2021 09:19:50: #1 finished! INFO @ Sat, 17 Apr 2021 09:19:50: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:19:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:19:51: #2 number of paired peaks: 477 WARNING @ Sat, 17 Apr 2021 09:19:51: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Sat, 17 Apr 2021 09:19:51: start model_add_line... INFO @ Sat, 17 Apr 2021 09:19:51: start X-correlation... INFO @ Sat, 17 Apr 2021 09:19:51: end of X-cor INFO @ Sat, 17 Apr 2021 09:19:51: #2 finished! INFO @ Sat, 17 Apr 2021 09:19:51: #2 predicted fragment length is 113 bps INFO @ Sat, 17 Apr 2021 09:19:51: #2 alternative fragment length(s) may be 113 bps INFO @ Sat, 17 Apr 2021 09:19:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.05_model.r WARNING @ Sat, 17 Apr 2021 09:19:51: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:19:51: #2 You may need to consider one of the other alternative d(s): 113 WARNING @ Sat, 17 Apr 2021 09:19:51: #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 09:19:51: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:19:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:19:53: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:19:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.05_peaks.xls INFO @ Sat, 17 Apr 2021 09:19:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:19:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.05_summits.bed INFO @ Sat, 17 Apr 2021 09:19:54: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1072 records, 4 fields): 3 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 09:20:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.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 09:20:03: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:20:03: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:20:09: 1000000 INFO @ Sat, 17 Apr 2021 09:20:15: 2000000 INFO @ Sat, 17 Apr 2021 09:20:20: 3000000 INFO @ Sat, 17 Apr 2021 09:20:21: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 09:20:21: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 09:20:21: #1 total tags in treatment: 1348601 INFO @ Sat, 17 Apr 2021 09:20:21: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:20:21: #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 09:20:21: #1 tags after filtering in treatment: 837029 INFO @ Sat, 17 Apr 2021 09:20:21: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 17 Apr 2021 09:20:21: #1 finished! INFO @ Sat, 17 Apr 2021 09:20:21: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:20:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:20:21: #2 number of paired peaks: 477 WARNING @ Sat, 17 Apr 2021 09:20:21: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Sat, 17 Apr 2021 09:20:21: start model_add_line... INFO @ Sat, 17 Apr 2021 09:20:21: start X-correlation... INFO @ Sat, 17 Apr 2021 09:20:21: end of X-cor INFO @ Sat, 17 Apr 2021 09:20:21: #2 finished! INFO @ Sat, 17 Apr 2021 09:20:21: #2 predicted fragment length is 113 bps INFO @ Sat, 17 Apr 2021 09:20:21: #2 alternative fragment length(s) may be 113 bps INFO @ Sat, 17 Apr 2021 09:20:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.10_model.r WARNING @ Sat, 17 Apr 2021 09:20:21: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:20:21: #2 You may need to consider one of the other alternative d(s): 113 WARNING @ Sat, 17 Apr 2021 09:20:21: #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 09:20:21: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:20:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:20:24: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:20:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.10_peaks.xls INFO @ Sat, 17 Apr 2021 09:20:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:20:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.10_summits.bed INFO @ Sat, 17 Apr 2021 09:20:25: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (718 records, 4 fields): 3 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 09:20:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.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 09:20:33: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:20:33: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 09:20:45: 1000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:20:57: 2000000 INFO @ Sat, 17 Apr 2021 09:21:07: 3000000 INFO @ Sat, 17 Apr 2021 09:21:09: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 09:21:09: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 09:21:09: #1 total tags in treatment: 1348601 INFO @ Sat, 17 Apr 2021 09:21:09: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:21:09: #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 09:21:09: #1 tags after filtering in treatment: 837029 INFO @ Sat, 17 Apr 2021 09:21:09: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 17 Apr 2021 09:21:09: #1 finished! INFO @ Sat, 17 Apr 2021 09:21:09: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:21:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:21:09: #2 number of paired peaks: 477 WARNING @ Sat, 17 Apr 2021 09:21:09: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Sat, 17 Apr 2021 09:21:09: start model_add_line... INFO @ Sat, 17 Apr 2021 09:21:09: start X-correlation... INFO @ Sat, 17 Apr 2021 09:21:09: end of X-cor INFO @ Sat, 17 Apr 2021 09:21:09: #2 finished! INFO @ Sat, 17 Apr 2021 09:21:09: #2 predicted fragment length is 113 bps INFO @ Sat, 17 Apr 2021 09:21:09: #2 alternative fragment length(s) may be 113 bps INFO @ Sat, 17 Apr 2021 09:21:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.20_model.r WARNING @ Sat, 17 Apr 2021 09:21:09: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:21:09: #2 You may need to consider one of the other alternative d(s): 113 WARNING @ Sat, 17 Apr 2021 09:21:09: #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 09:21:09: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:21:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:21:13: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:21:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.20_peaks.xls INFO @ Sat, 17 Apr 2021 09:21:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:21:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521490/SRX5521490.20_summits.bed INFO @ Sat, 17 Apr 2021 09:21:14: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (394 records, 4 fields): 4 millis CompletedMACS2peakCalling