Job ID = 12531708 SRX = SRX5521489 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2742034 spots for SRR8728300/SRR8728300.sra Written 2742034 spots for SRR8728300/SRR8728300.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: 00:02:36 2742034 reads; of these: 2742034 (100.00%) were paired; of these: 798272 (29.11%) aligned concordantly 0 times 1079802 (39.38%) aligned concordantly exactly 1 time 863960 (31.51%) aligned concordantly >1 times ---- 798272 pairs aligned concordantly 0 times; of these: 144838 (18.14%) aligned discordantly 1 time ---- 653434 pairs aligned 0 times concordantly or discordantly; of these: 1306868 mates make up the pairs; of these: 1043721 (79.86%) aligned 0 times 35156 (2.69%) aligned exactly 1 time 227991 (17.45%) aligned >1 times 80.97% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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] 413308 / 2073832 = 0.1993 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 09:20:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.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 09:20:09: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:20:09: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:20:15: 1000000 INFO @ Sat, 17 Apr 2021 09:20:22: 2000000 INFO @ Sat, 17 Apr 2021 09:20:28: 3000000 INFO @ Sat, 17 Apr 2021 09:20:32: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 09:20:32: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 09:20:32: #1 total tags in treatment: 1542279 INFO @ Sat, 17 Apr 2021 09:20:32: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:20:32: #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 09:20:32: #1 tags after filtering in treatment: 887182 INFO @ Sat, 17 Apr 2021 09:20:32: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 17 Apr 2021 09:20:32: #1 finished! INFO @ Sat, 17 Apr 2021 09:20:32: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:20:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:20:32: #2 number of paired peaks: 437 WARNING @ Sat, 17 Apr 2021 09:20:32: Fewer paired peaks (437) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 437 pairs to build model! INFO @ Sat, 17 Apr 2021 09:20:32: start model_add_line... INFO @ Sat, 17 Apr 2021 09:20:32: start X-correlation... INFO @ Sat, 17 Apr 2021 09:20:32: end of X-cor INFO @ Sat, 17 Apr 2021 09:20:32: #2 finished! INFO @ Sat, 17 Apr 2021 09:20:32: #2 predicted fragment length is 125 bps INFO @ Sat, 17 Apr 2021 09:20:32: #2 alternative fragment length(s) may be 4,125 bps INFO @ Sat, 17 Apr 2021 09:20:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.05_model.r WARNING @ Sat, 17 Apr 2021 09:20:32: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:20:32: #2 You may need to consider one of the other alternative d(s): 4,125 WARNING @ Sat, 17 Apr 2021 09:20:32: #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 09:20:32: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:20:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:20:36: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:20:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.05_peaks.xls INFO @ Sat, 17 Apr 2021 09:20:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:20:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.05_summits.bed INFO @ Sat, 17 Apr 2021 09:20:37: Done! 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 pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (1152 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:20:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.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 09:20:39: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:20:39: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:20:46: 1000000 INFO @ Sat, 17 Apr 2021 09:20:53: 2000000 INFO @ Sat, 17 Apr 2021 09:20:59: 3000000 INFO @ Sat, 17 Apr 2021 09:21:03: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 09:21:03: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 09:21:03: #1 total tags in treatment: 1542279 INFO @ Sat, 17 Apr 2021 09:21:03: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:21:03: #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 09:21:03: #1 tags after filtering in treatment: 887182 INFO @ Sat, 17 Apr 2021 09:21:03: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 17 Apr 2021 09:21:03: #1 finished! INFO @ Sat, 17 Apr 2021 09:21:03: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:21:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:21:04: #2 number of paired peaks: 437 WARNING @ Sat, 17 Apr 2021 09:21:04: Fewer paired peaks (437) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 437 pairs to build model! INFO @ Sat, 17 Apr 2021 09:21:04: start model_add_line... INFO @ Sat, 17 Apr 2021 09:21:04: start X-correlation... INFO @ Sat, 17 Apr 2021 09:21:04: end of X-cor INFO @ Sat, 17 Apr 2021 09:21:04: #2 finished! INFO @ Sat, 17 Apr 2021 09:21:04: #2 predicted fragment length is 125 bps INFO @ Sat, 17 Apr 2021 09:21:04: #2 alternative fragment length(s) may be 4,125 bps INFO @ Sat, 17 Apr 2021 09:21:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.10_model.r WARNING @ Sat, 17 Apr 2021 09:21:04: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:21:04: #2 You may need to consider one of the other alternative d(s): 4,125 WARNING @ Sat, 17 Apr 2021 09:21:04: #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 09:21:04: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:21:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:21:07: #3 Call peaks for each chromosome... 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 09:21:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.10_peaks.xls INFO @ Sat, 17 Apr 2021 09:21:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:21:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.10_summits.bed INFO @ Sat, 17 Apr 2021 09:21:08: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (719 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:21:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.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 09:21:09: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:21:09: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:21:16: 1000000 INFO @ Sat, 17 Apr 2021 09:21:23: 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 09:21:30: 3000000 INFO @ Sat, 17 Apr 2021 09:21:34: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 09:21:34: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 09:21:34: #1 total tags in treatment: 1542279 INFO @ Sat, 17 Apr 2021 09:21:34: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:21:34: #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 09:21:34: #1 tags after filtering in treatment: 887182 INFO @ Sat, 17 Apr 2021 09:21:34: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 17 Apr 2021 09:21:34: #1 finished! INFO @ Sat, 17 Apr 2021 09:21:34: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:21:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:21:34: #2 number of paired peaks: 437 WARNING @ Sat, 17 Apr 2021 09:21:34: Fewer paired peaks (437) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 437 pairs to build model! INFO @ Sat, 17 Apr 2021 09:21:34: start model_add_line... INFO @ Sat, 17 Apr 2021 09:21:34: start X-correlation... INFO @ Sat, 17 Apr 2021 09:21:34: end of X-cor INFO @ Sat, 17 Apr 2021 09:21:34: #2 finished! INFO @ Sat, 17 Apr 2021 09:21:34: #2 predicted fragment length is 125 bps INFO @ Sat, 17 Apr 2021 09:21:34: #2 alternative fragment length(s) may be 4,125 bps INFO @ Sat, 17 Apr 2021 09:21:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.20_model.r WARNING @ Sat, 17 Apr 2021 09:21:34: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:21:34: #2 You may need to consider one of the other alternative d(s): 4,125 WARNING @ Sat, 17 Apr 2021 09:21:34: #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 09:21:34: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:21:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:21:37: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:21:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.20_peaks.xls INFO @ Sat, 17 Apr 2021 09:21:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:21:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521489/SRX5521489.20_summits.bed INFO @ Sat, 17 Apr 2021 09:21:38: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (323 records, 4 fields): 2 millis CompletedMACS2peakCalling