Job ID = 7108746 SRX = SRX7960949 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7076320 spots for SRR11359454/SRR11359454.sra Written 7076320 spots for SRR11359454/SRR11359454.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: 00:03:00 7076320 reads; of these: 7076320 (100.00%) were unpaired; of these: 611425 (8.64%) aligned 0 times 4004301 (56.59%) aligned exactly 1 time 2460594 (34.77%) aligned >1 times 91.36% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3692463 / 6464895 = 0.5712 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 13:45:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.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 @ Wed, 22 Jul 2020 13:45:23: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:45:23: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:45:31: 1000000 INFO @ Wed, 22 Jul 2020 13:45:39: 2000000 INFO @ Wed, 22 Jul 2020 13:45:45: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:45:45: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:45:45: #1 total tags in treatment: 2772432 INFO @ Wed, 22 Jul 2020 13:45:45: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:45:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:45:45: #1 tags after filtering in treatment: 2772432 INFO @ Wed, 22 Jul 2020 13:45:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:45:45: #1 finished! INFO @ Wed, 22 Jul 2020 13:45:45: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:45:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:45:45: #2 number of paired peaks: 175 WARNING @ Wed, 22 Jul 2020 13:45:45: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Wed, 22 Jul 2020 13:45:45: start model_add_line... INFO @ Wed, 22 Jul 2020 13:45:45: start X-correlation... INFO @ Wed, 22 Jul 2020 13:45:45: end of X-cor INFO @ Wed, 22 Jul 2020 13:45:45: #2 finished! INFO @ Wed, 22 Jul 2020 13:45:45: #2 predicted fragment length is 214 bps INFO @ Wed, 22 Jul 2020 13:45:45: #2 alternative fragment length(s) may be 2,159,214,228,233,240,295,334,385,580 bps INFO @ Wed, 22 Jul 2020 13:45:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.05_model.r WARNING @ Wed, 22 Jul 2020 13:45:45: #2 Since the d (214) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:45:45: #2 You may need to consider one of the other alternative d(s): 2,159,214,228,233,240,295,334,385,580 WARNING @ Wed, 22 Jul 2020 13:45:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 13:45:45: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:45:45: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 13:45:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.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 @ Wed, 22 Jul 2020 13:45:53: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:45:53: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:45:53: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:45:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.05_peaks.xls INFO @ Wed, 22 Jul 2020 13:45:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:45:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.05_summits.bed INFO @ Wed, 22 Jul 2020 13:45:56: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (691 records, 4 fields): 74 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 13:46:02: 1000000 INFO @ Wed, 22 Jul 2020 13:46:10: 2000000 INFO @ Wed, 22 Jul 2020 13:46:17: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:46:17: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:46:17: #1 total tags in treatment: 2772432 INFO @ Wed, 22 Jul 2020 13:46:17: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:46:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:46:17: #1 tags after filtering in treatment: 2772432 INFO @ Wed, 22 Jul 2020 13:46:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:46:17: #1 finished! INFO @ Wed, 22 Jul 2020 13:46:17: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:46:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:46:17: #2 number of paired peaks: 175 WARNING @ Wed, 22 Jul 2020 13:46:17: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Wed, 22 Jul 2020 13:46:17: start model_add_line... INFO @ Wed, 22 Jul 2020 13:46:17: start X-correlation... INFO @ Wed, 22 Jul 2020 13:46:17: end of X-cor INFO @ Wed, 22 Jul 2020 13:46:17: #2 finished! INFO @ Wed, 22 Jul 2020 13:46:17: #2 predicted fragment length is 214 bps INFO @ Wed, 22 Jul 2020 13:46:17: #2 alternative fragment length(s) may be 2,159,214,228,233,240,295,334,385,580 bps INFO @ Wed, 22 Jul 2020 13:46:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.10_model.r WARNING @ Wed, 22 Jul 2020 13:46:17: #2 Since the d (214) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:46:17: #2 You may need to consider one of the other alternative d(s): 2,159,214,228,233,240,295,334,385,580 WARNING @ Wed, 22 Jul 2020 13:46:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 13:46:17: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:46:17: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 13:46:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.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 @ Wed, 22 Jul 2020 13:46:23: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:46:23: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:46:25: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:46:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.10_peaks.xls INFO @ Wed, 22 Jul 2020 13:46:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:46:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.10_summits.bed INFO @ Wed, 22 Jul 2020 13:46:28: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (421 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 13:46:31: 1000000 INFO @ Wed, 22 Jul 2020 13:46:39: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 13:46:44: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:46:44: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:46:44: #1 total tags in treatment: 2772432 INFO @ Wed, 22 Jul 2020 13:46:44: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:46:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:46:45: #1 tags after filtering in treatment: 2772432 INFO @ Wed, 22 Jul 2020 13:46:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:46:45: #1 finished! INFO @ Wed, 22 Jul 2020 13:46:45: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:46:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:46:45: #2 number of paired peaks: 175 WARNING @ Wed, 22 Jul 2020 13:46:45: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Wed, 22 Jul 2020 13:46:45: start model_add_line... INFO @ Wed, 22 Jul 2020 13:46:45: start X-correlation... INFO @ Wed, 22 Jul 2020 13:46:45: end of X-cor INFO @ Wed, 22 Jul 2020 13:46:45: #2 finished! INFO @ Wed, 22 Jul 2020 13:46:45: #2 predicted fragment length is 214 bps INFO @ Wed, 22 Jul 2020 13:46:45: #2 alternative fragment length(s) may be 2,159,214,228,233,240,295,334,385,580 bps INFO @ Wed, 22 Jul 2020 13:46:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.20_model.r WARNING @ Wed, 22 Jul 2020 13:46:45: #2 Since the d (214) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:46:45: #2 You may need to consider one of the other alternative d(s): 2,159,214,228,233,240,295,334,385,580 WARNING @ Wed, 22 Jul 2020 13:46:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 13:46:45: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:46:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 13:46:53: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:46:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.20_peaks.xls INFO @ Wed, 22 Jul 2020 13:46:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:46:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960949/SRX7960949.20_summits.bed INFO @ Wed, 22 Jul 2020 13:46:55: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (166 records, 4 fields): 10 millis CompletedMACS2peakCalling