Job ID = 7108468 SRX = SRX7960945 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6423286 spots for SRR11359450/SRR11359450.sra Written 6423286 spots for SRR11359450/SRR11359450.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: 00:02:13 6423286 reads; of these: 6423286 (100.00%) were unpaired; of these: 1623019 (25.27%) aligned 0 times 3345954 (52.09%) aligned exactly 1 time 1454313 (22.64%) aligned >1 times 74.73% overall alignment rate Time searching: 00:02:13 Overall time: 00:02:13 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_rmdupse_core] 2597647 / 4800267 = 0.5411 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 13:43:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.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 13:43:20: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:43:20: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:43:29: 1000000 INFO @ Wed, 22 Jul 2020 13:43:38: 2000000 INFO @ Wed, 22 Jul 2020 13:43:40: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:43:40: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:43:40: #1 total tags in treatment: 2202620 INFO @ Wed, 22 Jul 2020 13:43:40: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:43:40: #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 13:43:40: #1 tags after filtering in treatment: 2202620 INFO @ Wed, 22 Jul 2020 13:43:40: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:43:40: #1 finished! INFO @ Wed, 22 Jul 2020 13:43:40: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:43:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:43:40: #2 number of paired peaks: 190 WARNING @ Wed, 22 Jul 2020 13:43:40: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Wed, 22 Jul 2020 13:43:40: start model_add_line... INFO @ Wed, 22 Jul 2020 13:43:40: start X-correlation... INFO @ Wed, 22 Jul 2020 13:43:40: end of X-cor INFO @ Wed, 22 Jul 2020 13:43:40: #2 finished! INFO @ Wed, 22 Jul 2020 13:43:40: #2 predicted fragment length is 155 bps INFO @ Wed, 22 Jul 2020 13:43:40: #2 alternative fragment length(s) may be 0,110,118,133,155,173,230,524,541,564 bps INFO @ Wed, 22 Jul 2020 13:43:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.05_model.r WARNING @ Wed, 22 Jul 2020 13:43:40: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:43:40: #2 You may need to consider one of the other alternative d(s): 0,110,118,133,155,173,230,524,541,564 WARNING @ Wed, 22 Jul 2020 13:43:40: #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 13:43:40: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:43:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:43:45: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:43:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.05_peaks.xls INFO @ Wed, 22 Jul 2020 13:43:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:43:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.05_summits.bed INFO @ Wed, 22 Jul 2020 13:43:47: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (603 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 13:43:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.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 13:43:50: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:43:50: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:43:59: 1000000 INFO @ Wed, 22 Jul 2020 13:44:08: 2000000 INFO @ Wed, 22 Jul 2020 13:44:10: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:44:10: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:44:10: #1 total tags in treatment: 2202620 INFO @ Wed, 22 Jul 2020 13:44:10: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:44:10: #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 13:44:10: #1 tags after filtering in treatment: 2202620 INFO @ Wed, 22 Jul 2020 13:44:10: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:44:10: #1 finished! INFO @ Wed, 22 Jul 2020 13:44:10: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:44:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:44:10: #2 number of paired peaks: 190 WARNING @ Wed, 22 Jul 2020 13:44:10: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Wed, 22 Jul 2020 13:44:10: start model_add_line... INFO @ Wed, 22 Jul 2020 13:44:10: start X-correlation... INFO @ Wed, 22 Jul 2020 13:44:10: end of X-cor INFO @ Wed, 22 Jul 2020 13:44:10: #2 finished! INFO @ Wed, 22 Jul 2020 13:44:10: #2 predicted fragment length is 155 bps INFO @ Wed, 22 Jul 2020 13:44:10: #2 alternative fragment length(s) may be 0,110,118,133,155,173,230,524,541,564 bps INFO @ Wed, 22 Jul 2020 13:44:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.10_model.r WARNING @ Wed, 22 Jul 2020 13:44:10: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:44:10: #2 You may need to consider one of the other alternative d(s): 0,110,118,133,155,173,230,524,541,564 WARNING @ Wed, 22 Jul 2020 13:44:10: #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 13:44:10: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:44:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:44:15: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:44:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.10_peaks.xls INFO @ Wed, 22 Jul 2020 13:44:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:44:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.10_summits.bed INFO @ Wed, 22 Jul 2020 13:44:16: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (294 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 13:44:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.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 13:44:20: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:44:20: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:44:29: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 13:44:39: 2000000 INFO @ Wed, 22 Jul 2020 13:44:41: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:44:41: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:44:41: #1 total tags in treatment: 2202620 INFO @ Wed, 22 Jul 2020 13:44:41: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:44:41: #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 13:44:41: #1 tags after filtering in treatment: 2202620 INFO @ Wed, 22 Jul 2020 13:44:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:44:41: #1 finished! INFO @ Wed, 22 Jul 2020 13:44:41: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:44:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:44:41: #2 number of paired peaks: 190 WARNING @ Wed, 22 Jul 2020 13:44:41: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Wed, 22 Jul 2020 13:44:41: start model_add_line... INFO @ Wed, 22 Jul 2020 13:44:41: start X-correlation... INFO @ Wed, 22 Jul 2020 13:44:41: end of X-cor INFO @ Wed, 22 Jul 2020 13:44:41: #2 finished! INFO @ Wed, 22 Jul 2020 13:44:41: #2 predicted fragment length is 155 bps INFO @ Wed, 22 Jul 2020 13:44:41: #2 alternative fragment length(s) may be 0,110,118,133,155,173,230,524,541,564 bps INFO @ Wed, 22 Jul 2020 13:44:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.20_model.r WARNING @ Wed, 22 Jul 2020 13:44:41: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:44:41: #2 You may need to consider one of the other alternative d(s): 0,110,118,133,155,173,230,524,541,564 WARNING @ Wed, 22 Jul 2020 13:44:41: #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 13:44:41: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:44:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:44:45: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:44:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.20_peaks.xls INFO @ Wed, 22 Jul 2020 13:44:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:44:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960945/SRX7960945.20_summits.bed INFO @ Wed, 22 Jul 2020 13:44:47: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (63 records, 4 fields): 2 millis CompletedMACS2peakCalling