Job ID = 7097538 SRX = SRX1967615 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 4953393 spots for SRR3938353/SRR3938353.sra Written 4953393 spots for SRR3938353/SRR3938353.sra Read 3414035 spots for SRR3938354/SRR3938354.sra Written 3414035 spots for SRR3938354/SRR3938354.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: 00:01:20 8367428 reads; of these: 8367428 (100.00%) were unpaired; of these: 1683718 (20.12%) aligned 0 times 3654455 (43.67%) aligned exactly 1 time 3029255 (36.20%) aligned >1 times 79.88% overall alignment rate Time searching: 00:01:21 Overall time: 00:01:21 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] 5135441 / 6683710 = 0.7684 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 11:41:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.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 11:41:54: #1 read tag files... INFO @ Wed, 22 Jul 2020 11:41:54: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 11:42:00: 1000000 INFO @ Wed, 22 Jul 2020 11:42:04: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 11:42:04: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 11:42:04: #1 total tags in treatment: 1548269 INFO @ Wed, 22 Jul 2020 11:42:04: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 11:42:04: #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 11:42:04: #1 tags after filtering in treatment: 1548269 INFO @ Wed, 22 Jul 2020 11:42:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 11:42:04: #1 finished! INFO @ Wed, 22 Jul 2020 11:42:04: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 11:42:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 11:42:04: #2 number of paired peaks: 178 WARNING @ Wed, 22 Jul 2020 11:42:04: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Wed, 22 Jul 2020 11:42:04: start model_add_line... INFO @ Wed, 22 Jul 2020 11:42:04: start X-correlation... INFO @ Wed, 22 Jul 2020 11:42:04: end of X-cor INFO @ Wed, 22 Jul 2020 11:42:04: #2 finished! INFO @ Wed, 22 Jul 2020 11:42:04: #2 predicted fragment length is 61 bps INFO @ Wed, 22 Jul 2020 11:42:04: #2 alternative fragment length(s) may be 3,61,82,120,135 bps INFO @ Wed, 22 Jul 2020 11:42:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.05_model.r WARNING @ Wed, 22 Jul 2020 11:42:04: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 11:42:04: #2 You may need to consider one of the other alternative d(s): 3,61,82,120,135 WARNING @ Wed, 22 Jul 2020 11:42:04: #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 11:42:04: #3 Call peaks... INFO @ Wed, 22 Jul 2020 11:42:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 11:42:07: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 11:42:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.05_peaks.xls INFO @ Wed, 22 Jul 2020 11:42:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 11:42:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.05_summits.bed INFO @ Wed, 22 Jul 2020 11:42:08: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (147 records, 4 fields): 18 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 11:42:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.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 11:42:24: #1 read tag files... INFO @ Wed, 22 Jul 2020 11:42:24: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 11:42:30: 1000000 INFO @ Wed, 22 Jul 2020 11:42:33: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 11:42:33: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 11:42:33: #1 total tags in treatment: 1548269 INFO @ Wed, 22 Jul 2020 11:42:33: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 11:42:33: #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 11:42:33: #1 tags after filtering in treatment: 1548269 INFO @ Wed, 22 Jul 2020 11:42:33: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 11:42:33: #1 finished! INFO @ Wed, 22 Jul 2020 11:42:33: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 11:42:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 11:42:33: #2 number of paired peaks: 178 WARNING @ Wed, 22 Jul 2020 11:42:33: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Wed, 22 Jul 2020 11:42:33: start model_add_line... INFO @ Wed, 22 Jul 2020 11:42:33: start X-correlation... INFO @ Wed, 22 Jul 2020 11:42:33: end of X-cor INFO @ Wed, 22 Jul 2020 11:42:33: #2 finished! INFO @ Wed, 22 Jul 2020 11:42:33: #2 predicted fragment length is 61 bps INFO @ Wed, 22 Jul 2020 11:42:33: #2 alternative fragment length(s) may be 3,61,82,120,135 bps INFO @ Wed, 22 Jul 2020 11:42:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.10_model.r WARNING @ Wed, 22 Jul 2020 11:42:33: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 11:42:33: #2 You may need to consider one of the other alternative d(s): 3,61,82,120,135 WARNING @ Wed, 22 Jul 2020 11:42:33: #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 11:42:33: #3 Call peaks... INFO @ Wed, 22 Jul 2020 11:42:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 11:42:37: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 11:42:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.10_peaks.xls INFO @ Wed, 22 Jul 2020 11:42:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 11:42:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.10_summits.bed INFO @ Wed, 22 Jul 2020 11:42:38: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (112 records, 4 fields): 22 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 11:42:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.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 11:42:54: #1 read tag files... INFO @ Wed, 22 Jul 2020 11:42:54: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 11:43:00: 1000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 11:43:03: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 11:43:03: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 11:43:03: #1 total tags in treatment: 1548269 INFO @ Wed, 22 Jul 2020 11:43:03: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 11:43:03: #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 11:43:04: #1 tags after filtering in treatment: 1548269 INFO @ Wed, 22 Jul 2020 11:43:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 11:43:04: #1 finished! INFO @ Wed, 22 Jul 2020 11:43:04: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 11:43:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 11:43:04: #2 number of paired peaks: 178 WARNING @ Wed, 22 Jul 2020 11:43:04: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Wed, 22 Jul 2020 11:43:04: start model_add_line... INFO @ Wed, 22 Jul 2020 11:43:04: start X-correlation... INFO @ Wed, 22 Jul 2020 11:43:04: end of X-cor INFO @ Wed, 22 Jul 2020 11:43:04: #2 finished! INFO @ Wed, 22 Jul 2020 11:43:04: #2 predicted fragment length is 61 bps INFO @ Wed, 22 Jul 2020 11:43:04: #2 alternative fragment length(s) may be 3,61,82,120,135 bps INFO @ Wed, 22 Jul 2020 11:43:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.20_model.r WARNING @ Wed, 22 Jul 2020 11:43:04: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 11:43:04: #2 You may need to consider one of the other alternative d(s): 3,61,82,120,135 WARNING @ Wed, 22 Jul 2020 11:43:04: #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 11:43:04: #3 Call peaks... INFO @ Wed, 22 Jul 2020 11:43:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 11:43:07: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 11:43:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.20_peaks.xls INFO @ Wed, 22 Jul 2020 11:43:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 11:43:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX1967615/SRX1967615.20_summits.bed INFO @ Wed, 22 Jul 2020 11:43:08: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (75 records, 4 fields): 1 millis CompletedMACS2peakCalling