Job ID = 7099034 SRX = SRX6473473 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 2501542 spots for SRR9715596/SRR9715596.sra Written 2501542 spots for SRR9715596/SRR9715596.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: 00:00:29 2501542 reads; of these: 2501542 (100.00%) were unpaired; of these: 670991 (26.82%) aligned 0 times 1607423 (64.26%) aligned exactly 1 time 223128 (8.92%) aligned >1 times 73.18% overall alignment rate Time searching: 00:00:29 Overall time: 00:00:29 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] 574322 / 1830551 = 0.3137 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 12:02:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.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 12:02:36: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:02:36: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:02:43: 1000000 INFO @ Wed, 22 Jul 2020 12:02:45: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:02:45: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:02:45: #1 total tags in treatment: 1256229 INFO @ Wed, 22 Jul 2020 12:02:45: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:02:45: #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 12:02:45: #1 tags after filtering in treatment: 1256229 INFO @ Wed, 22 Jul 2020 12:02:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 12:02:45: #1 finished! INFO @ Wed, 22 Jul 2020 12:02:45: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:02:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:02:45: #2 number of paired peaks: 337 WARNING @ Wed, 22 Jul 2020 12:02:45: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Wed, 22 Jul 2020 12:02:45: start model_add_line... INFO @ Wed, 22 Jul 2020 12:02:45: start X-correlation... INFO @ Wed, 22 Jul 2020 12:02:45: end of X-cor INFO @ Wed, 22 Jul 2020 12:02:45: #2 finished! INFO @ Wed, 22 Jul 2020 12:02:45: #2 predicted fragment length is 154 bps INFO @ Wed, 22 Jul 2020 12:02:45: #2 alternative fragment length(s) may be 4,154 bps INFO @ Wed, 22 Jul 2020 12:02:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.05_model.r WARNING @ Wed, 22 Jul 2020 12:02:45: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:02:45: #2 You may need to consider one of the other alternative d(s): 4,154 WARNING @ Wed, 22 Jul 2020 12:02:45: #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 12:02:45: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:02:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:02:49: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:02:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.05_peaks.xls INFO @ Wed, 22 Jul 2020 12:02:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:02:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.05_summits.bed INFO @ Wed, 22 Jul 2020 12:02:50: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (676 records, 4 fields): 15 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 12:03:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.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 12:03:06: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:03:06: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:03:13: 1000000 INFO @ Wed, 22 Jul 2020 12:03:15: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:03:15: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:03:15: #1 total tags in treatment: 1256229 INFO @ Wed, 22 Jul 2020 12:03:15: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:03:15: #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 12:03:15: #1 tags after filtering in treatment: 1256229 INFO @ Wed, 22 Jul 2020 12:03:15: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 12:03:15: #1 finished! INFO @ Wed, 22 Jul 2020 12:03:15: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:03:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:03:15: #2 number of paired peaks: 337 WARNING @ Wed, 22 Jul 2020 12:03:15: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Wed, 22 Jul 2020 12:03:15: start model_add_line... INFO @ Wed, 22 Jul 2020 12:03:15: start X-correlation... INFO @ Wed, 22 Jul 2020 12:03:15: end of X-cor INFO @ Wed, 22 Jul 2020 12:03:15: #2 finished! INFO @ Wed, 22 Jul 2020 12:03:15: #2 predicted fragment length is 154 bps INFO @ Wed, 22 Jul 2020 12:03:15: #2 alternative fragment length(s) may be 4,154 bps INFO @ Wed, 22 Jul 2020 12:03:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.10_model.r WARNING @ Wed, 22 Jul 2020 12:03:15: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:03:15: #2 You may need to consider one of the other alternative d(s): 4,154 WARNING @ Wed, 22 Jul 2020 12:03:15: #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 12:03:15: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:03:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:03:18: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:03:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.10_peaks.xls INFO @ Wed, 22 Jul 2020 12:03:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:03:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.10_summits.bed INFO @ Wed, 22 Jul 2020 12:03:20: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (430 records, 4 fields): 2 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 12:03:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.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 12:03:36: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:03:36: #1 read treatment tags... 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 12:03:45: 1000000 INFO @ Wed, 22 Jul 2020 12:03:47: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:03:47: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:03:47: #1 total tags in treatment: 1256229 INFO @ Wed, 22 Jul 2020 12:03:47: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:03:47: #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 12:03:47: #1 tags after filtering in treatment: 1256229 INFO @ Wed, 22 Jul 2020 12:03:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 12:03:47: #1 finished! INFO @ Wed, 22 Jul 2020 12:03:47: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:03:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:03:47: #2 number of paired peaks: 337 WARNING @ Wed, 22 Jul 2020 12:03:47: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Wed, 22 Jul 2020 12:03:47: start model_add_line... INFO @ Wed, 22 Jul 2020 12:03:47: start X-correlation... INFO @ Wed, 22 Jul 2020 12:03:47: end of X-cor INFO @ Wed, 22 Jul 2020 12:03:47: #2 finished! INFO @ Wed, 22 Jul 2020 12:03:47: #2 predicted fragment length is 154 bps INFO @ Wed, 22 Jul 2020 12:03:47: #2 alternative fragment length(s) may be 4,154 bps INFO @ Wed, 22 Jul 2020 12:03:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.20_model.r WARNING @ Wed, 22 Jul 2020 12:03:47: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:03:47: #2 You may need to consider one of the other alternative d(s): 4,154 WARNING @ Wed, 22 Jul 2020 12:03:47: #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 12:03:47: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:03:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:03:51: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:03:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.20_peaks.xls INFO @ Wed, 22 Jul 2020 12:03:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:03:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6473473/SRX6473473.20_summits.bed INFO @ Wed, 22 Jul 2020 12:03:52: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (242 records, 4 fields): 1 millis CompletedMACS2peakCalling