Job ID = 14520312 SRX = SRX8421796 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 11721218 spots for SRR11872089/SRR11872089.sra Written 11721218 spots for SRR11872089/SRR11872089.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: 00:03:53 11721218 reads; of these: 11721218 (100.00%) were unpaired; of these: 682383 (5.82%) aligned 0 times 8106141 (69.16%) aligned exactly 1 time 2932694 (25.02%) aligned >1 times 94.18% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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 12 files... [bam_rmdupse_core] 6584572 / 11038835 = 0.5965 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:03:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.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, 15 Jan 2022 19:03:30: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:03:30: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:03:39: 1000000 INFO @ Sat, 15 Jan 2022 19:03:46: 2000000 INFO @ Sat, 15 Jan 2022 19:03:54: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:04:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.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, 15 Jan 2022 19:04:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:04:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:04:01: 4000000 INFO @ Sat, 15 Jan 2022 19:04:05: #1 tag size is determined as 151 bps INFO @ Sat, 15 Jan 2022 19:04:05: #1 tag size = 151 INFO @ Sat, 15 Jan 2022 19:04:05: #1 total tags in treatment: 4454263 INFO @ Sat, 15 Jan 2022 19:04:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:04:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:04:05: #1 tags after filtering in treatment: 4454263 INFO @ Sat, 15 Jan 2022 19:04:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 19:04:05: #1 finished! INFO @ Sat, 15 Jan 2022 19:04:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:04:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:04:05: #2 number of paired peaks: 139 WARNING @ Sat, 15 Jan 2022 19:04:05: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 15 Jan 2022 19:04:05: start model_add_line... INFO @ Sat, 15 Jan 2022 19:04:05: start X-correlation... INFO @ Sat, 15 Jan 2022 19:04:05: end of X-cor INFO @ Sat, 15 Jan 2022 19:04:05: #2 finished! INFO @ Sat, 15 Jan 2022 19:04:05: #2 predicted fragment length is 163 bps INFO @ Sat, 15 Jan 2022 19:04:05: #2 alternative fragment length(s) may be 2,39,76,113,141,163,192,226 bps INFO @ Sat, 15 Jan 2022 19:04:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.05_model.r WARNING @ Sat, 15 Jan 2022 19:04:05: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:04:05: #2 You may need to consider one of the other alternative d(s): 2,39,76,113,141,163,192,226 WARNING @ Sat, 15 Jan 2022 19:04:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 19:04:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:04:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:04:08: 1000000 INFO @ Sat, 15 Jan 2022 19:04:15: 2000000 INFO @ Sat, 15 Jan 2022 19:04:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:04:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:04:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:04:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.05_summits.bed INFO @ Sat, 15 Jan 2022 19:04:22: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (1430 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:04:23: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:04:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.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, 15 Jan 2022 19:04:30: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:04:30: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:04:30: 4000000 INFO @ Sat, 15 Jan 2022 19:04:34: #1 tag size is determined as 151 bps INFO @ Sat, 15 Jan 2022 19:04:34: #1 tag size = 151 INFO @ Sat, 15 Jan 2022 19:04:34: #1 total tags in treatment: 4454263 INFO @ Sat, 15 Jan 2022 19:04:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:04:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:04:34: #1 tags after filtering in treatment: 4454263 INFO @ Sat, 15 Jan 2022 19:04:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 19:04:34: #1 finished! INFO @ Sat, 15 Jan 2022 19:04:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:04:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:04:35: #2 number of paired peaks: 139 WARNING @ Sat, 15 Jan 2022 19:04:35: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 15 Jan 2022 19:04:35: start model_add_line... INFO @ Sat, 15 Jan 2022 19:04:35: start X-correlation... INFO @ Sat, 15 Jan 2022 19:04:35: end of X-cor INFO @ Sat, 15 Jan 2022 19:04:35: #2 finished! INFO @ Sat, 15 Jan 2022 19:04:35: #2 predicted fragment length is 163 bps INFO @ Sat, 15 Jan 2022 19:04:35: #2 alternative fragment length(s) may be 2,39,76,113,141,163,192,226 bps INFO @ Sat, 15 Jan 2022 19:04:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.10_model.r WARNING @ Sat, 15 Jan 2022 19:04:35: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:04:35: #2 You may need to consider one of the other alternative d(s): 2,39,76,113,141,163,192,226 WARNING @ Sat, 15 Jan 2022 19:04:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 19:04:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:04:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:04:38: 1000000 INFO @ Sat, 15 Jan 2022 19:04:46: 2000000 INFO @ Sat, 15 Jan 2022 19:04:48: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:04:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:04:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:04:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.10_summits.bed INFO @ Sat, 15 Jan 2022 19:04:51: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (1274 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:04:54: 3000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:05:02: 4000000 INFO @ Sat, 15 Jan 2022 19:05:05: #1 tag size is determined as 151 bps INFO @ Sat, 15 Jan 2022 19:05:05: #1 tag size = 151 INFO @ Sat, 15 Jan 2022 19:05:05: #1 total tags in treatment: 4454263 INFO @ Sat, 15 Jan 2022 19:05:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:05:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:05:06: #1 tags after filtering in treatment: 4454263 INFO @ Sat, 15 Jan 2022 19:05:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 19:05:06: #1 finished! INFO @ Sat, 15 Jan 2022 19:05:06: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:05:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:05:06: #2 number of paired peaks: 139 WARNING @ Sat, 15 Jan 2022 19:05:06: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 15 Jan 2022 19:05:06: start model_add_line... INFO @ Sat, 15 Jan 2022 19:05:06: start X-correlation... INFO @ Sat, 15 Jan 2022 19:05:06: end of X-cor INFO @ Sat, 15 Jan 2022 19:05:06: #2 finished! INFO @ Sat, 15 Jan 2022 19:05:06: #2 predicted fragment length is 163 bps INFO @ Sat, 15 Jan 2022 19:05:06: #2 alternative fragment length(s) may be 2,39,76,113,141,163,192,226 bps INFO @ Sat, 15 Jan 2022 19:05:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.20_model.r WARNING @ Sat, 15 Jan 2022 19:05:06: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:05:06: #2 You may need to consider one of the other alternative d(s): 2,39,76,113,141,163,192,226 WARNING @ Sat, 15 Jan 2022 19:05:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 19:05:06: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:05:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:05:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:05:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:05:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:05:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8421796/SRX8421796.20_summits.bed INFO @ Sat, 15 Jan 2022 19:05:23: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1027 records, 4 fields): 17 millis CompletedMACS2peakCalling