Job ID = 14521324 SRX = SRX9278490 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 1554830 spots for SRR12809888/SRR12809888.sra Written 1554830 spots for SRR12809888/SRR12809888.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: 00:00:45 1554830 reads; of these: 1554830 (100.00%) were unpaired; of these: 67284 (4.33%) aligned 0 times 1357688 (87.32%) aligned exactly 1 time 129858 (8.35%) aligned >1 times 95.67% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 132003 / 1487546 = 0.0887 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 20:51:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.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 20:51:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:51:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:51:54: 1000000 INFO @ Sat, 15 Jan 2022 20:51:57: #1 tag size is determined as 149 bps INFO @ Sat, 15 Jan 2022 20:51:57: #1 tag size = 149 INFO @ Sat, 15 Jan 2022 20:51:57: #1 total tags in treatment: 1355543 INFO @ Sat, 15 Jan 2022 20:51:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:51:57: #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 20:51:57: #1 tags after filtering in treatment: 1355543 INFO @ Sat, 15 Jan 2022 20:51:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:51:57: #1 finished! INFO @ Sat, 15 Jan 2022 20:51:57: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:51:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:51:57: #2 number of paired peaks: 252 WARNING @ Sat, 15 Jan 2022 20:51:57: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Sat, 15 Jan 2022 20:51:57: start model_add_line... INFO @ Sat, 15 Jan 2022 20:51:57: start X-correlation... INFO @ Sat, 15 Jan 2022 20:51:57: end of X-cor INFO @ Sat, 15 Jan 2022 20:51:57: #2 finished! INFO @ Sat, 15 Jan 2022 20:51:57: #2 predicted fragment length is 148 bps INFO @ Sat, 15 Jan 2022 20:51:57: #2 alternative fragment length(s) may be 4,148,184 bps INFO @ Sat, 15 Jan 2022 20:51:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.05_model.r WARNING @ Sat, 15 Jan 2022 20:51:57: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:51:57: #2 You may need to consider one of the other alternative d(s): 4,148,184 WARNING @ Sat, 15 Jan 2022 20:51:57: #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 20:51:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:51:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:52:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:52:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:52:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:52:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.05_summits.bed INFO @ Sat, 15 Jan 2022 20:52:02: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (652 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 20:52:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.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 20:52:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:52:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:52:22: 1000000 INFO @ Sat, 15 Jan 2022 20:52:25: #1 tag size is determined as 149 bps INFO @ Sat, 15 Jan 2022 20:52:25: #1 tag size = 149 INFO @ Sat, 15 Jan 2022 20:52:25: #1 total tags in treatment: 1355543 INFO @ Sat, 15 Jan 2022 20:52:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:52:25: #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 20:52:25: #1 tags after filtering in treatment: 1355543 INFO @ Sat, 15 Jan 2022 20:52:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:52:25: #1 finished! INFO @ Sat, 15 Jan 2022 20:52:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:52:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:52:25: #2 number of paired peaks: 252 WARNING @ Sat, 15 Jan 2022 20:52:25: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Sat, 15 Jan 2022 20:52:25: start model_add_line... INFO @ Sat, 15 Jan 2022 20:52:25: start X-correlation... INFO @ Sat, 15 Jan 2022 20:52:25: end of X-cor INFO @ Sat, 15 Jan 2022 20:52:25: #2 finished! INFO @ Sat, 15 Jan 2022 20:52:25: #2 predicted fragment length is 148 bps INFO @ Sat, 15 Jan 2022 20:52:25: #2 alternative fragment length(s) may be 4,148,184 bps INFO @ Sat, 15 Jan 2022 20:52:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.10_model.r WARNING @ Sat, 15 Jan 2022 20:52:25: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:52:25: #2 You may need to consider one of the other alternative d(s): 4,148,184 WARNING @ Sat, 15 Jan 2022 20:52:25: #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 20:52:25: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:52:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:52:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:52:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:52:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:52:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.10_summits.bed INFO @ Sat, 15 Jan 2022 20:52:30: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (390 records, 4 fields): 9 millis CompletedMACS2peakCalling 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 20:52:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.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 20:52:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:52:45: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:52:52: 1000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:52:55: #1 tag size is determined as 149 bps INFO @ Sat, 15 Jan 2022 20:52:55: #1 tag size = 149 INFO @ Sat, 15 Jan 2022 20:52:55: #1 total tags in treatment: 1355543 INFO @ Sat, 15 Jan 2022 20:52:55: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:52:55: #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 20:52:55: #1 tags after filtering in treatment: 1355543 INFO @ Sat, 15 Jan 2022 20:52:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:52:55: #1 finished! INFO @ Sat, 15 Jan 2022 20:52:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:52:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:52:55: #2 number of paired peaks: 252 WARNING @ Sat, 15 Jan 2022 20:52:55: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Sat, 15 Jan 2022 20:52:55: start model_add_line... INFO @ Sat, 15 Jan 2022 20:52:55: start X-correlation... INFO @ Sat, 15 Jan 2022 20:52:55: end of X-cor INFO @ Sat, 15 Jan 2022 20:52:55: #2 finished! INFO @ Sat, 15 Jan 2022 20:52:55: #2 predicted fragment length is 148 bps INFO @ Sat, 15 Jan 2022 20:52:55: #2 alternative fragment length(s) may be 4,148,184 bps INFO @ Sat, 15 Jan 2022 20:52:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.20_model.r WARNING @ Sat, 15 Jan 2022 20:52:55: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:52:55: #2 You may need to consider one of the other alternative d(s): 4,148,184 WARNING @ Sat, 15 Jan 2022 20:52:55: #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 20:52:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:52:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:52:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:53:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:53:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:53:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9278490/SRX9278490.20_summits.bed INFO @ Sat, 15 Jan 2022 20:53:00: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (234 records, 4 fields): 2 millis CompletedMACS2peakCalling