Job ID = 14521325 SRX = SRX9278491 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 1627347 spots for SRR12809889/SRR12809889.sra Written 1627347 spots for SRR12809889/SRR12809889.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 1627347 reads; of these: 1627347 (100.00%) were unpaired; of these: 43515 (2.67%) aligned 0 times 1437129 (88.31%) aligned exactly 1 time 146703 (9.01%) aligned >1 times 97.33% 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] 168299 / 1583832 = 0.1063 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 20:51:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.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 20:51:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:51:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:51:56: 1000000 INFO @ Sat, 15 Jan 2022 20:51:59: #1 tag size is determined as 147 bps INFO @ Sat, 15 Jan 2022 20:51:59: #1 tag size = 147 INFO @ Sat, 15 Jan 2022 20:51:59: #1 total tags in treatment: 1415533 INFO @ Sat, 15 Jan 2022 20:51:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:51:59: #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 20:51:59: #1 tags after filtering in treatment: 1415533 INFO @ Sat, 15 Jan 2022 20:51:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:51:59: #1 finished! INFO @ Sat, 15 Jan 2022 20:51:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:51:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:51:59: #2 number of paired peaks: 274 WARNING @ Sat, 15 Jan 2022 20:51:59: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Sat, 15 Jan 2022 20:51:59: start model_add_line... INFO @ Sat, 15 Jan 2022 20:51:59: start X-correlation... INFO @ Sat, 15 Jan 2022 20:51:59: end of X-cor INFO @ Sat, 15 Jan 2022 20:51:59: #2 finished! INFO @ Sat, 15 Jan 2022 20:51:59: #2 predicted fragment length is 178 bps INFO @ Sat, 15 Jan 2022 20:51:59: #2 alternative fragment length(s) may be 4,178 bps INFO @ Sat, 15 Jan 2022 20:51:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.05_model.r WARNING @ Sat, 15 Jan 2022 20:51:59: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:51:59: #2 You may need to consider one of the other alternative d(s): 4,178 WARNING @ Sat, 15 Jan 2022 20:51:59: #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 20:51:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:51:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:52:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:52:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:52:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:52:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.05_summits.bed INFO @ Sat, 15 Jan 2022 20:52:05: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (669 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 20:52:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.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 20:52:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:52:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:52:26: 1000000 INFO @ Sat, 15 Jan 2022 20:52:29: #1 tag size is determined as 147 bps INFO @ Sat, 15 Jan 2022 20:52:29: #1 tag size = 147 INFO @ Sat, 15 Jan 2022 20:52:29: #1 total tags in treatment: 1415533 INFO @ Sat, 15 Jan 2022 20:52:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:52:29: #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 20:52:30: #1 tags after filtering in treatment: 1415533 INFO @ Sat, 15 Jan 2022 20:52:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:52:30: #1 finished! INFO @ Sat, 15 Jan 2022 20:52:30: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:52:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:52:30: #2 number of paired peaks: 274 WARNING @ Sat, 15 Jan 2022 20:52:30: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Sat, 15 Jan 2022 20:52:30: start model_add_line... INFO @ Sat, 15 Jan 2022 20:52:30: start X-correlation... INFO @ Sat, 15 Jan 2022 20:52:30: end of X-cor INFO @ Sat, 15 Jan 2022 20:52:30: #2 finished! INFO @ Sat, 15 Jan 2022 20:52:30: #2 predicted fragment length is 178 bps INFO @ Sat, 15 Jan 2022 20:52:30: #2 alternative fragment length(s) may be 4,178 bps INFO @ Sat, 15 Jan 2022 20:52:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.10_model.r WARNING @ Sat, 15 Jan 2022 20:52:30: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:52:30: #2 You may need to consider one of the other alternative d(s): 4,178 WARNING @ Sat, 15 Jan 2022 20:52:30: #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 20:52:30: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:52:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:52:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:52:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:52:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:52:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.10_summits.bed INFO @ Sat, 15 Jan 2022 20:52:35: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (447 records, 4 fields): 2 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 20:52:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.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 20:52:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:52:48: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:52:55: 1000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:52:58: #1 tag size is determined as 147 bps INFO @ Sat, 15 Jan 2022 20:52:58: #1 tag size = 147 INFO @ Sat, 15 Jan 2022 20:52:58: #1 total tags in treatment: 1415533 INFO @ Sat, 15 Jan 2022 20:52:58: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:52:58: #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 20:52:58: #1 tags after filtering in treatment: 1415533 INFO @ Sat, 15 Jan 2022 20:52:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:52:58: #1 finished! INFO @ Sat, 15 Jan 2022 20:52:58: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:52:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:52:58: #2 number of paired peaks: 274 WARNING @ Sat, 15 Jan 2022 20:52:58: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Sat, 15 Jan 2022 20:52:58: start model_add_line... INFO @ Sat, 15 Jan 2022 20:52:58: start X-correlation... INFO @ Sat, 15 Jan 2022 20:52:58: end of X-cor INFO @ Sat, 15 Jan 2022 20:52:58: #2 finished! INFO @ Sat, 15 Jan 2022 20:52:58: #2 predicted fragment length is 178 bps INFO @ Sat, 15 Jan 2022 20:52:58: #2 alternative fragment length(s) may be 4,178 bps INFO @ Sat, 15 Jan 2022 20:52:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.20_model.r WARNING @ Sat, 15 Jan 2022 20:52:58: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:52:58: #2 You may need to consider one of the other alternative d(s): 4,178 WARNING @ Sat, 15 Jan 2022 20:52:58: #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 20:52:58: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:52:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:53:02: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:53:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:53:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:53:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9278491/SRX9278491.20_summits.bed INFO @ Sat, 15 Jan 2022 20:53:03: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (252 records, 4 fields): 2 millis CompletedMACS2peakCalling