Job ID = 14520587 SRX = SRX10705895 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 2300796 spots for SRR14352048/SRR14352048.sra Written 2300796 spots for SRR14352048/SRR14352048.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: 00:00:30 2300796 reads; of these: 2300796 (100.00%) were unpaired; of these: 514363 (22.36%) aligned 0 times 1555748 (67.62%) aligned exactly 1 time 230685 (10.03%) aligned >1 times 77.64% overall alignment rate Time searching: 00:00:30 Overall time: 00:00:30 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] 355032 / 1786433 = 0.1987 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 19:26:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.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 19:26:21: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:26:21: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:26:29: 1000000 INFO @ Sat, 15 Jan 2022 19:26:32: #1 tag size is determined as 82 bps INFO @ Sat, 15 Jan 2022 19:26:32: #1 tag size = 82 INFO @ Sat, 15 Jan 2022 19:26:32: #1 total tags in treatment: 1431401 INFO @ Sat, 15 Jan 2022 19:26:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:26:32: #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 19:26:32: #1 tags after filtering in treatment: 1431401 INFO @ Sat, 15 Jan 2022 19:26:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 19:26:32: #1 finished! INFO @ Sat, 15 Jan 2022 19:26:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:26:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:26:32: #2 number of paired peaks: 187 WARNING @ Sat, 15 Jan 2022 19:26:32: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sat, 15 Jan 2022 19:26:32: start model_add_line... INFO @ Sat, 15 Jan 2022 19:26:32: start X-correlation... INFO @ Sat, 15 Jan 2022 19:26:32: end of X-cor INFO @ Sat, 15 Jan 2022 19:26:32: #2 finished! INFO @ Sat, 15 Jan 2022 19:26:32: #2 predicted fragment length is 89 bps INFO @ Sat, 15 Jan 2022 19:26:32: #2 alternative fragment length(s) may be 4,89 bps INFO @ Sat, 15 Jan 2022 19:26:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.05_model.r WARNING @ Sat, 15 Jan 2022 19:26:32: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:26:32: #2 You may need to consider one of the other alternative d(s): 4,89 WARNING @ Sat, 15 Jan 2022 19:26:32: #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 19:26:32: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:26:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:26:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:26:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:26:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:26:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.05_summits.bed INFO @ Sat, 15 Jan 2022 19:26:37: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (1222 records, 4 fields): 32 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 19:26:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.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 19:26:51: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:26:51: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:26:59: 1000000 INFO @ Sat, 15 Jan 2022 19:27:02: #1 tag size is determined as 82 bps INFO @ Sat, 15 Jan 2022 19:27:02: #1 tag size = 82 INFO @ Sat, 15 Jan 2022 19:27:02: #1 total tags in treatment: 1431401 INFO @ Sat, 15 Jan 2022 19:27:02: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:27:02: #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 19:27:02: #1 tags after filtering in treatment: 1431401 INFO @ Sat, 15 Jan 2022 19:27:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 19:27:02: #1 finished! INFO @ Sat, 15 Jan 2022 19:27:02: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:27:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:27:02: #2 number of paired peaks: 187 WARNING @ Sat, 15 Jan 2022 19:27:02: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sat, 15 Jan 2022 19:27:02: start model_add_line... INFO @ Sat, 15 Jan 2022 19:27:02: start X-correlation... INFO @ Sat, 15 Jan 2022 19:27:02: end of X-cor INFO @ Sat, 15 Jan 2022 19:27:02: #2 finished! INFO @ Sat, 15 Jan 2022 19:27:02: #2 predicted fragment length is 89 bps INFO @ Sat, 15 Jan 2022 19:27:02: #2 alternative fragment length(s) may be 4,89 bps INFO @ Sat, 15 Jan 2022 19:27:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.10_model.r WARNING @ Sat, 15 Jan 2022 19:27:02: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:27:02: #2 You may need to consider one of the other alternative d(s): 4,89 WARNING @ Sat, 15 Jan 2022 19:27:02: #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 19:27:02: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:27:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:27:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:27:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:27:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:27:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.10_summits.bed INFO @ Sat, 15 Jan 2022 19:27:06: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (602 records, 4 fields): 36 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 19:27:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.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 19:27:21: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:27:21: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:27:28: 1000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:27:31: #1 tag size is determined as 82 bps INFO @ Sat, 15 Jan 2022 19:27:31: #1 tag size = 82 INFO @ Sat, 15 Jan 2022 19:27:31: #1 total tags in treatment: 1431401 INFO @ Sat, 15 Jan 2022 19:27:31: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:27:31: #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 19:27:31: #1 tags after filtering in treatment: 1431401 INFO @ Sat, 15 Jan 2022 19:27:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 19:27:31: #1 finished! INFO @ Sat, 15 Jan 2022 19:27:31: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:27:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:27:31: #2 number of paired peaks: 187 WARNING @ Sat, 15 Jan 2022 19:27:31: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sat, 15 Jan 2022 19:27:31: start model_add_line... INFO @ Sat, 15 Jan 2022 19:27:31: start X-correlation... INFO @ Sat, 15 Jan 2022 19:27:31: end of X-cor INFO @ Sat, 15 Jan 2022 19:27:31: #2 finished! INFO @ Sat, 15 Jan 2022 19:27:31: #2 predicted fragment length is 89 bps INFO @ Sat, 15 Jan 2022 19:27:31: #2 alternative fragment length(s) may be 4,89 bps INFO @ Sat, 15 Jan 2022 19:27:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.20_model.r WARNING @ Sat, 15 Jan 2022 19:27:31: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:27:31: #2 You may need to consider one of the other alternative d(s): 4,89 WARNING @ Sat, 15 Jan 2022 19:27:31: #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 19:27:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:27:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:27:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:27:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:27:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:27:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10705895/SRX10705895.20_summits.bed INFO @ Sat, 15 Jan 2022 19:27:36: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (261 records, 4 fields): 84 millis CompletedMACS2peakCalling