Job ID = 12531533 SRX = SRX2997384 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3502446 spots for SRR5819459/SRR5819459.sra Written 3502446 spots for SRR5819459/SRR5819459.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: 00:03:09 3502446 reads; of these: 3502446 (100.00%) were paired; of these: 1620503 (46.27%) aligned concordantly 0 times 1277054 (36.46%) aligned concordantly exactly 1 time 604889 (17.27%) aligned concordantly >1 times ---- 1620503 pairs aligned concordantly 0 times; of these: 297191 (18.34%) aligned discordantly 1 time ---- 1323312 pairs aligned 0 times concordantly or discordantly; of these: 2646624 mates make up the pairs; of these: 2292735 (86.63%) aligned 0 times 74992 (2.83%) aligned exactly 1 time 278897 (10.54%) aligned >1 times 67.27% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 368164 / 2154293 = 0.1709 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:10:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.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, 17 Apr 2021 08:10:36: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:10:36: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:10:46: 1000000 INFO @ Sat, 17 Apr 2021 08:10:57: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:11:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.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, 17 Apr 2021 08:11:06: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:11:06: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:11:08: 3000000 INFO @ Sat, 17 Apr 2021 08:11:19: 1000000 INFO @ Sat, 17 Apr 2021 08:11:21: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:11:21: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:11:21: #1 total tags in treatment: 1551324 INFO @ Sat, 17 Apr 2021 08:11:21: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:11:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:11:21: #1 tags after filtering in treatment: 906814 INFO @ Sat, 17 Apr 2021 08:11:21: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 17 Apr 2021 08:11:21: #1 finished! INFO @ Sat, 17 Apr 2021 08:11:21: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:11:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:11:21: #2 number of paired peaks: 453 WARNING @ Sat, 17 Apr 2021 08:11:21: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Sat, 17 Apr 2021 08:11:21: start model_add_line... INFO @ Sat, 17 Apr 2021 08:11:21: start X-correlation... INFO @ Sat, 17 Apr 2021 08:11:21: end of X-cor INFO @ Sat, 17 Apr 2021 08:11:21: #2 finished! INFO @ Sat, 17 Apr 2021 08:11:21: #2 predicted fragment length is 96 bps INFO @ Sat, 17 Apr 2021 08:11:21: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 17 Apr 2021 08:11:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.05_model.r WARNING @ Sat, 17 Apr 2021 08:11:21: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:11:21: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 17 Apr 2021 08:11:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:11:21: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:11:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:11:24: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:11:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.05_peaks.xls INFO @ Sat, 17 Apr 2021 08:11:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:11:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.05_summits.bed INFO @ Sat, 17 Apr 2021 08:11:25: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1992 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:11:30: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:11:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.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, 17 Apr 2021 08:11:36: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:11:36: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:11:42: 3000000 INFO @ Sat, 17 Apr 2021 08:11:47: 1000000 INFO @ Sat, 17 Apr 2021 08:11:54: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:11:54: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:11:54: #1 total tags in treatment: 1551324 INFO @ Sat, 17 Apr 2021 08:11:54: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:11:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:11:54: #1 tags after filtering in treatment: 906814 INFO @ Sat, 17 Apr 2021 08:11:54: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 17 Apr 2021 08:11:54: #1 finished! INFO @ Sat, 17 Apr 2021 08:11:54: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:11:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:11:54: #2 number of paired peaks: 453 WARNING @ Sat, 17 Apr 2021 08:11:54: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Sat, 17 Apr 2021 08:11:54: start model_add_line... INFO @ Sat, 17 Apr 2021 08:11:54: start X-correlation... INFO @ Sat, 17 Apr 2021 08:11:54: end of X-cor INFO @ Sat, 17 Apr 2021 08:11:54: #2 finished! INFO @ Sat, 17 Apr 2021 08:11:54: #2 predicted fragment length is 96 bps INFO @ Sat, 17 Apr 2021 08:11:54: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 17 Apr 2021 08:11:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.10_model.r WARNING @ Sat, 17 Apr 2021 08:11:54: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:11:54: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 17 Apr 2021 08:11:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:11:54: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:11:54: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 08:11:57: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:11:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.10_peaks.xls INFO @ Sat, 17 Apr 2021 08:11:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:11:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.10_summits.bed INFO @ Sat, 17 Apr 2021 08:11:58: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (1304 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:11:59: 2000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 08:12:10: 3000000 INFO @ Sat, 17 Apr 2021 08:12:19: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:12:19: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:12:19: #1 total tags in treatment: 1551324 INFO @ Sat, 17 Apr 2021 08:12:19: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:12:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:12:19: #1 tags after filtering in treatment: 906814 INFO @ Sat, 17 Apr 2021 08:12:19: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 17 Apr 2021 08:12:19: #1 finished! INFO @ Sat, 17 Apr 2021 08:12:19: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:12:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:12:20: #2 number of paired peaks: 453 WARNING @ Sat, 17 Apr 2021 08:12:20: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Sat, 17 Apr 2021 08:12:20: start model_add_line... INFO @ Sat, 17 Apr 2021 08:12:20: start X-correlation... INFO @ Sat, 17 Apr 2021 08:12:20: end of X-cor INFO @ Sat, 17 Apr 2021 08:12:20: #2 finished! INFO @ Sat, 17 Apr 2021 08:12:20: #2 predicted fragment length is 96 bps INFO @ Sat, 17 Apr 2021 08:12:20: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 17 Apr 2021 08:12:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.20_model.r WARNING @ Sat, 17 Apr 2021 08:12:20: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:12:20: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 17 Apr 2021 08:12:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:12:20: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:12:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:12:22: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:12:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.20_peaks.xls INFO @ Sat, 17 Apr 2021 08:12:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:12:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997384/SRX2997384.20_summits.bed INFO @ Sat, 17 Apr 2021 08:12:23: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (674 records, 4 fields): 2 millis CompletedMACS2peakCalling