Job ID = 12531541 SRX = SRX2997389 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4812628 spots for SRR5819464/SRR5819464.sra Written 4812628 spots for SRR5819464/SRR5819464.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: 00:03:48 4812628 reads; of these: 4812628 (100.00%) were paired; of these: 2025945 (42.10%) aligned concordantly 0 times 1832987 (38.09%) aligned concordantly exactly 1 time 953696 (19.82%) aligned concordantly >1 times ---- 2025945 pairs aligned concordantly 0 times; of these: 391618 (19.33%) aligned discordantly 1 time ---- 1634327 pairs aligned 0 times concordantly or discordantly; of these: 3268654 mates make up the pairs; of these: 2758731 (84.40%) aligned 0 times 95763 (2.93%) aligned exactly 1 time 414160 (12.67%) aligned >1 times 71.34% overall alignment rate Time searching: 00:03:48 Overall time: 00:03:48 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] 680729 / 3143938 = 0.2165 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 08:15:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.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 08:15:15: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:15:15: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:15:21: 1000000 INFO @ Sat, 17 Apr 2021 08:15:27: 2000000 INFO @ Sat, 17 Apr 2021 08:15:32: 3000000 INFO @ Sat, 17 Apr 2021 08:15:38: 4000000 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 08:15:44: 5000000 INFO @ Sat, 17 Apr 2021 08:15:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.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 08:15:45: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:15:45: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:15:47: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:15:47: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:15:47: #1 total tags in treatment: 2170342 INFO @ Sat, 17 Apr 2021 08:15:47: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:15:47: #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 08:15:47: #1 tags after filtering in treatment: 1166225 INFO @ Sat, 17 Apr 2021 08:15:47: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 17 Apr 2021 08:15:47: #1 finished! INFO @ Sat, 17 Apr 2021 08:15:47: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:15:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:15:47: #2 number of paired peaks: 350 WARNING @ Sat, 17 Apr 2021 08:15:47: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Sat, 17 Apr 2021 08:15:47: start model_add_line... INFO @ Sat, 17 Apr 2021 08:15:47: start X-correlation... INFO @ Sat, 17 Apr 2021 08:15:47: end of X-cor INFO @ Sat, 17 Apr 2021 08:15:47: #2 finished! INFO @ Sat, 17 Apr 2021 08:15:47: #2 predicted fragment length is 103 bps INFO @ Sat, 17 Apr 2021 08:15:47: #2 alternative fragment length(s) may be 103 bps INFO @ Sat, 17 Apr 2021 08:15:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.05_model.r WARNING @ Sat, 17 Apr 2021 08:15:47: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:15:47: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Sat, 17 Apr 2021 08:15:47: #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 08:15:47: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:15:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:15:50: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:15:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.05_peaks.xls INFO @ Sat, 17 Apr 2021 08:15:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:15:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.05_summits.bed INFO @ Sat, 17 Apr 2021 08:15:51: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (2229 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:15:53: 1000000 INFO @ Sat, 17 Apr 2021 08:16:00: 2000000 INFO @ Sat, 17 Apr 2021 08:16:07: 3000000 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 08:16:14: 4000000 INFO @ Sat, 17 Apr 2021 08:16:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.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 08:16:15: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:16:15: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:16:21: 5000000 INFO @ Sat, 17 Apr 2021 08:16:22: 1000000 INFO @ Sat, 17 Apr 2021 08:16:25: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:16:25: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:16:25: #1 total tags in treatment: 2170342 INFO @ Sat, 17 Apr 2021 08:16:25: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:16:25: #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 08:16:25: #1 tags after filtering in treatment: 1166225 INFO @ Sat, 17 Apr 2021 08:16:25: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 17 Apr 2021 08:16:25: #1 finished! INFO @ Sat, 17 Apr 2021 08:16:25: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:16:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:16:25: #2 number of paired peaks: 350 WARNING @ Sat, 17 Apr 2021 08:16:25: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Sat, 17 Apr 2021 08:16:25: start model_add_line... INFO @ Sat, 17 Apr 2021 08:16:25: start X-correlation... INFO @ Sat, 17 Apr 2021 08:16:25: end of X-cor INFO @ Sat, 17 Apr 2021 08:16:25: #2 finished! INFO @ Sat, 17 Apr 2021 08:16:25: #2 predicted fragment length is 103 bps INFO @ Sat, 17 Apr 2021 08:16:25: #2 alternative fragment length(s) may be 103 bps INFO @ Sat, 17 Apr 2021 08:16:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.10_model.r WARNING @ Sat, 17 Apr 2021 08:16:25: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:16:25: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Sat, 17 Apr 2021 08:16:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:16:25: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:16:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:16:28: 2000000 INFO @ Sat, 17 Apr 2021 08:16:29: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:16:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.10_peaks.xls INFO @ Sat, 17 Apr 2021 08:16:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:16:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.10_summits.bed INFO @ Sat, 17 Apr 2021 08:16:30: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1504 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:16:34: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 08:16:40: 4000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 08:16:46: 5000000 INFO @ Sat, 17 Apr 2021 08:16:49: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:16:49: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:16:49: #1 total tags in treatment: 2170342 INFO @ Sat, 17 Apr 2021 08:16:49: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:16:49: #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 08:16:49: #1 tags after filtering in treatment: 1166225 INFO @ Sat, 17 Apr 2021 08:16:49: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 17 Apr 2021 08:16:49: #1 finished! INFO @ Sat, 17 Apr 2021 08:16:49: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:16:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:16:49: #2 number of paired peaks: 350 WARNING @ Sat, 17 Apr 2021 08:16:49: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Sat, 17 Apr 2021 08:16:49: start model_add_line... INFO @ Sat, 17 Apr 2021 08:16:49: start X-correlation... INFO @ Sat, 17 Apr 2021 08:16:49: end of X-cor INFO @ Sat, 17 Apr 2021 08:16:49: #2 finished! INFO @ Sat, 17 Apr 2021 08:16:49: #2 predicted fragment length is 103 bps INFO @ Sat, 17 Apr 2021 08:16:49: #2 alternative fragment length(s) may be 103 bps INFO @ Sat, 17 Apr 2021 08:16:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.20_model.r WARNING @ Sat, 17 Apr 2021 08:16:49: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:16:49: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Sat, 17 Apr 2021 08:16:49: #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 08:16:49: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:16:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:16:52: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:16:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.20_peaks.xls INFO @ Sat, 17 Apr 2021 08:16:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:16:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997389/SRX2997389.20_summits.bed INFO @ Sat, 17 Apr 2021 08:16:53: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (841 records, 4 fields): 5 millis CompletedMACS2peakCalling