Job ID = 12531536 SRX = SRX2997386 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4151441 spots for SRR5819461/SRR5819461.sra Written 4151441 spots for SRR5819461/SRR5819461.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: 00:03:16 4151441 reads; of these: 4151441 (100.00%) were paired; of these: 1883920 (45.38%) aligned concordantly 0 times 1533000 (36.93%) aligned concordantly exactly 1 time 734521 (17.69%) aligned concordantly >1 times ---- 1883920 pairs aligned concordantly 0 times; of these: 359235 (19.07%) aligned discordantly 1 time ---- 1524685 pairs aligned 0 times concordantly or discordantly; of these: 3049370 mates make up the pairs; of these: 2613941 (85.72%) aligned 0 times 88494 (2.90%) aligned exactly 1 time 346935 (11.38%) aligned >1 times 68.52% overall alignment rate Time searching: 00:03:16 Overall time: 00:03:16 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] 500674 / 2595659 = 0.1929 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 08:12:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.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 08:12:04: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:12:04: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:12:09: 1000000 INFO @ Sat, 17 Apr 2021 08:12:14: 2000000 INFO @ Sat, 17 Apr 2021 08:12:19: 3000000 INFO @ Sat, 17 Apr 2021 08:12:24: 4000000 INFO @ Sat, 17 Apr 2021 08:12:28: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:12:28: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:12:28: #1 total tags in treatment: 1817804 INFO @ Sat, 17 Apr 2021 08:12:28: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:12:28: #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 08:12:28: #1 tags after filtering in treatment: 1034640 INFO @ Sat, 17 Apr 2021 08:12:28: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 17 Apr 2021 08:12:28: #1 finished! INFO @ Sat, 17 Apr 2021 08:12:28: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:12:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:12:28: #2 number of paired peaks: 397 WARNING @ Sat, 17 Apr 2021 08:12:28: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Sat, 17 Apr 2021 08:12:28: start model_add_line... INFO @ Sat, 17 Apr 2021 08:12:28: start X-correlation... INFO @ Sat, 17 Apr 2021 08:12:28: end of X-cor INFO @ Sat, 17 Apr 2021 08:12:28: #2 finished! INFO @ Sat, 17 Apr 2021 08:12:28: #2 predicted fragment length is 92 bps INFO @ Sat, 17 Apr 2021 08:12:28: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 17 Apr 2021 08:12:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.05_model.r WARNING @ Sat, 17 Apr 2021 08:12:28: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:12:28: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Sat, 17 Apr 2021 08:12:28: #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 08:12:28: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:12:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:12:31: #3 Call peaks for each chromosome... 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 08:12:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.05_peaks.xls INFO @ Sat, 17 Apr 2021 08:12:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:12:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.05_summits.bed INFO @ Sat, 17 Apr 2021 08:12:32: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (2088 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:12:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.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 08:12:34: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:12:34: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:12:39: 1000000 INFO @ Sat, 17 Apr 2021 08:12:44: 2000000 INFO @ Sat, 17 Apr 2021 08:12:49: 3000000 INFO @ Sat, 17 Apr 2021 08:12:54: 4000000 INFO @ Sat, 17 Apr 2021 08:12:58: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:12:58: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:12:58: #1 total tags in treatment: 1817804 INFO @ Sat, 17 Apr 2021 08:12:58: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:12:58: #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 08:12:58: #1 tags after filtering in treatment: 1034640 INFO @ Sat, 17 Apr 2021 08:12:58: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 17 Apr 2021 08:12:58: #1 finished! INFO @ Sat, 17 Apr 2021 08:12:58: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:12:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:12:58: #2 number of paired peaks: 397 WARNING @ Sat, 17 Apr 2021 08:12:58: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Sat, 17 Apr 2021 08:12:58: start model_add_line... INFO @ Sat, 17 Apr 2021 08:12:58: start X-correlation... INFO @ Sat, 17 Apr 2021 08:12:58: end of X-cor INFO @ Sat, 17 Apr 2021 08:12:58: #2 finished! INFO @ Sat, 17 Apr 2021 08:12:58: #2 predicted fragment length is 92 bps INFO @ Sat, 17 Apr 2021 08:12:58: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 17 Apr 2021 08:12:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.10_model.r WARNING @ Sat, 17 Apr 2021 08:12:58: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:12:58: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Sat, 17 Apr 2021 08:12:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:12:58: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:12:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:13:01: #3 Call peaks for each chromosome... 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 08:13:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.10_peaks.xls INFO @ Sat, 17 Apr 2021 08:13:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:13:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.10_summits.bed INFO @ Sat, 17 Apr 2021 08:13:02: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1357 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:13:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.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 08:13:04: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:13:04: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:13:09: 1000000 INFO @ Sat, 17 Apr 2021 08:13:14: 2000000 INFO @ Sat, 17 Apr 2021 08:13:19: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 08:13:24: 4000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 08:13:28: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:13:28: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:13:28: #1 total tags in treatment: 1817804 INFO @ Sat, 17 Apr 2021 08:13:28: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:13:28: #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 08:13:28: #1 tags after filtering in treatment: 1034640 INFO @ Sat, 17 Apr 2021 08:13:28: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 17 Apr 2021 08:13:28: #1 finished! INFO @ Sat, 17 Apr 2021 08:13:28: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:13:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:13:28: #2 number of paired peaks: 397 WARNING @ Sat, 17 Apr 2021 08:13:28: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Sat, 17 Apr 2021 08:13:28: start model_add_line... INFO @ Sat, 17 Apr 2021 08:13:28: start X-correlation... INFO @ Sat, 17 Apr 2021 08:13:28: end of X-cor INFO @ Sat, 17 Apr 2021 08:13:28: #2 finished! INFO @ Sat, 17 Apr 2021 08:13:28: #2 predicted fragment length is 92 bps INFO @ Sat, 17 Apr 2021 08:13:28: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 17 Apr 2021 08:13:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.20_model.r WARNING @ Sat, 17 Apr 2021 08:13:28: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:13:28: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Sat, 17 Apr 2021 08:13:28: #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 08:13:28: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:13:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:13:31: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:13:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.20_peaks.xls INFO @ Sat, 17 Apr 2021 08:13:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:13:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997386/SRX2997386.20_summits.bed INFO @ Sat, 17 Apr 2021 08:13:32: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (734 records, 4 fields): 3 millis CompletedMACS2peakCalling