Job ID = 14521984 SRX = SRX6950511 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3533056 spots for SRR10231159/SRR10231159.sra Written 3533056 spots for SRR10231159/SRR10231159.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: 00:04:13 3533056 reads; of these: 3533056 (100.00%) were paired; of these: 746214 (21.12%) aligned concordantly 0 times 2546926 (72.09%) aligned concordantly exactly 1 time 239916 (6.79%) aligned concordantly >1 times ---- 746214 pairs aligned concordantly 0 times; of these: 292726 (39.23%) aligned discordantly 1 time ---- 453488 pairs aligned 0 times concordantly or discordantly; of these: 906976 mates make up the pairs; of these: 814441 (89.80%) aligned 0 times 31626 (3.49%) aligned exactly 1 time 60909 (6.72%) aligned >1 times 88.47% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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_sort_core] merging from 8 files... [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] 357657 / 2438420 = 0.1467 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 22:04:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.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 22:04:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:04:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:04:17: 1000000 INFO @ Sat, 15 Jan 2022 22:04:25: 2000000 INFO @ Sat, 15 Jan 2022 22:04:33: 3000000 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 22:04:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.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 22:04:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:04:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:04:42: 4000000 INFO @ Sat, 15 Jan 2022 22:04:49: 1000000 INFO @ Sat, 15 Jan 2022 22:04:52: 5000000 INFO @ Sat, 15 Jan 2022 22:04:58: #1 tag size is determined as 81 bps INFO @ Sat, 15 Jan 2022 22:04:58: #1 tag size = 81 INFO @ Sat, 15 Jan 2022 22:04:58: #1 total tags in treatment: 2473799 INFO @ Sat, 15 Jan 2022 22:04:58: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:04:58: #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 22:04:58: #1 tags after filtering in treatment: 2046012 INFO @ Sat, 15 Jan 2022 22:04:58: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 15 Jan 2022 22:04:58: #1 finished! INFO @ Sat, 15 Jan 2022 22:04:58: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:04:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:04:58: #2 number of paired peaks: 193 WARNING @ Sat, 15 Jan 2022 22:04:58: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 15 Jan 2022 22:04:58: start model_add_line... INFO @ Sat, 15 Jan 2022 22:04:58: start X-correlation... INFO @ Sat, 15 Jan 2022 22:04:58: end of X-cor INFO @ Sat, 15 Jan 2022 22:04:58: #2 finished! INFO @ Sat, 15 Jan 2022 22:04:58: #2 predicted fragment length is 88 bps INFO @ Sat, 15 Jan 2022 22:04:58: #2 alternative fragment length(s) may be 3,88,118 bps INFO @ Sat, 15 Jan 2022 22:04:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.05_model.r WARNING @ Sat, 15 Jan 2022 22:04:58: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 22:04:58: #2 You may need to consider one of the other alternative d(s): 3,88,118 WARNING @ Sat, 15 Jan 2022 22:04:58: #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 22:04:58: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:04:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:05:00: 2000000 INFO @ Sat, 15 Jan 2022 22:05:02: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:05:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.05_peaks.xls INFO @ Sat, 15 Jan 2022 22:05:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:05:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.05_summits.bed INFO @ Sat, 15 Jan 2022 22:05:04: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (683 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 22:05:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.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 22:05:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:05:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:05:11: 3000000 INFO @ Sat, 15 Jan 2022 22:05:18: 1000000 INFO @ Sat, 15 Jan 2022 22:05:22: 4000000 INFO @ Sat, 15 Jan 2022 22:05:29: 2000000 INFO @ Sat, 15 Jan 2022 22:05:33: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:05:39: 3000000 INFO @ Sat, 15 Jan 2022 22:05:39: #1 tag size is determined as 81 bps INFO @ Sat, 15 Jan 2022 22:05:39: #1 tag size = 81 INFO @ Sat, 15 Jan 2022 22:05:39: #1 total tags in treatment: 2473799 INFO @ Sat, 15 Jan 2022 22:05:39: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:05:39: #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 22:05:39: #1 tags after filtering in treatment: 2046012 INFO @ Sat, 15 Jan 2022 22:05:39: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 15 Jan 2022 22:05:39: #1 finished! INFO @ Sat, 15 Jan 2022 22:05:39: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:05:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:05:39: #2 number of paired peaks: 193 WARNING @ Sat, 15 Jan 2022 22:05:39: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 15 Jan 2022 22:05:39: start model_add_line... INFO @ Sat, 15 Jan 2022 22:05:39: start X-correlation... INFO @ Sat, 15 Jan 2022 22:05:39: end of X-cor INFO @ Sat, 15 Jan 2022 22:05:39: #2 finished! INFO @ Sat, 15 Jan 2022 22:05:39: #2 predicted fragment length is 88 bps INFO @ Sat, 15 Jan 2022 22:05:39: #2 alternative fragment length(s) may be 3,88,118 bps INFO @ Sat, 15 Jan 2022 22:05:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.10_model.r WARNING @ Sat, 15 Jan 2022 22:05:39: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 22:05:39: #2 You may need to consider one of the other alternative d(s): 3,88,118 WARNING @ Sat, 15 Jan 2022 22:05:39: #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 22:05:39: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:05:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:05:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 22:05:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.10_peaks.xls INFO @ Sat, 15 Jan 2022 22:05:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:05:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.10_summits.bed INFO @ Sat, 15 Jan 2022 22:05:45: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (379 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:05:48: 4000000 INFO @ Sat, 15 Jan 2022 22:05:56: 5000000 INFO @ Sat, 15 Jan 2022 22:06:00: #1 tag size is determined as 81 bps INFO @ Sat, 15 Jan 2022 22:06:00: #1 tag size = 81 INFO @ Sat, 15 Jan 2022 22:06:00: #1 total tags in treatment: 2473799 INFO @ Sat, 15 Jan 2022 22:06:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:06:00: #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 22:06:00: #1 tags after filtering in treatment: 2046012 INFO @ Sat, 15 Jan 2022 22:06:00: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 15 Jan 2022 22:06:00: #1 finished! INFO @ Sat, 15 Jan 2022 22:06:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:06:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:06:00: #2 number of paired peaks: 193 WARNING @ Sat, 15 Jan 2022 22:06:00: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 15 Jan 2022 22:06:00: start model_add_line... INFO @ Sat, 15 Jan 2022 22:06:00: start X-correlation... INFO @ Sat, 15 Jan 2022 22:06:00: end of X-cor INFO @ Sat, 15 Jan 2022 22:06:00: #2 finished! INFO @ Sat, 15 Jan 2022 22:06:00: #2 predicted fragment length is 88 bps INFO @ Sat, 15 Jan 2022 22:06:00: #2 alternative fragment length(s) may be 3,88,118 bps INFO @ Sat, 15 Jan 2022 22:06:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.20_model.r WARNING @ Sat, 15 Jan 2022 22:06:00: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 22:06:00: #2 You may need to consider one of the other alternative d(s): 3,88,118 WARNING @ Sat, 15 Jan 2022 22:06:00: #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 22:06:00: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:06:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:06:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:06:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.20_peaks.xls INFO @ Sat, 15 Jan 2022 22:06:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:06:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6950511/SRX6950511.20_summits.bed INFO @ Sat, 15 Jan 2022 22:06:06: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 7 millis CompletedMACS2peakCalling