Job ID = 7102315 SRX = SRX6911519 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6444043 spots for SRR10191162/SRR10191162.sra Written 6444043 spots for SRR10191162/SRR10191162.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: 00:07:11 6444043 reads; of these: 6444043 (100.00%) were paired; of these: 1479513 (22.96%) aligned concordantly 0 times 4403167 (68.33%) aligned concordantly exactly 1 time 561363 (8.71%) aligned concordantly >1 times ---- 1479513 pairs aligned concordantly 0 times; of these: 149111 (10.08%) aligned discordantly 1 time ---- 1330402 pairs aligned 0 times concordantly or discordantly; of these: 2660804 mates make up the pairs; of these: 2490232 (93.59%) aligned 0 times 118023 (4.44%) aligned exactly 1 time 52549 (1.97%) aligned >1 times 80.68% overall alignment rate Time searching: 00:07:11 Overall time: 00:07:11 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] 1276220 / 5113231 = 0.2496 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 12:29:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.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 @ Wed, 22 Jul 2020 12:29:24: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:29:24: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:29:31: 1000000 INFO @ Wed, 22 Jul 2020 12:29:39: 2000000 INFO @ Wed, 22 Jul 2020 12:29:46: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 12:29:53: 4000000 INFO @ Wed, 22 Jul 2020 12:29:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.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 @ Wed, 22 Jul 2020 12:29:53: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:29:53: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:30:00: 5000000 INFO @ Wed, 22 Jul 2020 12:30:01: 1000000 INFO @ Wed, 22 Jul 2020 12:30:08: 6000000 INFO @ Wed, 22 Jul 2020 12:30:09: 2000000 INFO @ Wed, 22 Jul 2020 12:30:16: 7000000 INFO @ Wed, 22 Jul 2020 12:30:16: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 12:30:22: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:30:22: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:30:22: #1 total tags in treatment: 3710144 INFO @ Wed, 22 Jul 2020 12:30:22: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:30:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:30:22: #1 tags after filtering in treatment: 1840603 INFO @ Wed, 22 Jul 2020 12:30:22: #1 Redundant rate of treatment: 0.50 INFO @ Wed, 22 Jul 2020 12:30:22: #1 finished! INFO @ Wed, 22 Jul 2020 12:30:22: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:30:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:30:23: #2 number of paired peaks: 693 WARNING @ Wed, 22 Jul 2020 12:30:23: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Wed, 22 Jul 2020 12:30:23: start model_add_line... INFO @ Wed, 22 Jul 2020 12:30:23: start X-correlation... INFO @ Wed, 22 Jul 2020 12:30:23: end of X-cor INFO @ Wed, 22 Jul 2020 12:30:23: #2 finished! INFO @ Wed, 22 Jul 2020 12:30:23: #2 predicted fragment length is 149 bps INFO @ Wed, 22 Jul 2020 12:30:23: #2 alternative fragment length(s) may be 1,149 bps INFO @ Wed, 22 Jul 2020 12:30:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.05_model.r WARNING @ Wed, 22 Jul 2020 12:30:23: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:30:23: #2 You may need to consider one of the other alternative d(s): 1,149 WARNING @ Wed, 22 Jul 2020 12:30:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 12:30:23: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:30:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:30:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.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 @ Wed, 22 Jul 2020 12:30:23: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:30:23: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:30:24: 4000000 INFO @ Wed, 22 Jul 2020 12:30:31: 1000000 INFO @ Wed, 22 Jul 2020 12:30:31: 5000000 INFO @ Wed, 22 Jul 2020 12:30:33: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:30:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.05_peaks.xls INFO @ Wed, 22 Jul 2020 12:30:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:30:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.05_summits.bed INFO @ Wed, 22 Jul 2020 12:30:35: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (509 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 12:30:39: 6000000 INFO @ Wed, 22 Jul 2020 12:30:39: 2000000 INFO @ Wed, 22 Jul 2020 12:30:47: 7000000 INFO @ Wed, 22 Jul 2020 12:30:47: 3000000 INFO @ Wed, 22 Jul 2020 12:30:53: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:30:53: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:30:53: #1 total tags in treatment: 3710144 INFO @ Wed, 22 Jul 2020 12:30:53: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:30:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:30:53: #1 tags after filtering in treatment: 1840603 INFO @ Wed, 22 Jul 2020 12:30:53: #1 Redundant rate of treatment: 0.50 INFO @ Wed, 22 Jul 2020 12:30:53: #1 finished! INFO @ Wed, 22 Jul 2020 12:30:53: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:30:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:30:54: #2 number of paired peaks: 693 WARNING @ Wed, 22 Jul 2020 12:30:54: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Wed, 22 Jul 2020 12:30:54: start model_add_line... INFO @ Wed, 22 Jul 2020 12:30:54: start X-correlation... INFO @ Wed, 22 Jul 2020 12:30:54: end of X-cor INFO @ Wed, 22 Jul 2020 12:30:54: #2 finished! INFO @ Wed, 22 Jul 2020 12:30:54: #2 predicted fragment length is 149 bps INFO @ Wed, 22 Jul 2020 12:30:54: #2 alternative fragment length(s) may be 1,149 bps INFO @ Wed, 22 Jul 2020 12:30:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.10_model.r WARNING @ Wed, 22 Jul 2020 12:30:54: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:30:54: #2 You may need to consider one of the other alternative d(s): 1,149 WARNING @ Wed, 22 Jul 2020 12:30:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 12:30:54: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:30:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:30:55: 4000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 12:31:02: 5000000 INFO @ Wed, 22 Jul 2020 12:31:04: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:31:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.10_peaks.xls INFO @ Wed, 22 Jul 2020 12:31:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:31:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.10_summits.bed INFO @ Wed, 22 Jul 2020 12:31:06: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (153 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 12:31:10: 6000000 INFO @ Wed, 22 Jul 2020 12:31:17: 7000000 INFO @ Wed, 22 Jul 2020 12:31:23: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:31:23: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:31:23: #1 total tags in treatment: 3710144 INFO @ Wed, 22 Jul 2020 12:31:23: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:31:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:31:23: #1 tags after filtering in treatment: 1840603 INFO @ Wed, 22 Jul 2020 12:31:23: #1 Redundant rate of treatment: 0.50 INFO @ Wed, 22 Jul 2020 12:31:23: #1 finished! INFO @ Wed, 22 Jul 2020 12:31:23: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:31:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:31:24: #2 number of paired peaks: 693 WARNING @ Wed, 22 Jul 2020 12:31:24: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Wed, 22 Jul 2020 12:31:24: start model_add_line... INFO @ Wed, 22 Jul 2020 12:31:24: start X-correlation... INFO @ Wed, 22 Jul 2020 12:31:24: end of X-cor INFO @ Wed, 22 Jul 2020 12:31:24: #2 finished! INFO @ Wed, 22 Jul 2020 12:31:24: #2 predicted fragment length is 149 bps INFO @ Wed, 22 Jul 2020 12:31:24: #2 alternative fragment length(s) may be 1,149 bps INFO @ Wed, 22 Jul 2020 12:31:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.20_model.r WARNING @ Wed, 22 Jul 2020 12:31:24: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:31:24: #2 You may need to consider one of the other alternative d(s): 1,149 WARNING @ Wed, 22 Jul 2020 12:31:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 12:31:24: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:31:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:31:33: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:31:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.20_peaks.xls INFO @ Wed, 22 Jul 2020 12:31:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:31:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911519/SRX6911519.20_summits.bed INFO @ Wed, 22 Jul 2020 12:31:35: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (34 records, 4 fields): 1 millis CompletedMACS2peakCalling