Job ID = 7099566 SRX = SRX6911508 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18325476 spots for SRR10191135/SRR10191135.sra Written 18325476 spots for SRR10191135/SRR10191135.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: 00:17:38 18325476 reads; of these: 18325476 (100.00%) were paired; of these: 6257603 (34.15%) aligned concordantly 0 times 10619171 (57.95%) aligned concordantly exactly 1 time 1448702 (7.91%) aligned concordantly >1 times ---- 6257603 pairs aligned concordantly 0 times; of these: 504640 (8.06%) aligned discordantly 1 time ---- 5752963 pairs aligned 0 times concordantly or discordantly; of these: 11505926 mates make up the pairs; of these: 10385902 (90.27%) aligned 0 times 799073 (6.94%) aligned exactly 1 time 320951 (2.79%) aligned >1 times 71.66% overall alignment rate Time searching: 00:17:38 Overall time: 00:17:38 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 12 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] 6887448 / 12571389 = 0.5479 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 12:31:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.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 12:31:59: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:31:59: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:32:07: 1000000 INFO @ Wed, 22 Jul 2020 12:32:15: 2000000 INFO @ Wed, 22 Jul 2020 12:32:23: 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 12:32:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.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 12:32:28: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:32:28: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:32:31: 4000000 INFO @ Wed, 22 Jul 2020 12:32:36: 1000000 INFO @ Wed, 22 Jul 2020 12:32:40: 5000000 INFO @ Wed, 22 Jul 2020 12:32:44: 2000000 INFO @ Wed, 22 Jul 2020 12:32:48: 6000000 INFO @ Wed, 22 Jul 2020 12:32:52: 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 12:32:57: 7000000 INFO @ Wed, 22 Jul 2020 12:32:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.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 12:32:58: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:32:58: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:33:00: 4000000 INFO @ Wed, 22 Jul 2020 12:33:05: 8000000 INFO @ Wed, 22 Jul 2020 12:33:06: 1000000 INFO @ Wed, 22 Jul 2020 12:33:08: 5000000 INFO @ Wed, 22 Jul 2020 12:33:14: 9000000 INFO @ Wed, 22 Jul 2020 12:33:14: 2000000 INFO @ Wed, 22 Jul 2020 12:33:16: 6000000 INFO @ Wed, 22 Jul 2020 12:33:22: 3000000 INFO @ Wed, 22 Jul 2020 12:33:23: 10000000 INFO @ Wed, 22 Jul 2020 12:33:24: 7000000 INFO @ Wed, 22 Jul 2020 12:33:30: 4000000 INFO @ Wed, 22 Jul 2020 12:33:32: 8000000 INFO @ Wed, 22 Jul 2020 12:33:32: 11000000 INFO @ Wed, 22 Jul 2020 12:33:38: 5000000 INFO @ Wed, 22 Jul 2020 12:33:40: 9000000 INFO @ Wed, 22 Jul 2020 12:33:41: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 12:33:45: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:33:45: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:33:45: #1 total tags in treatment: 5370202 INFO @ Wed, 22 Jul 2020 12:33:45: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:33:45: #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 12:33:45: #1 tags after filtering in treatment: 1746433 INFO @ Wed, 22 Jul 2020 12:33:45: #1 Redundant rate of treatment: 0.67 INFO @ Wed, 22 Jul 2020 12:33:45: #1 finished! INFO @ Wed, 22 Jul 2020 12:33:45: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:33:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:33:46: #2 number of paired peaks: 962 WARNING @ Wed, 22 Jul 2020 12:33:46: Fewer paired peaks (962) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 962 pairs to build model! INFO @ Wed, 22 Jul 2020 12:33:46: start model_add_line... INFO @ Wed, 22 Jul 2020 12:33:46: start X-correlation... INFO @ Wed, 22 Jul 2020 12:33:46: end of X-cor INFO @ Wed, 22 Jul 2020 12:33:46: #2 finished! INFO @ Wed, 22 Jul 2020 12:33:46: #2 predicted fragment length is 168 bps INFO @ Wed, 22 Jul 2020 12:33:46: #2 alternative fragment length(s) may be 0,117,146,168 bps INFO @ Wed, 22 Jul 2020 12:33:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.05_model.r WARNING @ Wed, 22 Jul 2020 12:33:46: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:33:46: #2 You may need to consider one of the other alternative d(s): 0,117,146,168 WARNING @ Wed, 22 Jul 2020 12:33:46: #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 12:33:46: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:33:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:33:46: 6000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 12:33:48: 10000000 INFO @ Wed, 22 Jul 2020 12:33:54: 7000000 INFO @ Wed, 22 Jul 2020 12:33:54: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:33:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.05_peaks.xls INFO @ Wed, 22 Jul 2020 12:33:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:33:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.05_summits.bed INFO @ Wed, 22 Jul 2020 12:33:56: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (501 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 12:33:56: 11000000 INFO @ Wed, 22 Jul 2020 12:34:02: 8000000 INFO @ Wed, 22 Jul 2020 12:34:04: 12000000 INFO @ Wed, 22 Jul 2020 12:34:07: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:34:07: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:34:07: #1 total tags in treatment: 5370202 INFO @ Wed, 22 Jul 2020 12:34:07: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:34:07: #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 12:34:08: #1 tags after filtering in treatment: 1746433 INFO @ Wed, 22 Jul 2020 12:34:08: #1 Redundant rate of treatment: 0.67 INFO @ Wed, 22 Jul 2020 12:34:08: #1 finished! INFO @ Wed, 22 Jul 2020 12:34:08: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:34:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:34:08: #2 number of paired peaks: 962 WARNING @ Wed, 22 Jul 2020 12:34:08: Fewer paired peaks (962) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 962 pairs to build model! INFO @ Wed, 22 Jul 2020 12:34:08: start model_add_line... INFO @ Wed, 22 Jul 2020 12:34:08: start X-correlation... INFO @ Wed, 22 Jul 2020 12:34:08: end of X-cor INFO @ Wed, 22 Jul 2020 12:34:08: #2 finished! INFO @ Wed, 22 Jul 2020 12:34:08: #2 predicted fragment length is 168 bps INFO @ Wed, 22 Jul 2020 12:34:08: #2 alternative fragment length(s) may be 0,117,146,168 bps INFO @ Wed, 22 Jul 2020 12:34:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.10_model.r WARNING @ Wed, 22 Jul 2020 12:34:08: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:34:08: #2 You may need to consider one of the other alternative d(s): 0,117,146,168 WARNING @ Wed, 22 Jul 2020 12:34:08: #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 12:34:08: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:34:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:34:09: 9000000 INFO @ Wed, 22 Jul 2020 12:34:16: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:34:17: 10000000 INFO @ Wed, 22 Jul 2020 12:34:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.10_peaks.xls INFO @ Wed, 22 Jul 2020 12:34:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:34:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.10_summits.bed INFO @ Wed, 22 Jul 2020 12:34:18: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (433 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 12:34:24: 11000000 INFO @ Wed, 22 Jul 2020 12:34:31: 12000000 INFO @ Wed, 22 Jul 2020 12:34:34: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:34:34: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:34:34: #1 total tags in treatment: 5370202 INFO @ Wed, 22 Jul 2020 12:34:34: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:34:34: #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 12:34:34: #1 tags after filtering in treatment: 1746433 INFO @ Wed, 22 Jul 2020 12:34:34: #1 Redundant rate of treatment: 0.67 INFO @ Wed, 22 Jul 2020 12:34:34: #1 finished! INFO @ Wed, 22 Jul 2020 12:34:34: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:34:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:34:35: #2 number of paired peaks: 962 WARNING @ Wed, 22 Jul 2020 12:34:35: Fewer paired peaks (962) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 962 pairs to build model! INFO @ Wed, 22 Jul 2020 12:34:35: start model_add_line... INFO @ Wed, 22 Jul 2020 12:34:35: start X-correlation... INFO @ Wed, 22 Jul 2020 12:34:35: end of X-cor INFO @ Wed, 22 Jul 2020 12:34:35: #2 finished! INFO @ Wed, 22 Jul 2020 12:34:35: #2 predicted fragment length is 168 bps INFO @ Wed, 22 Jul 2020 12:34:35: #2 alternative fragment length(s) may be 0,117,146,168 bps INFO @ Wed, 22 Jul 2020 12:34:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.20_model.r WARNING @ Wed, 22 Jul 2020 12:34:35: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:34:35: #2 You may need to consider one of the other alternative d(s): 0,117,146,168 WARNING @ Wed, 22 Jul 2020 12:34:35: #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 12:34:35: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:34:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:34:43: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:34:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.20_peaks.xls INFO @ Wed, 22 Jul 2020 12:34:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:34:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911508/SRX6911508.20_summits.bed INFO @ Wed, 22 Jul 2020 12:34:44: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (296 records, 4 fields): 57 millis CompletedMACS2peakCalling