Job ID = 12531674 SRX = SRX4555046 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10786274 spots for SRR7696744/SRR7696744.sra Written 10786274 spots for SRR7696744/SRR7696744.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: 00:16:51 10786274 reads; of these: 10786274 (100.00%) were paired; of these: 723497 (6.71%) aligned concordantly 0 times 5339655 (49.50%) aligned concordantly exactly 1 time 4723122 (43.79%) aligned concordantly >1 times ---- 723497 pairs aligned concordantly 0 times; of these: 49140 (6.79%) aligned discordantly 1 time ---- 674357 pairs aligned 0 times concordantly or discordantly; of these: 1348714 mates make up the pairs; of these: 1083210 (80.31%) aligned 0 times 137760 (10.21%) aligned exactly 1 time 127744 (9.47%) aligned >1 times 94.98% overall alignment rate Time searching: 00:16:51 Overall time: 00:16:51 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 16 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] 1941827 / 4915282 = 0.3951 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 09:29:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.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 09:29:22: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:29:22: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:29:28: 1000000 INFO @ Sat, 17 Apr 2021 09:29:35: 2000000 INFO @ Sat, 17 Apr 2021 09:29:41: 3000000 INFO @ Sat, 17 Apr 2021 09:29:47: 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 09:29:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.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 09:29:52: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:29:52: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:29:53: 5000000 INFO @ Sat, 17 Apr 2021 09:30:00: 1000000 INFO @ Sat, 17 Apr 2021 09:30:01: 6000000 INFO @ Sat, 17 Apr 2021 09:30:07: 2000000 INFO @ Sat, 17 Apr 2021 09:30:07: 7000000 INFO @ Sat, 17 Apr 2021 09:30:13: 3000000 INFO @ Sat, 17 Apr 2021 09:30:13: 8000000 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 09:30:20: 9000000 INFO @ Sat, 17 Apr 2021 09:30:20: 4000000 INFO @ Sat, 17 Apr 2021 09:30:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.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 09:30:22: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:30:22: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:30:26: 10000000 INFO @ Sat, 17 Apr 2021 09:30:27: 5000000 INFO @ Sat, 17 Apr 2021 09:30:29: 1000000 INFO @ Sat, 17 Apr 2021 09:30:33: 11000000 INFO @ Sat, 17 Apr 2021 09:30:34: 6000000 INFO @ Sat, 17 Apr 2021 09:30:35: 2000000 INFO @ Sat, 17 Apr 2021 09:30:39: 12000000 INFO @ Sat, 17 Apr 2021 09:30:41: 7000000 INFO @ Sat, 17 Apr 2021 09:30:42: 3000000 INFO @ Sat, 17 Apr 2021 09:30:46: 13000000 INFO @ Sat, 17 Apr 2021 09:30:47: 8000000 INFO @ Sat, 17 Apr 2021 09:30:48: 4000000 INFO @ Sat, 17 Apr 2021 09:30:53: 14000000 INFO @ Sat, 17 Apr 2021 09:30:54: 9000000 INFO @ Sat, 17 Apr 2021 09:30:55: 5000000 INFO @ Sat, 17 Apr 2021 09:31:00: 15000000 INFO @ Sat, 17 Apr 2021 09:31:01: 10000000 INFO @ Sat, 17 Apr 2021 09:31:02: 6000000 INFO @ Sat, 17 Apr 2021 09:31:07: 16000000 INFO @ Sat, 17 Apr 2021 09:31:08: 11000000 INFO @ Sat, 17 Apr 2021 09:31:08: 7000000 INFO @ Sat, 17 Apr 2021 09:31:11: #1 tag size is determined as 75 bps INFO @ Sat, 17 Apr 2021 09:31:11: #1 tag size = 75 INFO @ Sat, 17 Apr 2021 09:31:11: #1 total tags in treatment: 8123411 INFO @ Sat, 17 Apr 2021 09:31:11: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:31:11: #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 09:31:11: #1 tags after filtering in treatment: 2148849 INFO @ Sat, 17 Apr 2021 09:31:11: #1 Redundant rate of treatment: 0.74 INFO @ Sat, 17 Apr 2021 09:31:11: #1 finished! INFO @ Sat, 17 Apr 2021 09:31:11: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:31:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:31:11: #2 number of paired peaks: 169 WARNING @ Sat, 17 Apr 2021 09:31:11: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 17 Apr 2021 09:31:11: start model_add_line... INFO @ Sat, 17 Apr 2021 09:31:11: start X-correlation... INFO @ Sat, 17 Apr 2021 09:31:11: end of X-cor INFO @ Sat, 17 Apr 2021 09:31:11: #2 finished! INFO @ Sat, 17 Apr 2021 09:31:11: #2 predicted fragment length is 46 bps INFO @ Sat, 17 Apr 2021 09:31:11: #2 alternative fragment length(s) may be 4,17,46 bps INFO @ Sat, 17 Apr 2021 09:31:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.05_model.r WARNING @ Sat, 17 Apr 2021 09:31:11: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:31:11: #2 You may need to consider one of the other alternative d(s): 4,17,46 WARNING @ Sat, 17 Apr 2021 09:31:11: #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 09:31:11: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:31:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:31:14: 12000000 INFO @ Sat, 17 Apr 2021 09:31:14: 8000000 INFO @ Sat, 17 Apr 2021 09:31:15: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:31:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.05_peaks.xls INFO @ Sat, 17 Apr 2021 09:31:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:31:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.05_summits.bed INFO @ Sat, 17 Apr 2021 09:31:17: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (2835 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:31:20: 9000000 INFO @ Sat, 17 Apr 2021 09:31:20: 13000000 INFO @ Sat, 17 Apr 2021 09:31:26: 10000000 INFO @ Sat, 17 Apr 2021 09:31:26: 14000000 INFO @ Sat, 17 Apr 2021 09:31:32: 11000000 INFO @ Sat, 17 Apr 2021 09:31:33: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 09:31:38: 12000000 INFO @ Sat, 17 Apr 2021 09:31:39: 16000000 INFO @ Sat, 17 Apr 2021 09:31:43: #1 tag size is determined as 75 bps INFO @ Sat, 17 Apr 2021 09:31:43: #1 tag size = 75 INFO @ Sat, 17 Apr 2021 09:31:43: #1 total tags in treatment: 8123411 INFO @ Sat, 17 Apr 2021 09:31:43: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:31:43: #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 09:31:43: #1 tags after filtering in treatment: 2148849 INFO @ Sat, 17 Apr 2021 09:31:43: #1 Redundant rate of treatment: 0.74 INFO @ Sat, 17 Apr 2021 09:31:43: #1 finished! INFO @ Sat, 17 Apr 2021 09:31:43: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:31:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:31:43: #2 number of paired peaks: 169 WARNING @ Sat, 17 Apr 2021 09:31:43: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 17 Apr 2021 09:31:43: start model_add_line... INFO @ Sat, 17 Apr 2021 09:31:43: start X-correlation... INFO @ Sat, 17 Apr 2021 09:31:43: end of X-cor INFO @ Sat, 17 Apr 2021 09:31:43: #2 finished! INFO @ Sat, 17 Apr 2021 09:31:43: #2 predicted fragment length is 46 bps INFO @ Sat, 17 Apr 2021 09:31:43: #2 alternative fragment length(s) may be 4,17,46 bps INFO @ Sat, 17 Apr 2021 09:31:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.10_model.r WARNING @ Sat, 17 Apr 2021 09:31:43: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:31:43: #2 You may need to consider one of the other alternative d(s): 4,17,46 WARNING @ Sat, 17 Apr 2021 09:31:43: #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 09:31:43: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:31:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:31:44: 13000000 INFO @ Sat, 17 Apr 2021 09:31:47: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:31:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.10_peaks.xls INFO @ Sat, 17 Apr 2021 09:31:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:31:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.10_summits.bed INFO @ Sat, 17 Apr 2021 09:31:49: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1598 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:31:51: 14000000 INFO @ Sat, 17 Apr 2021 09:31:57: 15000000 INFO @ Sat, 17 Apr 2021 09:32:03: 16000000 INFO @ Sat, 17 Apr 2021 09:32:08: #1 tag size is determined as 75 bps INFO @ Sat, 17 Apr 2021 09:32:08: #1 tag size = 75 INFO @ Sat, 17 Apr 2021 09:32:08: #1 total tags in treatment: 8123411 INFO @ Sat, 17 Apr 2021 09:32:08: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:32:08: #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 09:32:08: #1 tags after filtering in treatment: 2148849 INFO @ Sat, 17 Apr 2021 09:32:08: #1 Redundant rate of treatment: 0.74 INFO @ Sat, 17 Apr 2021 09:32:08: #1 finished! INFO @ Sat, 17 Apr 2021 09:32:08: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:32:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:32:08: #2 number of paired peaks: 169 WARNING @ Sat, 17 Apr 2021 09:32:08: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 17 Apr 2021 09:32:08: start model_add_line... INFO @ Sat, 17 Apr 2021 09:32:08: start X-correlation... INFO @ Sat, 17 Apr 2021 09:32:08: end of X-cor INFO @ Sat, 17 Apr 2021 09:32:08: #2 finished! INFO @ Sat, 17 Apr 2021 09:32:08: #2 predicted fragment length is 46 bps INFO @ Sat, 17 Apr 2021 09:32:08: #2 alternative fragment length(s) may be 4,17,46 bps INFO @ Sat, 17 Apr 2021 09:32:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.20_model.r WARNING @ Sat, 17 Apr 2021 09:32:08: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:32:08: #2 You may need to consider one of the other alternative d(s): 4,17,46 WARNING @ Sat, 17 Apr 2021 09:32:08: #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 09:32:08: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:32:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:32:12: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:32:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.20_peaks.xls INFO @ Sat, 17 Apr 2021 09:32:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:32:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555046/SRX4555046.20_summits.bed INFO @ Sat, 17 Apr 2021 09:32:14: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (401 records, 4 fields): 2 millis CompletedMACS2peakCalling