Job ID = 12531663 SRX = SRX4555036 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14894730 spots for SRR7696731/SRR7696731.sra Written 14894730 spots for SRR7696731/SRR7696731.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: 00:18:19 14894730 reads; of these: 14894730 (100.00%) were paired; of these: 953882 (6.40%) aligned concordantly 0 times 6509488 (43.70%) aligned concordantly exactly 1 time 7431360 (49.89%) aligned concordantly >1 times ---- 953882 pairs aligned concordantly 0 times; of these: 57936 (6.07%) aligned discordantly 1 time ---- 895946 pairs aligned 0 times concordantly or discordantly; of these: 1791892 mates make up the pairs; of these: 1441880 (80.47%) aligned 0 times 171101 (9.55%) aligned exactly 1 time 178911 (9.98%) aligned >1 times 95.16% overall alignment rate Time searching: 00:18:19 Overall time: 00:18:19 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 20 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] 2667062 / 5984870 = 0.4456 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 09:26:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.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 09:26:53: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:26:53: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:27:01: 1000000 INFO @ Sat, 17 Apr 2021 09:27:08: 2000000 INFO @ Sat, 17 Apr 2021 09:27:16: 3000000 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 09:27:23: 4000000 INFO @ Sat, 17 Apr 2021 09:27:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.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 09:27:23: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:27:23: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:27:32: 5000000 INFO @ Sat, 17 Apr 2021 09:27:32: 1000000 INFO @ Sat, 17 Apr 2021 09:27:40: 6000000 INFO @ Sat, 17 Apr 2021 09:27:41: 2000000 INFO @ Sat, 17 Apr 2021 09:27:48: 7000000 INFO @ Sat, 17 Apr 2021 09:27:49: 3000000 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 09:27:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.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 09:27:53: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:27:53: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:27:57: 8000000 INFO @ Sat, 17 Apr 2021 09:27:58: 4000000 INFO @ Sat, 17 Apr 2021 09:28:02: 1000000 INFO @ Sat, 17 Apr 2021 09:28:06: 9000000 INFO @ Sat, 17 Apr 2021 09:28:07: 5000000 INFO @ Sat, 17 Apr 2021 09:28:12: 2000000 INFO @ Sat, 17 Apr 2021 09:28:15: 10000000 INFO @ Sat, 17 Apr 2021 09:28:16: 6000000 INFO @ Sat, 17 Apr 2021 09:28:21: 3000000 INFO @ Sat, 17 Apr 2021 09:28:24: 11000000 INFO @ Sat, 17 Apr 2021 09:28:25: 7000000 INFO @ Sat, 17 Apr 2021 09:28:30: 4000000 INFO @ Sat, 17 Apr 2021 09:28:32: 12000000 INFO @ Sat, 17 Apr 2021 09:28:34: 8000000 INFO @ Sat, 17 Apr 2021 09:28:39: 5000000 INFO @ Sat, 17 Apr 2021 09:28:41: 13000000 INFO @ Sat, 17 Apr 2021 09:28:43: 9000000 INFO @ Sat, 17 Apr 2021 09:28:48: 6000000 INFO @ Sat, 17 Apr 2021 09:28:50: 14000000 INFO @ Sat, 17 Apr 2021 09:28:51: 10000000 INFO @ Sat, 17 Apr 2021 09:28:57: 7000000 INFO @ Sat, 17 Apr 2021 09:28:58: 15000000 INFO @ Sat, 17 Apr 2021 09:29:00: 11000000 INFO @ Sat, 17 Apr 2021 09:29:06: 8000000 INFO @ Sat, 17 Apr 2021 09:29:07: 16000000 INFO @ Sat, 17 Apr 2021 09:29:08: 12000000 INFO @ Sat, 17 Apr 2021 09:29:14: 9000000 INFO @ Sat, 17 Apr 2021 09:29:15: 17000000 INFO @ Sat, 17 Apr 2021 09:29:16: 13000000 INFO @ Sat, 17 Apr 2021 09:29:22: 10000000 INFO @ Sat, 17 Apr 2021 09:29:23: 18000000 INFO @ Sat, 17 Apr 2021 09:29:25: 14000000 INFO @ Sat, 17 Apr 2021 09:29:30: 11000000 INFO @ Sat, 17 Apr 2021 09:29:32: 19000000 INFO @ Sat, 17 Apr 2021 09:29:33: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 09:29:39: 12000000 INFO @ Sat, 17 Apr 2021 09:29:40: 20000000 INFO @ Sat, 17 Apr 2021 09:29:41: 16000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:29:47: 13000000 INFO @ Sat, 17 Apr 2021 09:29:49: 21000000 INFO @ Sat, 17 Apr 2021 09:29:49: 17000000 INFO @ Sat, 17 Apr 2021 09:29:55: 14000000 INFO @ Sat, 17 Apr 2021 09:29:58: 18000000 INFO @ Sat, 17 Apr 2021 09:29:58: 22000000 INFO @ Sat, 17 Apr 2021 09:30:03: 15000000 INFO @ Sat, 17 Apr 2021 09:30:06: 19000000 INFO @ Sat, 17 Apr 2021 09:30:06: 23000000 INFO @ Sat, 17 Apr 2021 09:30:07: #1 tag size is determined as 97 bps INFO @ Sat, 17 Apr 2021 09:30:07: #1 tag size = 97 INFO @ Sat, 17 Apr 2021 09:30:07: #1 total tags in treatment: 11276928 INFO @ Sat, 17 Apr 2021 09:30:07: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:30:07: #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 09:30:07: #1 tags after filtering in treatment: 2503650 INFO @ Sat, 17 Apr 2021 09:30:07: #1 Redundant rate of treatment: 0.78 INFO @ Sat, 17 Apr 2021 09:30:07: #1 finished! INFO @ Sat, 17 Apr 2021 09:30:07: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:30:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:30:07: #2 number of paired peaks: 131 WARNING @ Sat, 17 Apr 2021 09:30:07: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Sat, 17 Apr 2021 09:30:07: start model_add_line... INFO @ Sat, 17 Apr 2021 09:30:07: start X-correlation... INFO @ Sat, 17 Apr 2021 09:30:07: end of X-cor INFO @ Sat, 17 Apr 2021 09:30:07: #2 finished! INFO @ Sat, 17 Apr 2021 09:30:07: #2 predicted fragment length is 46 bps INFO @ Sat, 17 Apr 2021 09:30:07: #2 alternative fragment length(s) may be 4,17,46 bps INFO @ Sat, 17 Apr 2021 09:30:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.05_model.r WARNING @ Sat, 17 Apr 2021 09:30:07: #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 09:30:07: #2 You may need to consider one of the other alternative d(s): 4,17,46 WARNING @ Sat, 17 Apr 2021 09:30:07: #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 09:30:07: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:30:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:30:11: 16000000 INFO @ Sat, 17 Apr 2021 09:30:13: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:30:14: 20000000 INFO @ Sat, 17 Apr 2021 09:30:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.05_peaks.xls INFO @ Sat, 17 Apr 2021 09:30:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:30:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.05_summits.bed INFO @ Sat, 17 Apr 2021 09:30:16: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (3119 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:30:19: 17000000 INFO @ Sat, 17 Apr 2021 09:30:23: 21000000 INFO @ Sat, 17 Apr 2021 09:30:27: 18000000 INFO @ Sat, 17 Apr 2021 09:30:31: 22000000 INFO @ Sat, 17 Apr 2021 09:30:35: 19000000 INFO @ Sat, 17 Apr 2021 09:30:40: 23000000 INFO @ Sat, 17 Apr 2021 09:30:40: #1 tag size is determined as 97 bps INFO @ Sat, 17 Apr 2021 09:30:40: #1 tag size = 97 INFO @ Sat, 17 Apr 2021 09:30:40: #1 total tags in treatment: 11276928 INFO @ Sat, 17 Apr 2021 09:30:40: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:30:40: #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 09:30:40: #1 tags after filtering in treatment: 2503650 INFO @ Sat, 17 Apr 2021 09:30:40: #1 Redundant rate of treatment: 0.78 INFO @ Sat, 17 Apr 2021 09:30:40: #1 finished! INFO @ Sat, 17 Apr 2021 09:30:40: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:30:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:30:40: #2 number of paired peaks: 131 WARNING @ Sat, 17 Apr 2021 09:30:40: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Sat, 17 Apr 2021 09:30:40: start model_add_line... INFO @ Sat, 17 Apr 2021 09:30:41: start X-correlation... INFO @ Sat, 17 Apr 2021 09:30:41: end of X-cor INFO @ Sat, 17 Apr 2021 09:30:41: #2 finished! INFO @ Sat, 17 Apr 2021 09:30:41: #2 predicted fragment length is 46 bps INFO @ Sat, 17 Apr 2021 09:30:41: #2 alternative fragment length(s) may be 4,17,46 bps INFO @ Sat, 17 Apr 2021 09:30:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.10_model.r WARNING @ Sat, 17 Apr 2021 09:30:41: #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 09:30:41: #2 You may need to consider one of the other alternative d(s): 4,17,46 WARNING @ Sat, 17 Apr 2021 09:30:41: #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 09:30:41: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:30:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:30:43: 20000000 INFO @ Sat, 17 Apr 2021 09:30:46: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:30:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.10_peaks.xls INFO @ Sat, 17 Apr 2021 09:30:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:30:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.10_summits.bed INFO @ Sat, 17 Apr 2021 09:30:49: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1874 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:30:51: 21000000 INFO @ Sat, 17 Apr 2021 09:30:59: 22000000 INFO @ Sat, 17 Apr 2021 09:31:06: 23000000 INFO @ Sat, 17 Apr 2021 09:31:06: #1 tag size is determined as 97 bps INFO @ Sat, 17 Apr 2021 09:31:06: #1 tag size = 97 INFO @ Sat, 17 Apr 2021 09:31:06: #1 total tags in treatment: 11276928 INFO @ Sat, 17 Apr 2021 09:31:06: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:31:06: #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 09:31:07: #1 tags after filtering in treatment: 2503650 INFO @ Sat, 17 Apr 2021 09:31:07: #1 Redundant rate of treatment: 0.78 INFO @ Sat, 17 Apr 2021 09:31:07: #1 finished! INFO @ Sat, 17 Apr 2021 09:31:07: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:31:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:31:07: #2 number of paired peaks: 131 WARNING @ Sat, 17 Apr 2021 09:31:07: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Sat, 17 Apr 2021 09:31:07: start model_add_line... INFO @ Sat, 17 Apr 2021 09:31:07: start X-correlation... INFO @ Sat, 17 Apr 2021 09:31:07: end of X-cor INFO @ Sat, 17 Apr 2021 09:31:07: #2 finished! INFO @ Sat, 17 Apr 2021 09:31:07: #2 predicted fragment length is 46 bps INFO @ Sat, 17 Apr 2021 09:31:07: #2 alternative fragment length(s) may be 4,17,46 bps INFO @ Sat, 17 Apr 2021 09:31:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.20_model.r WARNING @ Sat, 17 Apr 2021 09:31:07: #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 09:31:07: #2 You may need to consider one of the other alternative d(s): 4,17,46 WARNING @ Sat, 17 Apr 2021 09:31:07: #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 09:31:07: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:31:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:31:12: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:31:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.20_peaks.xls INFO @ Sat, 17 Apr 2021 09:31:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:31:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555036/SRX4555036.20_summits.bed INFO @ Sat, 17 Apr 2021 09:31:15: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (560 records, 4 fields): 2 millis CompletedMACS2peakCalling