Job ID = 7106895 SRX = SRX6911539 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19682937 spots for SRR10191150/SRR10191150.sra Written 19682937 spots for SRR10191150/SRR10191150.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: 00:16:48 19682937 reads; of these: 19682937 (100.00%) were paired; of these: 6650744 (33.79%) aligned concordantly 0 times 10401928 (52.85%) aligned concordantly exactly 1 time 2630265 (13.36%) aligned concordantly >1 times ---- 6650744 pairs aligned concordantly 0 times; of these: 461818 (6.94%) aligned discordantly 1 time ---- 6188926 pairs aligned 0 times concordantly or discordantly; of these: 12377852 mates make up the pairs; of these: 11678032 (94.35%) aligned 0 times 382170 (3.09%) aligned exactly 1 time 317650 (2.57%) aligned >1 times 70.33% overall alignment rate Time searching: 00:16:48 Overall time: 00:16:48 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] 3056493 / 13492735 = 0.2265 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 13:13:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.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 13:13:49: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:13:49: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:13:56: 1000000 INFO @ Wed, 22 Jul 2020 13:14:05: 2000000 INFO @ Wed, 22 Jul 2020 13:14:13: 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 13:14:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.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 13:14:19: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:14:19: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:14:21: 4000000 INFO @ Wed, 22 Jul 2020 13:14:27: 1000000 INFO @ Wed, 22 Jul 2020 13:14:29: 5000000 INFO @ Wed, 22 Jul 2020 13:14:35: 2000000 INFO @ Wed, 22 Jul 2020 13:14:38: 6000000 INFO @ Wed, 22 Jul 2020 13:14:42: 3000000 INFO @ Wed, 22 Jul 2020 13:14:46: 7000000 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 13:14:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.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 13:14:49: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:14:49: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:14:50: 4000000 INFO @ Wed, 22 Jul 2020 13:14:55: 8000000 INFO @ Wed, 22 Jul 2020 13:14:57: 1000000 INFO @ Wed, 22 Jul 2020 13:14:58: 5000000 INFO @ Wed, 22 Jul 2020 13:15:03: 9000000 INFO @ Wed, 22 Jul 2020 13:15:05: 2000000 INFO @ Wed, 22 Jul 2020 13:15:06: 6000000 INFO @ Wed, 22 Jul 2020 13:15:12: 10000000 INFO @ Wed, 22 Jul 2020 13:15:13: 3000000 INFO @ Wed, 22 Jul 2020 13:15:14: 7000000 INFO @ Wed, 22 Jul 2020 13:15:20: 11000000 INFO @ Wed, 22 Jul 2020 13:15:21: 4000000 INFO @ Wed, 22 Jul 2020 13:15:22: 8000000 INFO @ Wed, 22 Jul 2020 13:15:29: 12000000 INFO @ Wed, 22 Jul 2020 13:15:29: 5000000 INFO @ Wed, 22 Jul 2020 13:15:29: 9000000 INFO @ Wed, 22 Jul 2020 13:15:37: 6000000 INFO @ Wed, 22 Jul 2020 13:15:37: 10000000 INFO @ Wed, 22 Jul 2020 13:15:37: 13000000 INFO @ Wed, 22 Jul 2020 13:15:45: 7000000 INFO @ Wed, 22 Jul 2020 13:15:45: 11000000 INFO @ Wed, 22 Jul 2020 13:15:46: 14000000 INFO @ Wed, 22 Jul 2020 13:15:53: 8000000 INFO @ Wed, 22 Jul 2020 13:15:53: 12000000 INFO @ Wed, 22 Jul 2020 13:15:54: 15000000 INFO @ Wed, 22 Jul 2020 13:16:01: 9000000 INFO @ Wed, 22 Jul 2020 13:16:01: 13000000 INFO @ Wed, 22 Jul 2020 13:16:03: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 13:16:08: 10000000 INFO @ Wed, 22 Jul 2020 13:16:08: 14000000 INFO @ Wed, 22 Jul 2020 13:16:11: 17000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 13:16:16: 11000000 INFO @ Wed, 22 Jul 2020 13:16:16: 15000000 INFO @ Wed, 22 Jul 2020 13:16:19: 18000000 INFO @ Wed, 22 Jul 2020 13:16:24: 16000000 INFO @ Wed, 22 Jul 2020 13:16:24: 12000000 INFO @ Wed, 22 Jul 2020 13:16:28: 19000000 INFO @ Wed, 22 Jul 2020 13:16:32: 17000000 INFO @ Wed, 22 Jul 2020 13:16:32: 13000000 INFO @ Wed, 22 Jul 2020 13:16:36: 20000000 INFO @ Wed, 22 Jul 2020 13:16:39: 18000000 INFO @ Wed, 22 Jul 2020 13:16:40: 14000000 INFO @ Wed, 22 Jul 2020 13:16:44: 21000000 INFO @ Wed, 22 Jul 2020 13:16:47: 15000000 INFO @ Wed, 22 Jul 2020 13:16:47: 19000000 INFO @ Wed, 22 Jul 2020 13:16:49: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:16:49: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:16:49: #1 total tags in treatment: 10021550 INFO @ Wed, 22 Jul 2020 13:16:49: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:16:49: #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 13:16:49: #1 tags after filtering in treatment: 4024157 INFO @ Wed, 22 Jul 2020 13:16:49: #1 Redundant rate of treatment: 0.60 INFO @ Wed, 22 Jul 2020 13:16:49: #1 finished! INFO @ Wed, 22 Jul 2020 13:16:49: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:16:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:16:50: #2 number of paired peaks: 258 WARNING @ Wed, 22 Jul 2020 13:16:50: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Wed, 22 Jul 2020 13:16:50: start model_add_line... INFO @ Wed, 22 Jul 2020 13:16:50: start X-correlation... INFO @ Wed, 22 Jul 2020 13:16:50: end of X-cor INFO @ Wed, 22 Jul 2020 13:16:50: #2 finished! INFO @ Wed, 22 Jul 2020 13:16:50: #2 predicted fragment length is 121 bps INFO @ Wed, 22 Jul 2020 13:16:50: #2 alternative fragment length(s) may be 24,47,76,97,121,140,163,202,226,265,269,272,313,319,359,375,413,428,457,534,570 bps INFO @ Wed, 22 Jul 2020 13:16:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.05_model.r WARNING @ Wed, 22 Jul 2020 13:16:50: #2 Since the d (121) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:16:50: #2 You may need to consider one of the other alternative d(s): 24,47,76,97,121,140,163,202,226,265,269,272,313,319,359,375,413,428,457,534,570 WARNING @ Wed, 22 Jul 2020 13:16:50: #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 13:16:50: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:16:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:16:55: 16000000 INFO @ Wed, 22 Jul 2020 13:16:55: 20000000 INFO @ Wed, 22 Jul 2020 13:17:01: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:17:02: 17000000 INFO @ Wed, 22 Jul 2020 13:17:02: 21000000 INFO @ Wed, 22 Jul 2020 13:17:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.05_peaks.xls INFO @ Wed, 22 Jul 2020 13:17:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:17:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.05_summits.bed INFO @ Wed, 22 Jul 2020 13:17:04: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (510 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 13:17:06: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:17:06: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:17:06: #1 total tags in treatment: 10021550 INFO @ Wed, 22 Jul 2020 13:17:06: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:17:06: #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 13:17:06: #1 tags after filtering in treatment: 4024157 INFO @ Wed, 22 Jul 2020 13:17:06: #1 Redundant rate of treatment: 0.60 INFO @ Wed, 22 Jul 2020 13:17:06: #1 finished! INFO @ Wed, 22 Jul 2020 13:17:06: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:17:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:17:07: #2 number of paired peaks: 258 WARNING @ Wed, 22 Jul 2020 13:17:07: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Wed, 22 Jul 2020 13:17:07: start model_add_line... INFO @ Wed, 22 Jul 2020 13:17:07: start X-correlation... INFO @ Wed, 22 Jul 2020 13:17:07: end of X-cor INFO @ Wed, 22 Jul 2020 13:17:07: #2 finished! INFO @ Wed, 22 Jul 2020 13:17:07: #2 predicted fragment length is 121 bps INFO @ Wed, 22 Jul 2020 13:17:07: #2 alternative fragment length(s) may be 24,47,76,97,121,140,163,202,226,265,269,272,313,319,359,375,413,428,457,534,570 bps INFO @ Wed, 22 Jul 2020 13:17:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.10_model.r WARNING @ Wed, 22 Jul 2020 13:17:07: #2 Since the d (121) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:17:07: #2 You may need to consider one of the other alternative d(s): 24,47,76,97,121,140,163,202,226,265,269,272,313,319,359,375,413,428,457,534,570 WARNING @ Wed, 22 Jul 2020 13:17:07: #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 13:17:07: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:17:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:17:09: 18000000 INFO @ Wed, 22 Jul 2020 13:17:16: 19000000 INFO @ Wed, 22 Jul 2020 13:17:19: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:17:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.10_peaks.xls INFO @ Wed, 22 Jul 2020 13:17:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:17:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.10_summits.bed INFO @ Wed, 22 Jul 2020 13:17:22: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (231 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 13:17:23: 20000000 INFO @ Wed, 22 Jul 2020 13:17:29: 21000000 INFO @ Wed, 22 Jul 2020 13:17:32: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:17:32: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:17:32: #1 total tags in treatment: 10021550 INFO @ Wed, 22 Jul 2020 13:17:32: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:17:32: #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 13:17:33: #1 tags after filtering in treatment: 4024157 INFO @ Wed, 22 Jul 2020 13:17:33: #1 Redundant rate of treatment: 0.60 INFO @ Wed, 22 Jul 2020 13:17:33: #1 finished! INFO @ Wed, 22 Jul 2020 13:17:33: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:17:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:17:33: #2 number of paired peaks: 258 WARNING @ Wed, 22 Jul 2020 13:17:33: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Wed, 22 Jul 2020 13:17:33: start model_add_line... INFO @ Wed, 22 Jul 2020 13:17:33: start X-correlation... INFO @ Wed, 22 Jul 2020 13:17:33: end of X-cor INFO @ Wed, 22 Jul 2020 13:17:33: #2 finished! INFO @ Wed, 22 Jul 2020 13:17:33: #2 predicted fragment length is 121 bps INFO @ Wed, 22 Jul 2020 13:17:33: #2 alternative fragment length(s) may be 24,47,76,97,121,140,163,202,226,265,269,272,313,319,359,375,413,428,457,534,570 bps INFO @ Wed, 22 Jul 2020 13:17:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.20_model.r WARNING @ Wed, 22 Jul 2020 13:17:33: #2 Since the d (121) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:17:33: #2 You may need to consider one of the other alternative d(s): 24,47,76,97,121,140,163,202,226,265,269,272,313,319,359,375,413,428,457,534,570 WARNING @ Wed, 22 Jul 2020 13:17:33: #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 13:17:33: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:17:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:17:45: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:17:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.20_peaks.xls INFO @ Wed, 22 Jul 2020 13:17:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:17:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911539/SRX6911539.20_summits.bed INFO @ Wed, 22 Jul 2020 13:17:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (55 records, 4 fields): 20 millis CompletedMACS2peakCalling