Job ID = 14520573 SRX = SRX11781068 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:22:52 prefetch.2.10.7: 1) Downloading 'SRR15481011'... 2022-01-15T10:22:52 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:23:53 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:23:53 prefetch.2.10.7: 1) 'SRR15481011' was downloaded successfully 2022-01-15T10:23:53 prefetch.2.10.7: 'SRR15481011' has 0 unresolved dependencies Read 11608489 spots for SRR15481011/SRR15481011.sra Written 11608489 spots for SRR15481011/SRR15481011.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: 00:52:35 11608489 reads; of these: 11608489 (100.00%) were paired; of these: 1935011 (16.67%) aligned concordantly 0 times 4114599 (35.44%) aligned concordantly exactly 1 time 5558879 (47.89%) aligned concordantly >1 times ---- 1935011 pairs aligned concordantly 0 times; of these: 34473 (1.78%) aligned discordantly 1 time ---- 1900538 pairs aligned 0 times concordantly or discordantly; of these: 3801076 mates make up the pairs; of these: 2965466 (78.02%) aligned 0 times 359313 (9.45%) aligned exactly 1 time 476297 (12.53%) aligned >1 times 87.23% overall alignment rate Time searching: 00:52:35 Overall time: 00:52:35 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] 1203420 / 9707082 = 0.1240 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:34:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.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, 15 Jan 2022 20:34:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:34:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:34:11: 1000000 INFO @ Sat, 15 Jan 2022 20:34:21: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:34:30: 3000000 INFO @ Sat, 15 Jan 2022 20:34:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.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, 15 Jan 2022 20:34:31: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:34:31: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:34:39: 4000000 INFO @ Sat, 15 Jan 2022 20:34:41: 1000000 INFO @ Sat, 15 Jan 2022 20:34:49: 5000000 INFO @ Sat, 15 Jan 2022 20:34:52: 2000000 INFO @ Sat, 15 Jan 2022 20:34:58: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:35:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.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, 15 Jan 2022 20:35:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:35:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:35:01: 3000000 INFO @ Sat, 15 Jan 2022 20:35:08: 7000000 INFO @ Sat, 15 Jan 2022 20:35:12: 4000000 INFO @ Sat, 15 Jan 2022 20:35:14: 1000000 INFO @ Sat, 15 Jan 2022 20:35:18: 8000000 INFO @ Sat, 15 Jan 2022 20:35:22: 5000000 INFO @ Sat, 15 Jan 2022 20:35:26: 2000000 INFO @ Sat, 15 Jan 2022 20:35:27: 9000000 INFO @ Sat, 15 Jan 2022 20:35:32: 6000000 INFO @ Sat, 15 Jan 2022 20:35:37: 10000000 INFO @ Sat, 15 Jan 2022 20:35:39: 3000000 INFO @ Sat, 15 Jan 2022 20:35:42: 7000000 INFO @ Sat, 15 Jan 2022 20:35:47: 11000000 INFO @ Sat, 15 Jan 2022 20:35:51: 4000000 INFO @ Sat, 15 Jan 2022 20:35:53: 8000000 INFO @ Sat, 15 Jan 2022 20:35:56: 12000000 INFO @ Sat, 15 Jan 2022 20:36:03: 9000000 INFO @ Sat, 15 Jan 2022 20:36:04: 5000000 INFO @ Sat, 15 Jan 2022 20:36:06: 13000000 INFO @ Sat, 15 Jan 2022 20:36:13: 10000000 INFO @ Sat, 15 Jan 2022 20:36:15: 6000000 INFO @ Sat, 15 Jan 2022 20:36:16: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:36:23: 11000000 INFO @ Sat, 15 Jan 2022 20:36:25: 15000000 INFO @ Sat, 15 Jan 2022 20:36:27: 7000000 INFO @ Sat, 15 Jan 2022 20:36:33: 12000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:36:35: 16000000 INFO @ Sat, 15 Jan 2022 20:36:40: 8000000 INFO @ Sat, 15 Jan 2022 20:36:44: 13000000 INFO @ Sat, 15 Jan 2022 20:36:45: 17000000 INFO @ Sat, 15 Jan 2022 20:36:51: 9000000 INFO @ Sat, 15 Jan 2022 20:36:52: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:36:52: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:36:52: #1 total tags in treatment: 8471985 INFO @ Sat, 15 Jan 2022 20:36:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:36:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:36:52: #1 tags after filtering in treatment: 3286340 INFO @ Sat, 15 Jan 2022 20:36:52: #1 Redundant rate of treatment: 0.61 INFO @ Sat, 15 Jan 2022 20:36:52: #1 finished! INFO @ Sat, 15 Jan 2022 20:36:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:36:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:36:53: #2 number of paired peaks: 180 WARNING @ Sat, 15 Jan 2022 20:36:53: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sat, 15 Jan 2022 20:36:53: start model_add_line... INFO @ Sat, 15 Jan 2022 20:36:53: start X-correlation... INFO @ Sat, 15 Jan 2022 20:36:53: end of X-cor INFO @ Sat, 15 Jan 2022 20:36:53: #2 finished! INFO @ Sat, 15 Jan 2022 20:36:53: #2 predicted fragment length is 60 bps INFO @ Sat, 15 Jan 2022 20:36:53: #2 alternative fragment length(s) may be 60,77,92,99,130,136,147,169,173,177,211,232,249,291,310,356,402,452,480,500,530 bps INFO @ Sat, 15 Jan 2022 20:36:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.05_model.r WARNING @ Sat, 15 Jan 2022 20:36:53: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:36:53: #2 You may need to consider one of the other alternative d(s): 60,77,92,99,130,136,147,169,173,177,211,232,249,291,310,356,402,452,480,500,530 WARNING @ Sat, 15 Jan 2022 20:36:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 20:36:53: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:36:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:36:54: 14000000 INFO @ Sat, 15 Jan 2022 20:37:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:37:03: 15000000 INFO @ Sat, 15 Jan 2022 20:37:03: 10000000 INFO @ Sat, 15 Jan 2022 20:37:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:37:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:37:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.05_summits.bed INFO @ Sat, 15 Jan 2022 20:37:04: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (386 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:37:12: 16000000 INFO @ Sat, 15 Jan 2022 20:37:15: 11000000 INFO @ Sat, 15 Jan 2022 20:37:22: 17000000 INFO @ Sat, 15 Jan 2022 20:37:27: 12000000 INFO @ Sat, 15 Jan 2022 20:37:30: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:37:30: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:37:30: #1 total tags in treatment: 8471985 INFO @ Sat, 15 Jan 2022 20:37:30: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:37:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:37:30: #1 tags after filtering in treatment: 3286340 INFO @ Sat, 15 Jan 2022 20:37:30: #1 Redundant rate of treatment: 0.61 INFO @ Sat, 15 Jan 2022 20:37:30: #1 finished! INFO @ Sat, 15 Jan 2022 20:37:30: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:37:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:37:31: #2 number of paired peaks: 180 WARNING @ Sat, 15 Jan 2022 20:37:31: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sat, 15 Jan 2022 20:37:31: start model_add_line... INFO @ Sat, 15 Jan 2022 20:37:31: start X-correlation... INFO @ Sat, 15 Jan 2022 20:37:31: end of X-cor INFO @ Sat, 15 Jan 2022 20:37:31: #2 finished! INFO @ Sat, 15 Jan 2022 20:37:31: #2 predicted fragment length is 60 bps INFO @ Sat, 15 Jan 2022 20:37:31: #2 alternative fragment length(s) may be 60,77,92,99,130,136,147,169,173,177,211,232,249,291,310,356,402,452,480,500,530 bps INFO @ Sat, 15 Jan 2022 20:37:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.10_model.r WARNING @ Sat, 15 Jan 2022 20:37:31: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:37:31: #2 You may need to consider one of the other alternative d(s): 60,77,92,99,130,136,147,169,173,177,211,232,249,291,310,356,402,452,480,500,530 WARNING @ Sat, 15 Jan 2022 20:37:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 20:37:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:37:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:37:39: 13000000 INFO @ Sat, 15 Jan 2022 20:37:39: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:37:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:37:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:37:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.10_summits.bed INFO @ Sat, 15 Jan 2022 20:37:42: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (103 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:37:50: 14000000 INFO @ Sat, 15 Jan 2022 20:38:01: 15000000 INFO @ Sat, 15 Jan 2022 20:38:12: 16000000 INFO @ Sat, 15 Jan 2022 20:38:23: 17000000 INFO @ Sat, 15 Jan 2022 20:38:32: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:38:32: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:38:32: #1 total tags in treatment: 8471985 INFO @ Sat, 15 Jan 2022 20:38:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:38:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:38:32: #1 tags after filtering in treatment: 3286340 INFO @ Sat, 15 Jan 2022 20:38:32: #1 Redundant rate of treatment: 0.61 INFO @ Sat, 15 Jan 2022 20:38:32: #1 finished! INFO @ Sat, 15 Jan 2022 20:38:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:38:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:38:33: #2 number of paired peaks: 180 WARNING @ Sat, 15 Jan 2022 20:38:33: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sat, 15 Jan 2022 20:38:33: start model_add_line... INFO @ Sat, 15 Jan 2022 20:38:33: start X-correlation... INFO @ Sat, 15 Jan 2022 20:38:33: end of X-cor INFO @ Sat, 15 Jan 2022 20:38:33: #2 finished! INFO @ Sat, 15 Jan 2022 20:38:33: #2 predicted fragment length is 60 bps INFO @ Sat, 15 Jan 2022 20:38:33: #2 alternative fragment length(s) may be 60,77,92,99,130,136,147,169,173,177,211,232,249,291,310,356,402,452,480,500,530 bps INFO @ Sat, 15 Jan 2022 20:38:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.20_model.r WARNING @ Sat, 15 Jan 2022 20:38:33: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:38:33: #2 You may need to consider one of the other alternative d(s): 60,77,92,99,130,136,147,169,173,177,211,232,249,291,310,356,402,452,480,500,530 WARNING @ Sat, 15 Jan 2022 20:38:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 20:38:33: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:38:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:38:41: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:38:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:38:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:38:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781068/SRX11781068.20_summits.bed INFO @ Sat, 15 Jan 2022 20:38:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (13 records, 4 fields): 5 millis CompletedMACS2peakCalling