Job ID = 12531668 SRX = SRX4555040 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7668046 spots for SRR7696737/SRR7696737.sra Written 7668046 spots for SRR7696737/SRR7696737.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: 00:08:40 7668046 reads; of these: 7668046 (100.00%) were paired; of these: 377983 (4.93%) aligned concordantly 0 times 2649830 (34.56%) aligned concordantly exactly 1 time 4640233 (60.51%) aligned concordantly >1 times ---- 377983 pairs aligned concordantly 0 times; of these: 26005 (6.88%) aligned discordantly 1 time ---- 351978 pairs aligned 0 times concordantly or discordantly; of these: 703956 mates make up the pairs; of these: 507141 (72.04%) aligned 0 times 94956 (13.49%) aligned exactly 1 time 101859 (14.47%) aligned >1 times 96.69% overall alignment rate Time searching: 00:08:40 Overall time: 00:08:40 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] 1707291 / 3242337 = 0.5266 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 09:14:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.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 09:14:18: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:14:18: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:14:26: 1000000 INFO @ Sat, 17 Apr 2021 09:14:34: 2000000 INFO @ Sat, 17 Apr 2021 09:14:41: 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 09:14:49: 4000000 INFO @ Sat, 17 Apr 2021 09:14:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.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 09:14:49: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:14:49: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:14:57: 5000000 INFO @ Sat, 17 Apr 2021 09:14:58: 1000000 INFO @ Sat, 17 Apr 2021 09:15:06: 6000000 INFO @ Sat, 17 Apr 2021 09:15:08: 2000000 INFO @ Sat, 17 Apr 2021 09:15:15: 7000000 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 09:15:18: 3000000 INFO @ Sat, 17 Apr 2021 09:15:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.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 09:15:18: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:15:18: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:15:24: 8000000 INFO @ Sat, 17 Apr 2021 09:15:27: 4000000 INFO @ Sat, 17 Apr 2021 09:15:28: 1000000 INFO @ Sat, 17 Apr 2021 09:15:33: 9000000 INFO @ Sat, 17 Apr 2021 09:15:36: 5000000 INFO @ Sat, 17 Apr 2021 09:15:37: 2000000 INFO @ Sat, 17 Apr 2021 09:15:42: 10000000 INFO @ Sat, 17 Apr 2021 09:15:45: 6000000 INFO @ Sat, 17 Apr 2021 09:15:47: 3000000 INFO @ Sat, 17 Apr 2021 09:15:52: 11000000 INFO @ Sat, 17 Apr 2021 09:15:54: 7000000 INFO @ Sat, 17 Apr 2021 09:15:56: #1 tag size is determined as 110 bps INFO @ Sat, 17 Apr 2021 09:15:56: #1 tag size = 110 INFO @ Sat, 17 Apr 2021 09:15:56: #1 total tags in treatment: 5585534 INFO @ Sat, 17 Apr 2021 09:15:56: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:15:56: #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 09:15:56: #1 tags after filtering in treatment: 1158922 INFO @ Sat, 17 Apr 2021 09:15:56: #1 Redundant rate of treatment: 0.79 INFO @ Sat, 17 Apr 2021 09:15:56: #1 finished! INFO @ Sat, 17 Apr 2021 09:15:56: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:15:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:15:56: #2 number of paired peaks: 408 WARNING @ Sat, 17 Apr 2021 09:15:56: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Sat, 17 Apr 2021 09:15:56: start model_add_line... INFO @ Sat, 17 Apr 2021 09:15:56: start X-correlation... INFO @ Sat, 17 Apr 2021 09:15:56: end of X-cor INFO @ Sat, 17 Apr 2021 09:15:56: #2 finished! INFO @ Sat, 17 Apr 2021 09:15:56: #2 predicted fragment length is 66 bps INFO @ Sat, 17 Apr 2021 09:15:56: #2 alternative fragment length(s) may be 66 bps INFO @ Sat, 17 Apr 2021 09:15:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.05_model.r WARNING @ Sat, 17 Apr 2021 09:15:56: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:15:56: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sat, 17 Apr 2021 09:15:56: #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 09:15:56: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:15:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:15:56: 4000000 INFO @ Sat, 17 Apr 2021 09:15:59: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:16:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.05_peaks.xls INFO @ Sat, 17 Apr 2021 09:16:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:16:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.05_summits.bed INFO @ Sat, 17 Apr 2021 09:16:01: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (2163 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:16:02: 8000000 INFO @ Sat, 17 Apr 2021 09:16:05: 5000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:16:11: 9000000 INFO @ Sat, 17 Apr 2021 09:16:14: 6000000 INFO @ Sat, 17 Apr 2021 09:16:20: 10000000 INFO @ Sat, 17 Apr 2021 09:16:22: 7000000 INFO @ Sat, 17 Apr 2021 09:16:29: 11000000 INFO @ Sat, 17 Apr 2021 09:16:31: 8000000 INFO @ Sat, 17 Apr 2021 09:16:33: #1 tag size is determined as 110 bps INFO @ Sat, 17 Apr 2021 09:16:33: #1 tag size = 110 INFO @ Sat, 17 Apr 2021 09:16:33: #1 total tags in treatment: 5585534 INFO @ Sat, 17 Apr 2021 09:16:33: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:16:33: #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 09:16:34: #1 tags after filtering in treatment: 1158922 INFO @ Sat, 17 Apr 2021 09:16:34: #1 Redundant rate of treatment: 0.79 INFO @ Sat, 17 Apr 2021 09:16:34: #1 finished! INFO @ Sat, 17 Apr 2021 09:16:34: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:16:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:16:34: #2 number of paired peaks: 408 WARNING @ Sat, 17 Apr 2021 09:16:34: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Sat, 17 Apr 2021 09:16:34: start model_add_line... INFO @ Sat, 17 Apr 2021 09:16:34: start X-correlation... INFO @ Sat, 17 Apr 2021 09:16:34: end of X-cor INFO @ Sat, 17 Apr 2021 09:16:34: #2 finished! INFO @ Sat, 17 Apr 2021 09:16:34: #2 predicted fragment length is 66 bps INFO @ Sat, 17 Apr 2021 09:16:34: #2 alternative fragment length(s) may be 66 bps INFO @ Sat, 17 Apr 2021 09:16:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.10_model.r WARNING @ Sat, 17 Apr 2021 09:16:34: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:16:34: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sat, 17 Apr 2021 09:16:34: #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 09:16:34: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:16:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:16:37: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:16:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.10_peaks.xls INFO @ Sat, 17 Apr 2021 09:16:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:16:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.10_summits.bed INFO @ Sat, 17 Apr 2021 09:16:38: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1323 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:16:39: 9000000 INFO @ Sat, 17 Apr 2021 09:16:47: 10000000 INFO @ Sat, 17 Apr 2021 09:16:55: 11000000 INFO @ Sat, 17 Apr 2021 09:16:58: #1 tag size is determined as 110 bps INFO @ Sat, 17 Apr 2021 09:16:58: #1 tag size = 110 INFO @ Sat, 17 Apr 2021 09:16:58: #1 total tags in treatment: 5585534 INFO @ Sat, 17 Apr 2021 09:16:58: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:16:58: #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 09:16:59: #1 tags after filtering in treatment: 1158922 INFO @ Sat, 17 Apr 2021 09:16:59: #1 Redundant rate of treatment: 0.79 INFO @ Sat, 17 Apr 2021 09:16:59: #1 finished! INFO @ Sat, 17 Apr 2021 09:16:59: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:16:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:16:59: #2 number of paired peaks: 408 WARNING @ Sat, 17 Apr 2021 09:16:59: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Sat, 17 Apr 2021 09:16:59: start model_add_line... INFO @ Sat, 17 Apr 2021 09:16:59: start X-correlation... INFO @ Sat, 17 Apr 2021 09:16:59: end of X-cor INFO @ Sat, 17 Apr 2021 09:16:59: #2 finished! INFO @ Sat, 17 Apr 2021 09:16:59: #2 predicted fragment length is 66 bps INFO @ Sat, 17 Apr 2021 09:16:59: #2 alternative fragment length(s) may be 66 bps INFO @ Sat, 17 Apr 2021 09:16:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.20_model.r WARNING @ Sat, 17 Apr 2021 09:16:59: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:16:59: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sat, 17 Apr 2021 09:16:59: #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 09:16:59: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:16:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:17:02: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:17:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.20_peaks.xls INFO @ Sat, 17 Apr 2021 09:17:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:17:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555040/SRX4555040.20_summits.bed INFO @ Sat, 17 Apr 2021 09:17:03: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (591 records, 4 fields): 5 millis CompletedMACS2peakCalling