Job ID = 14521234 SRX = SRX8245389 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9880457 spots for SRR11684600/SRR11684600.sra Written 9880457 spots for SRR11684600/SRR11684600.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: 00:05:21 9880457 reads; of these: 9880457 (100.00%) were paired; of these: 5434748 (55.01%) aligned concordantly 0 times 3930918 (39.78%) aligned concordantly exactly 1 time 514791 (5.21%) aligned concordantly >1 times ---- 5434748 pairs aligned concordantly 0 times; of these: 21785 (0.40%) aligned discordantly 1 time ---- 5412963 pairs aligned 0 times concordantly or discordantly; of these: 10825926 mates make up the pairs; of these: 7197006 (66.48%) aligned 0 times 3166838 (29.25%) aligned exactly 1 time 462082 (4.27%) aligned >1 times 63.58% overall alignment rate Time searching: 00:05:21 Overall time: 00:05:21 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 8 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] 328319 / 4466738 = 0.0735 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 20:54:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.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 20:54:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:54:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:54:21: 1000000 INFO @ Sat, 15 Jan 2022 20:54:27: 2000000 INFO @ Sat, 15 Jan 2022 20:54:33: 3000000 INFO @ Sat, 15 Jan 2022 20:54:40: 4000000 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 20:54:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.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 20:54:44: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:54:44: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:54:46: 5000000 INFO @ Sat, 15 Jan 2022 20:54:51: 1000000 INFO @ Sat, 15 Jan 2022 20:54:53: 6000000 INFO @ Sat, 15 Jan 2022 20:54:57: 2000000 INFO @ Sat, 15 Jan 2022 20:55:00: 7000000 INFO @ Sat, 15 Jan 2022 20:55:03: 3000000 INFO @ Sat, 15 Jan 2022 20:55:07: 8000000 INFO @ Sat, 15 Jan 2022 20:55:08: 4000000 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 20:55:14: 9000000 INFO @ Sat, 15 Jan 2022 20:55:14: 5000000 INFO @ Sat, 15 Jan 2022 20:55:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.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 20:55:14: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:55:14: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:55:20: 6000000 INFO @ Sat, 15 Jan 2022 20:55:21: 10000000 INFO @ Sat, 15 Jan 2022 20:55:21: 1000000 INFO @ Sat, 15 Jan 2022 20:55:26: 7000000 INFO @ Sat, 15 Jan 2022 20:55:28: 11000000 INFO @ Sat, 15 Jan 2022 20:55:28: 2000000 INFO @ Sat, 15 Jan 2022 20:55:33: 8000000 INFO @ Sat, 15 Jan 2022 20:55:34: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:55:34: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:55:34: #1 total tags in treatment: 4118967 INFO @ Sat, 15 Jan 2022 20:55:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:55:34: #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 20:55:34: #1 tags after filtering in treatment: 2529674 INFO @ Sat, 15 Jan 2022 20:55:34: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 15 Jan 2022 20:55:34: #1 finished! INFO @ Sat, 15 Jan 2022 20:55:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:55:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:55:35: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 20:55:35: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 20:55:35: start model_add_line... INFO @ Sat, 15 Jan 2022 20:55:35: start X-correlation... INFO @ Sat, 15 Jan 2022 20:55:35: end of X-cor INFO @ Sat, 15 Jan 2022 20:55:35: #2 finished! INFO @ Sat, 15 Jan 2022 20:55:35: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 20:55:35: #2 alternative fragment length(s) may be 50,122,201,215,247,272,291,308,310,336,380,393,425,448,469,486,508,556,571 bps INFO @ Sat, 15 Jan 2022 20:55:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.05_model.r WARNING @ Sat, 15 Jan 2022 20:55:35: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:55:35: #2 You may need to consider one of the other alternative d(s): 50,122,201,215,247,272,291,308,310,336,380,393,425,448,469,486,508,556,571 WARNING @ Sat, 15 Jan 2022 20:55:35: #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 20:55:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:55:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:55:35: 3000000 INFO @ Sat, 15 Jan 2022 20:55:39: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:55:39: 9000000 INFO @ Sat, 15 Jan 2022 20:55:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:55:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:55:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.05_summits.bed INFO @ Sat, 15 Jan 2022 20:55:40: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (49 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:55:42: 4000000 INFO @ Sat, 15 Jan 2022 20:55:45: 10000000 INFO @ Sat, 15 Jan 2022 20:55:48: 5000000 INFO @ Sat, 15 Jan 2022 20:55:51: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:55:55: 6000000 INFO @ Sat, 15 Jan 2022 20:55:56: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:55:56: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:55:56: #1 total tags in treatment: 4118967 INFO @ Sat, 15 Jan 2022 20:55:56: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:55:56: #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 20:55:57: #1 tags after filtering in treatment: 2529674 INFO @ Sat, 15 Jan 2022 20:55:57: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 15 Jan 2022 20:55:57: #1 finished! INFO @ Sat, 15 Jan 2022 20:55:57: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:55:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:55:57: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 20:55:57: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 20:55:57: start model_add_line... INFO @ Sat, 15 Jan 2022 20:55:57: start X-correlation... INFO @ Sat, 15 Jan 2022 20:55:57: end of X-cor INFO @ Sat, 15 Jan 2022 20:55:57: #2 finished! INFO @ Sat, 15 Jan 2022 20:55:57: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 20:55:57: #2 alternative fragment length(s) may be 50,122,201,215,247,272,291,308,310,336,380,393,425,448,469,486,508,556,571 bps INFO @ Sat, 15 Jan 2022 20:55:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.10_model.r WARNING @ Sat, 15 Jan 2022 20:55:57: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:55:57: #2 You may need to consider one of the other alternative d(s): 50,122,201,215,247,272,291,308,310,336,380,393,425,448,469,486,508,556,571 WARNING @ Sat, 15 Jan 2022 20:55:57: #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 20:55:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:55:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:56:01: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:56:01: 7000000 INFO @ Sat, 15 Jan 2022 20:56:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:56:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:56:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.10_summits.bed INFO @ Sat, 15 Jan 2022 20:56:03: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (5 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:56:08: 8000000 INFO @ Sat, 15 Jan 2022 20:56:14: 9000000 INFO @ Sat, 15 Jan 2022 20:56:20: 10000000 INFO @ Sat, 15 Jan 2022 20:56:26: 11000000 INFO @ Sat, 15 Jan 2022 20:56:31: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:56:31: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:56:31: #1 total tags in treatment: 4118967 INFO @ Sat, 15 Jan 2022 20:56:31: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:56:31: #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 20:56:32: #1 tags after filtering in treatment: 2529674 INFO @ Sat, 15 Jan 2022 20:56:32: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 15 Jan 2022 20:56:32: #1 finished! INFO @ Sat, 15 Jan 2022 20:56:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:56:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:56:32: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 20:56:32: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 20:56:32: start model_add_line... INFO @ Sat, 15 Jan 2022 20:56:32: start X-correlation... INFO @ Sat, 15 Jan 2022 20:56:32: end of X-cor INFO @ Sat, 15 Jan 2022 20:56:32: #2 finished! INFO @ Sat, 15 Jan 2022 20:56:32: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 20:56:32: #2 alternative fragment length(s) may be 50,122,201,215,247,272,291,308,310,336,380,393,425,448,469,486,508,556,571 bps INFO @ Sat, 15 Jan 2022 20:56:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.20_model.r WARNING @ Sat, 15 Jan 2022 20:56:32: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:56:32: #2 You may need to consider one of the other alternative d(s): 50,122,201,215,247,272,291,308,310,336,380,393,425,448,469,486,508,556,571 WARNING @ Sat, 15 Jan 2022 20:56:32: #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 20:56:32: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:56:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:56:36: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:56:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:56:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:56:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245389/SRX8245389.20_summits.bed INFO @ Sat, 15 Jan 2022 20:56:37: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (3 records, 4 fields): 40 millis CompletedMACS2peakCalling