Job ID = 14520828 SRX = SRX8245535 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10223600 spots for SRR11684746/SRR11684746.sra Written 10223600 spots for SRR11684746/SRR11684746.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: 00:04:50 10223600 reads; of these: 10223600 (100.00%) were paired; of these: 6466549 (63.25%) aligned concordantly 0 times 3393060 (33.19%) aligned concordantly exactly 1 time 363991 (3.56%) aligned concordantly >1 times ---- 6466549 pairs aligned concordantly 0 times; of these: 28522 (0.44%) aligned discordantly 1 time ---- 6438027 pairs aligned 0 times concordantly or discordantly; of these: 12876054 mates make up the pairs; of these: 8804321 (68.38%) aligned 0 times 3582787 (27.83%) aligned exactly 1 time 488946 (3.80%) aligned >1 times 56.94% overall alignment rate Time searching: 00:04:50 Overall time: 00:04:50 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] 334326 / 3784972 = 0.0883 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 20:10:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.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 20:10:34: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:10:34: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:10:38: 1000000 INFO @ Sat, 15 Jan 2022 20:10:43: 2000000 INFO @ Sat, 15 Jan 2022 20:10:48: 3000000 INFO @ Sat, 15 Jan 2022 20:10:52: 4000000 INFO @ Sat, 15 Jan 2022 20:10:57: 5000000 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 20:11:02: 6000000 INFO @ Sat, 15 Jan 2022 20:11:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.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 20:11:04: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:11:04: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:11:07: 7000000 INFO @ Sat, 15 Jan 2022 20:11:09: 1000000 INFO @ Sat, 15 Jan 2022 20:11:12: 8000000 INFO @ Sat, 15 Jan 2022 20:11:14: 2000000 INFO @ Sat, 15 Jan 2022 20:11:18: 9000000 INFO @ Sat, 15 Jan 2022 20:11:19: 3000000 INFO @ Sat, 15 Jan 2022 20:11:23: 10000000 INFO @ Sat, 15 Jan 2022 20:11:25: 4000000 INFO @ Sat, 15 Jan 2022 20:11:28: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:11:28: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:11:28: #1 total tags in treatment: 3423848 INFO @ Sat, 15 Jan 2022 20:11:28: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:11:28: #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 20:11:28: #1 tags after filtering in treatment: 1935257 INFO @ Sat, 15 Jan 2022 20:11:28: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 20:11:28: #1 finished! INFO @ Sat, 15 Jan 2022 20:11:28: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:11:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:11:28: #2 number of paired peaks: 175 WARNING @ Sat, 15 Jan 2022 20:11:28: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Jan 2022 20:11:28: start model_add_line... INFO @ Sat, 15 Jan 2022 20:11:28: start X-correlation... INFO @ Sat, 15 Jan 2022 20:11:29: end of X-cor INFO @ Sat, 15 Jan 2022 20:11:29: #2 finished! INFO @ Sat, 15 Jan 2022 20:11:29: #2 predicted fragment length is 60 bps INFO @ Sat, 15 Jan 2022 20:11:29: #2 alternative fragment length(s) may be 26,60,122,160,176,193,208,238,257,302,342,348,378,397,479,504,510,519,565,584 bps INFO @ Sat, 15 Jan 2022 20:11:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.05_model.r WARNING @ Sat, 15 Jan 2022 20:11:29: #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 20:11:29: #2 You may need to consider one of the other alternative d(s): 26,60,122,160,176,193,208,238,257,302,342,348,378,397,479,504,510,519,565,584 WARNING @ Sat, 15 Jan 2022 20:11:29: #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 20:11:29: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:11:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:11:30: 5000000 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 20:11:32: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:11:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:11:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:11:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.05_summits.bed INFO @ Sat, 15 Jan 2022 20:11:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (50 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:11:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.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 20:11:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:11:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:11:35: 6000000 INFO @ Sat, 15 Jan 2022 20:11:40: 1000000 INFO @ Sat, 15 Jan 2022 20:11:40: 7000000 INFO @ Sat, 15 Jan 2022 20:11:46: 8000000 INFO @ Sat, 15 Jan 2022 20:11:47: 2000000 INFO @ Sat, 15 Jan 2022 20:11:52: 9000000 INFO @ Sat, 15 Jan 2022 20:11:53: 3000000 INFO @ Sat, 15 Jan 2022 20:11:58: 10000000 INFO @ Sat, 15 Jan 2022 20:12:00: 4000000 INFO @ Sat, 15 Jan 2022 20:12:04: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:12:04: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:12:04: #1 total tags in treatment: 3423848 INFO @ Sat, 15 Jan 2022 20:12:04: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:12:04: #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 20:12:04: #1 tags after filtering in treatment: 1935257 INFO @ Sat, 15 Jan 2022 20:12:04: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 20:12:04: #1 finished! INFO @ Sat, 15 Jan 2022 20:12:04: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:12:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:12:04: #2 number of paired peaks: 175 WARNING @ Sat, 15 Jan 2022 20:12:04: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Jan 2022 20:12:04: start model_add_line... INFO @ Sat, 15 Jan 2022 20:12:04: start X-correlation... INFO @ Sat, 15 Jan 2022 20:12:04: end of X-cor INFO @ Sat, 15 Jan 2022 20:12:04: #2 finished! INFO @ Sat, 15 Jan 2022 20:12:04: #2 predicted fragment length is 60 bps INFO @ Sat, 15 Jan 2022 20:12:04: #2 alternative fragment length(s) may be 26,60,122,160,176,193,208,238,257,302,342,348,378,397,479,504,510,519,565,584 bps INFO @ Sat, 15 Jan 2022 20:12:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.10_model.r WARNING @ Sat, 15 Jan 2022 20:12:04: #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 20:12:04: #2 You may need to consider one of the other alternative d(s): 26,60,122,160,176,193,208,238,257,302,342,348,378,397,479,504,510,519,565,584 WARNING @ Sat, 15 Jan 2022 20:12:04: #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 20:12:04: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:12:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:12:06: 5000000 INFO @ Sat, 15 Jan 2022 20:12:07: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:12:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:12:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:12:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.10_summits.bed INFO @ Sat, 15 Jan 2022 20:12:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 201 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:12:12: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:12:18: 7000000 INFO @ Sat, 15 Jan 2022 20:12:24: 8000000 INFO @ Sat, 15 Jan 2022 20:12:30: 9000000 INFO @ Sat, 15 Jan 2022 20:12:37: 10000000 INFO @ Sat, 15 Jan 2022 20:12:42: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:12:42: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:12:42: #1 total tags in treatment: 3423848 INFO @ Sat, 15 Jan 2022 20:12:42: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:12:42: #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 20:12:42: #1 tags after filtering in treatment: 1935257 INFO @ Sat, 15 Jan 2022 20:12:42: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 20:12:42: #1 finished! INFO @ Sat, 15 Jan 2022 20:12:42: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:12:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:12:43: #2 number of paired peaks: 175 WARNING @ Sat, 15 Jan 2022 20:12:43: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Jan 2022 20:12:43: start model_add_line... INFO @ Sat, 15 Jan 2022 20:12:43: start X-correlation... INFO @ Sat, 15 Jan 2022 20:12:43: end of X-cor INFO @ Sat, 15 Jan 2022 20:12:43: #2 finished! INFO @ Sat, 15 Jan 2022 20:12:43: #2 predicted fragment length is 60 bps INFO @ Sat, 15 Jan 2022 20:12:43: #2 alternative fragment length(s) may be 26,60,122,160,176,193,208,238,257,302,342,348,378,397,479,504,510,519,565,584 bps INFO @ Sat, 15 Jan 2022 20:12:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.20_model.r WARNING @ Sat, 15 Jan 2022 20:12:43: #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 20:12:43: #2 You may need to consider one of the other alternative d(s): 26,60,122,160,176,193,208,238,257,302,342,348,378,397,479,504,510,519,565,584 WARNING @ Sat, 15 Jan 2022 20:12:43: #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 20:12:43: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:12:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:12:46: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:12:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:12:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:12:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245535/SRX8245535.20_summits.bed INFO @ Sat, 15 Jan 2022 20:12:47: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling