Job ID = 14520536 SRX = SRX9144938 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10596218 spots for SRR12664296/SRR12664296.sra Written 10596218 spots for SRR12664296/SRR12664296.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: 00:13:54 10596218 reads; of these: 10596218 (100.00%) were paired; of these: 392265 (3.70%) aligned concordantly 0 times 8184436 (77.24%) aligned concordantly exactly 1 time 2019517 (19.06%) aligned concordantly >1 times ---- 392265 pairs aligned concordantly 0 times; of these: 39357 (10.03%) aligned discordantly 1 time ---- 352908 pairs aligned 0 times concordantly or discordantly; of these: 705816 mates make up the pairs; of these: 600624 (85.10%) aligned 0 times 60848 (8.62%) aligned exactly 1 time 44344 (6.28%) aligned >1 times 97.17% overall alignment rate Time searching: 00:13:54 Overall time: 00:13:54 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 16 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] 3958656 / 10238323 = 0.3867 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 19:41:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.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 19:41:59: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:41:59: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:42:08: 1000000 INFO @ Sat, 15 Jan 2022 19:42:17: 2000000 INFO @ Sat, 15 Jan 2022 19:42:26: 3000000 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 19:42:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.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 19:42:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:42:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:42:35: 4000000 INFO @ Sat, 15 Jan 2022 19:42:38: 1000000 INFO @ Sat, 15 Jan 2022 19:42:45: 5000000 INFO @ Sat, 15 Jan 2022 19:42:47: 2000000 INFO @ Sat, 15 Jan 2022 19:42:55: 6000000 INFO @ Sat, 15 Jan 2022 19:42:56: 3000000 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 19:43:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.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 19:43:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:43:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:43:05: 7000000 INFO @ Sat, 15 Jan 2022 19:43:05: 4000000 INFO @ Sat, 15 Jan 2022 19:43:10: 1000000 INFO @ Sat, 15 Jan 2022 19:43:14: 5000000 INFO @ Sat, 15 Jan 2022 19:43:15: 8000000 INFO @ Sat, 15 Jan 2022 19:43:21: 2000000 INFO @ Sat, 15 Jan 2022 19:43:23: 6000000 INFO @ Sat, 15 Jan 2022 19:43:25: 9000000 INFO @ Sat, 15 Jan 2022 19:43:31: 3000000 INFO @ Sat, 15 Jan 2022 19:43:33: 7000000 INFO @ Sat, 15 Jan 2022 19:43:35: 10000000 INFO @ Sat, 15 Jan 2022 19:43:42: 4000000 INFO @ Sat, 15 Jan 2022 19:43:42: 8000000 INFO @ Sat, 15 Jan 2022 19:43:45: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:43:51: 9000000 INFO @ Sat, 15 Jan 2022 19:43:52: 5000000 INFO @ Sat, 15 Jan 2022 19:43:54: 12000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:44:00: 10000000 INFO @ Sat, 15 Jan 2022 19:44:01: #1 tag size is determined as 151 bps INFO @ Sat, 15 Jan 2022 19:44:01: #1 tag size = 151 INFO @ Sat, 15 Jan 2022 19:44:01: #1 total tags in treatment: 6256959 INFO @ Sat, 15 Jan 2022 19:44:01: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:44:01: #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 19:44:01: #1 tags after filtering in treatment: 3396834 INFO @ Sat, 15 Jan 2022 19:44:01: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 15 Jan 2022 19:44:01: #1 finished! INFO @ Sat, 15 Jan 2022 19:44:01: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:44:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:44:01: #2 number of paired peaks: 136 WARNING @ Sat, 15 Jan 2022 19:44:01: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sat, 15 Jan 2022 19:44:01: start model_add_line... INFO @ Sat, 15 Jan 2022 19:44:01: start X-correlation... INFO @ Sat, 15 Jan 2022 19:44:01: end of X-cor INFO @ Sat, 15 Jan 2022 19:44:01: #2 finished! INFO @ Sat, 15 Jan 2022 19:44:01: #2 predicted fragment length is 209 bps INFO @ Sat, 15 Jan 2022 19:44:01: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 15 Jan 2022 19:44:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.05_model.r WARNING @ Sat, 15 Jan 2022 19:44:01: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:44:01: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Sat, 15 Jan 2022 19:44:01: #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 19:44:01: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:44:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:44:02: 6000000 INFO @ Sat, 15 Jan 2022 19:44:09: 11000000 INFO @ Sat, 15 Jan 2022 19:44:11: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:44:12: 7000000 INFO @ Sat, 15 Jan 2022 19:44:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:44:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:44:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.05_summits.bed INFO @ Sat, 15 Jan 2022 19:44:14: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1689 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:44:18: 12000000 INFO @ Sat, 15 Jan 2022 19:44:22: 8000000 INFO @ Sat, 15 Jan 2022 19:44:24: #1 tag size is determined as 151 bps INFO @ Sat, 15 Jan 2022 19:44:24: #1 tag size = 151 INFO @ Sat, 15 Jan 2022 19:44:24: #1 total tags in treatment: 6256959 INFO @ Sat, 15 Jan 2022 19:44:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:44:24: #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 19:44:24: #1 tags after filtering in treatment: 3396834 INFO @ Sat, 15 Jan 2022 19:44:24: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 15 Jan 2022 19:44:24: #1 finished! INFO @ Sat, 15 Jan 2022 19:44:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:44:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:44:24: #2 number of paired peaks: 136 WARNING @ Sat, 15 Jan 2022 19:44:24: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sat, 15 Jan 2022 19:44:24: start model_add_line... INFO @ Sat, 15 Jan 2022 19:44:24: start X-correlation... INFO @ Sat, 15 Jan 2022 19:44:24: end of X-cor INFO @ Sat, 15 Jan 2022 19:44:24: #2 finished! INFO @ Sat, 15 Jan 2022 19:44:24: #2 predicted fragment length is 209 bps INFO @ Sat, 15 Jan 2022 19:44:24: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 15 Jan 2022 19:44:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.10_model.r WARNING @ Sat, 15 Jan 2022 19:44:24: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:44:24: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Sat, 15 Jan 2022 19:44:24: #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 19:44:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:44:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:44:31: 9000000 INFO @ Sat, 15 Jan 2022 19:44:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:44:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:44:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:44:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.10_summits.bed INFO @ Sat, 15 Jan 2022 19:44:37: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1176 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:44:41: 10000000 INFO @ Sat, 15 Jan 2022 19:44:50: 11000000 INFO @ Sat, 15 Jan 2022 19:44:59: 12000000 INFO @ Sat, 15 Jan 2022 19:45:05: #1 tag size is determined as 151 bps INFO @ Sat, 15 Jan 2022 19:45:05: #1 tag size = 151 INFO @ Sat, 15 Jan 2022 19:45:05: #1 total tags in treatment: 6256959 INFO @ Sat, 15 Jan 2022 19:45:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:45:05: #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 19:45:05: #1 tags after filtering in treatment: 3396834 INFO @ Sat, 15 Jan 2022 19:45:05: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 15 Jan 2022 19:45:05: #1 finished! INFO @ Sat, 15 Jan 2022 19:45:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:45:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:45:05: #2 number of paired peaks: 136 WARNING @ Sat, 15 Jan 2022 19:45:05: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sat, 15 Jan 2022 19:45:05: start model_add_line... INFO @ Sat, 15 Jan 2022 19:45:05: start X-correlation... INFO @ Sat, 15 Jan 2022 19:45:05: end of X-cor INFO @ Sat, 15 Jan 2022 19:45:05: #2 finished! INFO @ Sat, 15 Jan 2022 19:45:05: #2 predicted fragment length is 209 bps INFO @ Sat, 15 Jan 2022 19:45:05: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 15 Jan 2022 19:45:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.20_model.r WARNING @ Sat, 15 Jan 2022 19:45:05: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:45:05: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Sat, 15 Jan 2022 19:45:05: #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 19:45:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:45:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:45:15: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:45:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:45:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:45:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9144938/SRX9144938.20_summits.bed INFO @ Sat, 15 Jan 2022 19:45:18: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (771 records, 4 fields): 3 millis CompletedMACS2peakCalling