Job ID = 14520769 SRX = SRX9038693 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19763888 spots for SRR12549474/SRR12549474.sra Written 19763888 spots for SRR12549474/SRR12549474.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: 00:16:02 19763888 reads; of these: 19763888 (100.00%) were paired; of these: 12139361 (61.42%) aligned concordantly 0 times 1518781 (7.68%) aligned concordantly exactly 1 time 6105746 (30.89%) aligned concordantly >1 times ---- 12139361 pairs aligned concordantly 0 times; of these: 240883 (1.98%) aligned discordantly 1 time ---- 11898478 pairs aligned 0 times concordantly or discordantly; of these: 23796956 mates make up the pairs; of these: 20965302 (88.10%) aligned 0 times 171204 (0.72%) aligned exactly 1 time 2660450 (11.18%) aligned >1 times 46.96% overall alignment rate Time searching: 00:16:02 Overall time: 00:16:02 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] 3545435 / 7837803 = 0.4524 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 20:16:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.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 20:16:21: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:16:21: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:16:31: 1000000 INFO @ Sat, 15 Jan 2022 20:16:40: 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 20:16:50: 3000000 INFO @ Sat, 15 Jan 2022 20:16:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.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 20:16:51: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:16:51: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:17:00: 4000000 INFO @ Sat, 15 Jan 2022 20:17:02: 1000000 INFO @ Sat, 15 Jan 2022 20:17:10: 5000000 INFO @ Sat, 15 Jan 2022 20:17:12: 2000000 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 20:17:21: 6000000 INFO @ Sat, 15 Jan 2022 20:17:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.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 20:17:21: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:17:21: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:17:23: 3000000 INFO @ Sat, 15 Jan 2022 20:17:31: 7000000 INFO @ Sat, 15 Jan 2022 20:17:32: 1000000 INFO @ Sat, 15 Jan 2022 20:17:33: 4000000 INFO @ Sat, 15 Jan 2022 20:17:42: 8000000 INFO @ Sat, 15 Jan 2022 20:17:43: 2000000 INFO @ Sat, 15 Jan 2022 20:17:44: 5000000 INFO @ Sat, 15 Jan 2022 20:17:52: 9000000 INFO @ Sat, 15 Jan 2022 20:17:53: 3000000 INFO @ Sat, 15 Jan 2022 20:17:54: 6000000 INFO @ Sat, 15 Jan 2022 20:18:03: 10000000 INFO @ Sat, 15 Jan 2022 20:18:04: 4000000 INFO @ Sat, 15 Jan 2022 20:18:05: 7000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:18:14: 11000000 INFO @ Sat, 15 Jan 2022 20:18:14: 5000000 INFO @ Sat, 15 Jan 2022 20:18:15: 8000000 INFO @ Sat, 15 Jan 2022 20:18:19: #1 tag size is determined as 151 bps INFO @ Sat, 15 Jan 2022 20:18:19: #1 tag size = 151 INFO @ Sat, 15 Jan 2022 20:18:19: #1 total tags in treatment: 4107072 INFO @ Sat, 15 Jan 2022 20:18:19: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:18:19: #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 20:18:19: #1 tags after filtering in treatment: 1103800 INFO @ Sat, 15 Jan 2022 20:18:19: #1 Redundant rate of treatment: 0.73 INFO @ Sat, 15 Jan 2022 20:18:19: #1 finished! INFO @ Sat, 15 Jan 2022 20:18:19: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:18:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:18:19: #2 number of paired peaks: 246 WARNING @ Sat, 15 Jan 2022 20:18:19: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Sat, 15 Jan 2022 20:18:19: start model_add_line... INFO @ Sat, 15 Jan 2022 20:18:19: start X-correlation... INFO @ Sat, 15 Jan 2022 20:18:19: end of X-cor INFO @ Sat, 15 Jan 2022 20:18:19: #2 finished! INFO @ Sat, 15 Jan 2022 20:18:19: #2 predicted fragment length is 235 bps INFO @ Sat, 15 Jan 2022 20:18:19: #2 alternative fragment length(s) may be 4,235 bps INFO @ Sat, 15 Jan 2022 20:18:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.05_model.r WARNING @ Sat, 15 Jan 2022 20:18:19: #2 Since the d (235) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:18:19: #2 You may need to consider one of the other alternative d(s): 4,235 WARNING @ Sat, 15 Jan 2022 20:18:19: #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 20:18:19: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:18:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:18:23: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:18:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:18:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:18:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.05_summits.bed INFO @ Sat, 15 Jan 2022 20:18:24: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (464 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:18:25: 6000000 INFO @ Sat, 15 Jan 2022 20:18:26: 9000000 INFO @ Sat, 15 Jan 2022 20:18:36: 7000000 INFO @ Sat, 15 Jan 2022 20:18:36: 10000000 INFO @ Sat, 15 Jan 2022 20:18:46: 8000000 INFO @ Sat, 15 Jan 2022 20:18:47: 11000000 INFO @ Sat, 15 Jan 2022 20:18:52: #1 tag size is determined as 151 bps INFO @ Sat, 15 Jan 2022 20:18:52: #1 tag size = 151 INFO @ Sat, 15 Jan 2022 20:18:52: #1 total tags in treatment: 4107072 INFO @ Sat, 15 Jan 2022 20:18:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:18:52: #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 20:18:52: #1 tags after filtering in treatment: 1103800 INFO @ Sat, 15 Jan 2022 20:18:52: #1 Redundant rate of treatment: 0.73 INFO @ Sat, 15 Jan 2022 20:18:52: #1 finished! INFO @ Sat, 15 Jan 2022 20:18:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:18:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:18:52: #2 number of paired peaks: 246 WARNING @ Sat, 15 Jan 2022 20:18:52: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Sat, 15 Jan 2022 20:18:52: start model_add_line... INFO @ Sat, 15 Jan 2022 20:18:52: start X-correlation... INFO @ Sat, 15 Jan 2022 20:18:52: end of X-cor INFO @ Sat, 15 Jan 2022 20:18:52: #2 finished! INFO @ Sat, 15 Jan 2022 20:18:52: #2 predicted fragment length is 235 bps INFO @ Sat, 15 Jan 2022 20:18:52: #2 alternative fragment length(s) may be 4,235 bps INFO @ Sat, 15 Jan 2022 20:18:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.10_model.r WARNING @ Sat, 15 Jan 2022 20:18:52: #2 Since the d (235) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:18:52: #2 You may need to consider one of the other alternative d(s): 4,235 WARNING @ Sat, 15 Jan 2022 20:18:52: #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 20:18:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:18:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:18:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:18:56: 9000000 INFO @ Sat, 15 Jan 2022 20:18:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:18:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:18:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.10_summits.bed INFO @ Sat, 15 Jan 2022 20:18:57: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (268 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:19:06: 10000000 INFO @ Sat, 15 Jan 2022 20:19:15: 11000000 INFO @ Sat, 15 Jan 2022 20:19:19: #1 tag size is determined as 151 bps INFO @ Sat, 15 Jan 2022 20:19:19: #1 tag size = 151 INFO @ Sat, 15 Jan 2022 20:19:19: #1 total tags in treatment: 4107072 INFO @ Sat, 15 Jan 2022 20:19:19: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:19:19: #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 20:19:20: #1 tags after filtering in treatment: 1103800 INFO @ Sat, 15 Jan 2022 20:19:20: #1 Redundant rate of treatment: 0.73 INFO @ Sat, 15 Jan 2022 20:19:20: #1 finished! INFO @ Sat, 15 Jan 2022 20:19:20: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:19:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:19:20: #2 number of paired peaks: 246 WARNING @ Sat, 15 Jan 2022 20:19:20: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Sat, 15 Jan 2022 20:19:20: start model_add_line... INFO @ Sat, 15 Jan 2022 20:19:20: start X-correlation... INFO @ Sat, 15 Jan 2022 20:19:20: end of X-cor INFO @ Sat, 15 Jan 2022 20:19:20: #2 finished! INFO @ Sat, 15 Jan 2022 20:19:20: #2 predicted fragment length is 235 bps INFO @ Sat, 15 Jan 2022 20:19:20: #2 alternative fragment length(s) may be 4,235 bps INFO @ Sat, 15 Jan 2022 20:19:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.20_model.r WARNING @ Sat, 15 Jan 2022 20:19:20: #2 Since the d (235) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:19:20: #2 You may need to consider one of the other alternative d(s): 4,235 WARNING @ Sat, 15 Jan 2022 20:19:20: #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 20:19:20: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:19:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:19:23: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:19:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:19:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:19:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9038693/SRX9038693.20_summits.bed INFO @ Sat, 15 Jan 2022 20:19:24: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (161 records, 4 fields): 2 millis CompletedMACS2peakCalling