Job ID = 12531690 SRX = SRX4555058 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9473839 spots for SRR7696759/SRR7696759.sra Written 9473839 spots for SRR7696759/SRR7696759.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: 00:11:10 9473839 reads; of these: 9473839 (100.00%) were paired; of these: 562164 (5.93%) aligned concordantly 0 times 4347705 (45.89%) aligned concordantly exactly 1 time 4563970 (48.17%) aligned concordantly >1 times ---- 562164 pairs aligned concordantly 0 times; of these: 36091 (6.42%) aligned discordantly 1 time ---- 526073 pairs aligned 0 times concordantly or discordantly; of these: 1052146 mates make up the pairs; of these: 845255 (80.34%) aligned 0 times 103200 (9.81%) aligned exactly 1 time 103691 (9.86%) aligned >1 times 95.54% overall alignment rate Time searching: 00:11:10 Overall time: 00:11:10 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] 1785258 / 4362018 = 0.4093 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 09:28:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.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 09:28:26: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:28:26: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:28:32: 1000000 INFO @ Sat, 17 Apr 2021 09:28:37: 2000000 INFO @ Sat, 17 Apr 2021 09:28:43: 3000000 INFO @ Sat, 17 Apr 2021 09:28:49: 4000000 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 09:28:55: 5000000 INFO @ Sat, 17 Apr 2021 09:28:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.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 09:28:56: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:28:56: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:29:01: 6000000 INFO @ Sat, 17 Apr 2021 09:29:02: 1000000 INFO @ Sat, 17 Apr 2021 09:29:06: 7000000 INFO @ Sat, 17 Apr 2021 09:29:08: 2000000 INFO @ Sat, 17 Apr 2021 09:29:12: 8000000 INFO @ Sat, 17 Apr 2021 09:29:14: 3000000 INFO @ Sat, 17 Apr 2021 09:29:18: 9000000 INFO @ Sat, 17 Apr 2021 09:29:20: 4000000 INFO @ Sat, 17 Apr 2021 09:29:23: 10000000 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 09:29:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.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 09:29:26: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:29:26: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:29:26: 5000000 INFO @ Sat, 17 Apr 2021 09:29:29: 11000000 INFO @ Sat, 17 Apr 2021 09:29:32: 1000000 INFO @ Sat, 17 Apr 2021 09:29:32: 6000000 INFO @ Sat, 17 Apr 2021 09:29:36: 12000000 INFO @ Sat, 17 Apr 2021 09:29:38: 7000000 INFO @ Sat, 17 Apr 2021 09:29:39: 2000000 INFO @ Sat, 17 Apr 2021 09:29:42: 13000000 INFO @ Sat, 17 Apr 2021 09:29:44: 8000000 INFO @ Sat, 17 Apr 2021 09:29:45: 3000000 INFO @ Sat, 17 Apr 2021 09:29:48: 14000000 INFO @ Sat, 17 Apr 2021 09:29:49: 9000000 INFO @ Sat, 17 Apr 2021 09:29:51: 4000000 INFO @ Sat, 17 Apr 2021 09:29:52: #1 tag size is determined as 99 bps INFO @ Sat, 17 Apr 2021 09:29:52: #1 tag size = 99 INFO @ Sat, 17 Apr 2021 09:29:52: #1 total tags in treatment: 7128235 INFO @ Sat, 17 Apr 2021 09:29:52: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:29:52: #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 09:29:52: #1 tags after filtering in treatment: 1915724 INFO @ Sat, 17 Apr 2021 09:29:52: #1 Redundant rate of treatment: 0.73 INFO @ Sat, 17 Apr 2021 09:29:52: #1 finished! INFO @ Sat, 17 Apr 2021 09:29:52: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:29:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:29:52: #2 number of paired peaks: 211 WARNING @ Sat, 17 Apr 2021 09:29:52: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Sat, 17 Apr 2021 09:29:52: start model_add_line... INFO @ Sat, 17 Apr 2021 09:29:52: start X-correlation... INFO @ Sat, 17 Apr 2021 09:29:52: end of X-cor INFO @ Sat, 17 Apr 2021 09:29:52: #2 finished! INFO @ Sat, 17 Apr 2021 09:29:52: #2 predicted fragment length is 53 bps INFO @ Sat, 17 Apr 2021 09:29:52: #2 alternative fragment length(s) may be 4,12,53 bps INFO @ Sat, 17 Apr 2021 09:29:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.05_model.r WARNING @ Sat, 17 Apr 2021 09:29:52: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:29:52: #2 You may need to consider one of the other alternative d(s): 4,12,53 WARNING @ Sat, 17 Apr 2021 09:29:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:29:52: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:29:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:29:55: 10000000 INFO @ Sat, 17 Apr 2021 09:29:56: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:29:57: 5000000 INFO @ Sat, 17 Apr 2021 09:29:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.05_peaks.xls INFO @ Sat, 17 Apr 2021 09:29:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:29:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.05_summits.bed INFO @ Sat, 17 Apr 2021 09:29:58: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (2630 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:30:01: 11000000 INFO @ Sat, 17 Apr 2021 09:30:03: 6000000 INFO @ Sat, 17 Apr 2021 09:30:07: 12000000 INFO @ Sat, 17 Apr 2021 09:30:09: 7000000 INFO @ Sat, 17 Apr 2021 09:30:13: 13000000 INFO @ Sat, 17 Apr 2021 09:30:15: 8000000 INFO @ Sat, 17 Apr 2021 09:30:19: 14000000 INFO @ Sat, 17 Apr 2021 09:30:20: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 09:30:22: #1 tag size is determined as 99 bps INFO @ Sat, 17 Apr 2021 09:30:22: #1 tag size = 99 INFO @ Sat, 17 Apr 2021 09:30:22: #1 total tags in treatment: 7128235 INFO @ Sat, 17 Apr 2021 09:30:22: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:30:22: #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 09:30:22: #1 tags after filtering in treatment: 1915724 INFO @ Sat, 17 Apr 2021 09:30:22: #1 Redundant rate of treatment: 0.73 INFO @ Sat, 17 Apr 2021 09:30:22: #1 finished! INFO @ Sat, 17 Apr 2021 09:30:22: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:30:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:30:22: #2 number of paired peaks: 211 WARNING @ Sat, 17 Apr 2021 09:30:22: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Sat, 17 Apr 2021 09:30:22: start model_add_line... INFO @ Sat, 17 Apr 2021 09:30:22: start X-correlation... INFO @ Sat, 17 Apr 2021 09:30:22: end of X-cor INFO @ Sat, 17 Apr 2021 09:30:22: #2 finished! INFO @ Sat, 17 Apr 2021 09:30:22: #2 predicted fragment length is 53 bps INFO @ Sat, 17 Apr 2021 09:30:22: #2 alternative fragment length(s) may be 4,12,53 bps INFO @ Sat, 17 Apr 2021 09:30:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.10_model.r WARNING @ Sat, 17 Apr 2021 09:30:22: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:30:22: #2 You may need to consider one of the other alternative d(s): 4,12,53 WARNING @ Sat, 17 Apr 2021 09:30:22: #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 09:30:22: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:30:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:30:26: 10000000 INFO @ Sat, 17 Apr 2021 09:30:26: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:30:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.10_peaks.xls INFO @ Sat, 17 Apr 2021 09:30:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:30:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.10_summits.bed INFO @ Sat, 17 Apr 2021 09:30:28: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1496 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:30:32: 11000000 INFO @ Sat, 17 Apr 2021 09:30:37: 12000000 INFO @ Sat, 17 Apr 2021 09:30:43: 13000000 INFO @ Sat, 17 Apr 2021 09:30:49: 14000000 INFO @ Sat, 17 Apr 2021 09:30:53: #1 tag size is determined as 99 bps INFO @ Sat, 17 Apr 2021 09:30:53: #1 tag size = 99 INFO @ Sat, 17 Apr 2021 09:30:53: #1 total tags in treatment: 7128235 INFO @ Sat, 17 Apr 2021 09:30:53: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:30:53: #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 09:30:53: #1 tags after filtering in treatment: 1915724 INFO @ Sat, 17 Apr 2021 09:30:53: #1 Redundant rate of treatment: 0.73 INFO @ Sat, 17 Apr 2021 09:30:53: #1 finished! INFO @ Sat, 17 Apr 2021 09:30:53: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:30:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:30:53: #2 number of paired peaks: 211 WARNING @ Sat, 17 Apr 2021 09:30:53: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Sat, 17 Apr 2021 09:30:53: start model_add_line... INFO @ Sat, 17 Apr 2021 09:30:53: start X-correlation... INFO @ Sat, 17 Apr 2021 09:30:53: end of X-cor INFO @ Sat, 17 Apr 2021 09:30:53: #2 finished! INFO @ Sat, 17 Apr 2021 09:30:53: #2 predicted fragment length is 53 bps INFO @ Sat, 17 Apr 2021 09:30:53: #2 alternative fragment length(s) may be 4,12,53 bps INFO @ Sat, 17 Apr 2021 09:30:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.20_model.r WARNING @ Sat, 17 Apr 2021 09:30:53: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:30:53: #2 You may need to consider one of the other alternative d(s): 4,12,53 WARNING @ Sat, 17 Apr 2021 09:30:53: #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 09:30:53: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:30:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:30:57: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:30:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.20_peaks.xls INFO @ Sat, 17 Apr 2021 09:30:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:30:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555058/SRX4555058.20_summits.bed INFO @ Sat, 17 Apr 2021 09:30:58: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (468 records, 4 fields): 3 millis CompletedMACS2peakCalling