Job ID = 14520428 SRX = SRX11781024 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:05:06 prefetch.2.10.7: 1) Downloading 'SRR15480967'... 2022-01-15T10:05:06 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:05:34 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:05:35 prefetch.2.10.7: 'SRR15480967' is valid 2022-01-15T10:05:35 prefetch.2.10.7: 1) 'SRR15480967' was downloaded successfully 2022-01-15T10:05:35 prefetch.2.10.7: 'SRR15480967' has 0 unresolved dependencies Read 7629678 spots for SRR15480967/SRR15480967.sra Written 7629678 spots for SRR15480967/SRR15480967.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: 00:05:32 7629678 reads; of these: 7629678 (100.00%) were paired; of these: 1467801 (19.24%) aligned concordantly 0 times 3743807 (49.07%) aligned concordantly exactly 1 time 2418070 (31.69%) aligned concordantly >1 times ---- 1467801 pairs aligned concordantly 0 times; of these: 73930 (5.04%) aligned discordantly 1 time ---- 1393871 pairs aligned 0 times concordantly or discordantly; of these: 2787742 mates make up the pairs; of these: 2374041 (85.16%) aligned 0 times 321075 (11.52%) aligned exactly 1 time 92626 (3.32%) aligned >1 times 84.44% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 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] 2553491 / 6223415 = 0.4103 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 19:15:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.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 19:15:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:15:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:15:15: 1000000 INFO @ Sat, 15 Jan 2022 19:15:22: 2000000 INFO @ Sat, 15 Jan 2022 19:15:28: 3000000 INFO @ Sat, 15 Jan 2022 19:15:34: 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 19:15:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.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 19:15:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:15:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:15:40: 5000000 INFO @ Sat, 15 Jan 2022 19:15:47: 1000000 INFO @ Sat, 15 Jan 2022 19:15:47: 6000000 INFO @ Sat, 15 Jan 2022 19:15:54: 2000000 INFO @ Sat, 15 Jan 2022 19:15:55: 7000000 INFO @ Sat, 15 Jan 2022 19:16:00: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:16:00: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:16:00: #1 total tags in treatment: 3630594 INFO @ Sat, 15 Jan 2022 19:16:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:16:00: #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 19:16:00: #1 tags after filtering in treatment: 1710195 INFO @ Sat, 15 Jan 2022 19:16:00: #1 Redundant rate of treatment: 0.53 INFO @ Sat, 15 Jan 2022 19:16:00: #1 finished! INFO @ Sat, 15 Jan 2022 19:16:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:16:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:16:01: #2 number of paired peaks: 184 WARNING @ Sat, 15 Jan 2022 19:16:01: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Sat, 15 Jan 2022 19:16:01: start model_add_line... INFO @ Sat, 15 Jan 2022 19:16:01: start X-correlation... INFO @ Sat, 15 Jan 2022 19:16:01: end of X-cor INFO @ Sat, 15 Jan 2022 19:16:01: #2 finished! INFO @ Sat, 15 Jan 2022 19:16:01: #2 predicted fragment length is 111 bps INFO @ Sat, 15 Jan 2022 19:16:01: #2 alternative fragment length(s) may be 0,99,111,150,232,274,476,544,558 bps INFO @ Sat, 15 Jan 2022 19:16:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.05_model.r WARNING @ Sat, 15 Jan 2022 19:16:01: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:16:01: #2 You may need to consider one of the other alternative d(s): 0,99,111,150,232,274,476,544,558 WARNING @ Sat, 15 Jan 2022 19:16:01: #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 19:16:01: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:16:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:16:02: 3000000 INFO @ Sat, 15 Jan 2022 19:16:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:16:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:16:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:16:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.05_summits.bed BedGraph に変換中... INFO @ Sat, 15 Jan 2022 19:16:07: Done! 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 pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (131 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:16:08: 4000000 INFO @ Sat, 15 Jan 2022 19:16:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.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 19:16:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:16:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:16:16: 5000000 INFO @ Sat, 15 Jan 2022 19:16:18: 1000000 INFO @ Sat, 15 Jan 2022 19:16:24: 6000000 INFO @ Sat, 15 Jan 2022 19:16:27: 2000000 INFO @ Sat, 15 Jan 2022 19:16:32: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:16:36: 3000000 INFO @ Sat, 15 Jan 2022 19:16:38: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:16:38: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:16:38: #1 total tags in treatment: 3630594 INFO @ Sat, 15 Jan 2022 19:16:38: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:16:38: #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 19:16:38: #1 tags after filtering in treatment: 1710195 INFO @ Sat, 15 Jan 2022 19:16:38: #1 Redundant rate of treatment: 0.53 INFO @ Sat, 15 Jan 2022 19:16:38: #1 finished! INFO @ Sat, 15 Jan 2022 19:16:38: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:16:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:16:38: #2 number of paired peaks: 184 WARNING @ Sat, 15 Jan 2022 19:16:38: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Sat, 15 Jan 2022 19:16:38: start model_add_line... INFO @ Sat, 15 Jan 2022 19:16:38: start X-correlation... INFO @ Sat, 15 Jan 2022 19:16:38: end of X-cor INFO @ Sat, 15 Jan 2022 19:16:38: #2 finished! INFO @ Sat, 15 Jan 2022 19:16:38: #2 predicted fragment length is 111 bps INFO @ Sat, 15 Jan 2022 19:16:38: #2 alternative fragment length(s) may be 0,99,111,150,232,274,476,544,558 bps INFO @ Sat, 15 Jan 2022 19:16:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.10_model.r WARNING @ Sat, 15 Jan 2022 19:16:38: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:16:38: #2 You may need to consider one of the other alternative d(s): 0,99,111,150,232,274,476,544,558 WARNING @ Sat, 15 Jan 2022 19:16:38: #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 19:16:38: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:16:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:16:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:16:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:16:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:16:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.10_summits.bed INFO @ Sat, 15 Jan 2022 19:16:43: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (34 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:16:45: 4000000 INFO @ Sat, 15 Jan 2022 19:16:53: 5000000 INFO @ Sat, 15 Jan 2022 19:17:01: 6000000 INFO @ Sat, 15 Jan 2022 19:17:09: 7000000 INFO @ Sat, 15 Jan 2022 19:17:15: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:17:15: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:17:15: #1 total tags in treatment: 3630594 INFO @ Sat, 15 Jan 2022 19:17:15: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:17:15: #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 19:17:15: #1 tags after filtering in treatment: 1710195 INFO @ Sat, 15 Jan 2022 19:17:15: #1 Redundant rate of treatment: 0.53 INFO @ Sat, 15 Jan 2022 19:17:15: #1 finished! INFO @ Sat, 15 Jan 2022 19:17:15: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:17:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:17:16: #2 number of paired peaks: 184 WARNING @ Sat, 15 Jan 2022 19:17:16: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Sat, 15 Jan 2022 19:17:16: start model_add_line... INFO @ Sat, 15 Jan 2022 19:17:16: start X-correlation... INFO @ Sat, 15 Jan 2022 19:17:16: end of X-cor INFO @ Sat, 15 Jan 2022 19:17:16: #2 finished! INFO @ Sat, 15 Jan 2022 19:17:16: #2 predicted fragment length is 111 bps INFO @ Sat, 15 Jan 2022 19:17:16: #2 alternative fragment length(s) may be 0,99,111,150,232,274,476,544,558 bps INFO @ Sat, 15 Jan 2022 19:17:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.20_model.r WARNING @ Sat, 15 Jan 2022 19:17:16: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:17:16: #2 You may need to consider one of the other alternative d(s): 0,99,111,150,232,274,476,544,558 WARNING @ Sat, 15 Jan 2022 19:17:16: #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 19:17:16: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:17:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:17:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:17:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:17:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:17:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781024/SRX11781024.20_summits.bed INFO @ Sat, 15 Jan 2022 19:17:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (8 records, 4 fields): 2 millis CompletedMACS2peakCalling