Job ID = 14521167 SRX = SRX10468508 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4335327 spots for SRR14094819/SRR14094819.sra Written 4335327 spots for SRR14094819/SRR14094819.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: 00:02:11 4335327 reads; of these: 4335327 (100.00%) were paired; of these: 853000 (19.68%) aligned concordantly 0 times 3137840 (72.38%) aligned concordantly exactly 1 time 344487 (7.95%) aligned concordantly >1 times ---- 853000 pairs aligned concordantly 0 times; of these: 48421 (5.68%) aligned discordantly 1 time ---- 804579 pairs aligned 0 times concordantly or discordantly; of these: 1609158 mates make up the pairs; of these: 1506474 (93.62%) aligned 0 times 81278 (5.05%) aligned exactly 1 time 21406 (1.33%) aligned >1 times 82.63% overall alignment rate Time searching: 00:02:11 Overall time: 00:02:11 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_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] 105449 / 3497755 = 0.0301 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 20:37:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.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 20:37:32: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:37:32: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:37:37: 1000000 INFO @ Sat, 15 Jan 2022 20:37:43: 2000000 INFO @ Sat, 15 Jan 2022 20:37:48: 3000000 INFO @ Sat, 15 Jan 2022 20:37:53: 4000000 INFO @ Sat, 15 Jan 2022 20:37:58: 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 20:38:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.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 20:38:02: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:38:02: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:38:03: 6000000 INFO @ Sat, 15 Jan 2022 20:38:08: 1000000 INFO @ Sat, 15 Jan 2022 20:38:08: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:38:08: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:38:08: #1 total tags in treatment: 3377113 INFO @ Sat, 15 Jan 2022 20:38:08: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:38:08: #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 20:38:08: #1 tags after filtering in treatment: 2812796 INFO @ Sat, 15 Jan 2022 20:38:08: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 15 Jan 2022 20:38:08: #1 finished! INFO @ Sat, 15 Jan 2022 20:38:08: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:38:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:38:08: #2 number of paired peaks: 158 WARNING @ Sat, 15 Jan 2022 20:38:08: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 15 Jan 2022 20:38:08: start model_add_line... INFO @ Sat, 15 Jan 2022 20:38:08: start X-correlation... INFO @ Sat, 15 Jan 2022 20:38:08: end of X-cor INFO @ Sat, 15 Jan 2022 20:38:08: #2 finished! INFO @ Sat, 15 Jan 2022 20:38:08: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 20:38:08: #2 alternative fragment length(s) may be 3,35 bps INFO @ Sat, 15 Jan 2022 20:38:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.05_model.r WARNING @ Sat, 15 Jan 2022 20:38:08: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:38:08: #2 You may need to consider one of the other alternative d(s): 3,35 WARNING @ Sat, 15 Jan 2022 20:38:08: #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 20:38:08: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:38:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:38:12: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:38:13: 2000000 INFO @ Sat, 15 Jan 2022 20:38:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:38:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:38:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.05_summits.bed INFO @ Sat, 15 Jan 2022 20:38:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:38:18: 3000000 INFO @ Sat, 15 Jan 2022 20:38:23: 4000000 INFO @ Sat, 15 Jan 2022 20:38:28: 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 20:38:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.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 20:38:32: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:38:32: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:38:33: 6000000 INFO @ Sat, 15 Jan 2022 20:38:37: 1000000 INFO @ Sat, 15 Jan 2022 20:38:38: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:38:38: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:38:38: #1 total tags in treatment: 3377113 INFO @ Sat, 15 Jan 2022 20:38:38: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:38:38: #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 20:38:38: #1 tags after filtering in treatment: 2812796 INFO @ Sat, 15 Jan 2022 20:38:38: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 15 Jan 2022 20:38:38: #1 finished! INFO @ Sat, 15 Jan 2022 20:38:38: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:38:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:38:38: #2 number of paired peaks: 158 WARNING @ Sat, 15 Jan 2022 20:38:38: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 15 Jan 2022 20:38:38: start model_add_line... INFO @ Sat, 15 Jan 2022 20:38:38: start X-correlation... INFO @ Sat, 15 Jan 2022 20:38:38: end of X-cor INFO @ Sat, 15 Jan 2022 20:38:38: #2 finished! INFO @ Sat, 15 Jan 2022 20:38:38: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 20:38:38: #2 alternative fragment length(s) may be 3,35 bps INFO @ Sat, 15 Jan 2022 20:38:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.10_model.r WARNING @ Sat, 15 Jan 2022 20:38:38: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:38:38: #2 You may need to consider one of the other alternative d(s): 3,35 WARNING @ Sat, 15 Jan 2022 20:38:38: #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 20:38:38: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:38:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:38:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:38:42: 2000000 INFO @ Sat, 15 Jan 2022 20:38:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:38:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:38:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.10_summits.bed INFO @ Sat, 15 Jan 2022 20:38:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:38:48: 3000000 INFO @ Sat, 15 Jan 2022 20:38:52: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:38:57: 5000000 INFO @ Sat, 15 Jan 2022 20:39:02: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:39:06: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:39:06: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:39:06: #1 total tags in treatment: 3377113 INFO @ Sat, 15 Jan 2022 20:39:06: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:39:06: #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 20:39:06: #1 tags after filtering in treatment: 2812796 INFO @ Sat, 15 Jan 2022 20:39:06: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 15 Jan 2022 20:39:06: #1 finished! INFO @ Sat, 15 Jan 2022 20:39:06: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:39:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:39:06: #2 number of paired peaks: 158 WARNING @ Sat, 15 Jan 2022 20:39:06: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 15 Jan 2022 20:39:06: start model_add_line... INFO @ Sat, 15 Jan 2022 20:39:06: start X-correlation... INFO @ Sat, 15 Jan 2022 20:39:07: end of X-cor INFO @ Sat, 15 Jan 2022 20:39:07: #2 finished! INFO @ Sat, 15 Jan 2022 20:39:07: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 20:39:07: #2 alternative fragment length(s) may be 3,35 bps INFO @ Sat, 15 Jan 2022 20:39:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.20_model.r WARNING @ Sat, 15 Jan 2022 20:39:07: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:39:07: #2 You may need to consider one of the other alternative d(s): 3,35 WARNING @ Sat, 15 Jan 2022 20:39:07: #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 20:39:07: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:39:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:39:11: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:39:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:39:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:39:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468508/SRX10468508.20_summits.bed INFO @ Sat, 15 Jan 2022 20:39:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling