Job ID = 14521839 SRX = ERX4439552 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2544641 spots for ERR4501481/ERR4501481.sra Written 2544641 spots for ERR4501481/ERR4501481.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: 00:02:42 2544641 reads; of these: 2544641 (100.00%) were paired; of these: 1381288 (54.28%) aligned concordantly 0 times 882804 (34.69%) aligned concordantly exactly 1 time 280549 (11.03%) aligned concordantly >1 times ---- 1381288 pairs aligned concordantly 0 times; of these: 243419 (17.62%) aligned discordantly 1 time ---- 1137869 pairs aligned 0 times concordantly or discordantly; of these: 2275738 mates make up the pairs; of these: 1807429 (79.42%) aligned 0 times 192644 (8.47%) aligned exactly 1 time 275665 (12.11%) aligned >1 times 64.49% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 133739 / 1378344 = 0.0970 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 21:48:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.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 21:48:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:48:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:48:09: 1000000 INFO @ Sat, 15 Jan 2022 21:48:17: 2000000 INFO @ Sat, 15 Jan 2022 21:48:26: 3000000 INFO @ Sat, 15 Jan 2022 21:48:26: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:48:26: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:48:26: #1 total tags in treatment: 1058948 INFO @ Sat, 15 Jan 2022 21:48:26: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:48:26: #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 21:48:26: #1 tags after filtering in treatment: 697166 INFO @ Sat, 15 Jan 2022 21:48:26: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 21:48:26: #1 finished! INFO @ Sat, 15 Jan 2022 21:48:26: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:48:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:48:26: #2 number of paired peaks: 531 WARNING @ Sat, 15 Jan 2022 21:48:26: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Sat, 15 Jan 2022 21:48:26: start model_add_line... INFO @ Sat, 15 Jan 2022 21:48:26: start X-correlation... INFO @ Sat, 15 Jan 2022 21:48:26: end of X-cor INFO @ Sat, 15 Jan 2022 21:48:26: #2 finished! INFO @ Sat, 15 Jan 2022 21:48:26: #2 predicted fragment length is 149 bps INFO @ Sat, 15 Jan 2022 21:48:26: #2 alternative fragment length(s) may be 149 bps INFO @ Sat, 15 Jan 2022 21:48:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.05_model.r WARNING @ Sat, 15 Jan 2022 21:48:26: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:48:26: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Sat, 15 Jan 2022 21:48:26: #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 21:48:26: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:48:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:48:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:48:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:48:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:48:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.05_summits.bed INFO @ Sat, 15 Jan 2022 21:48:29: 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 (865 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:48:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.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 21:48:31: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:48:31: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:48:39: 1000000 INFO @ Sat, 15 Jan 2022 21:48:45: 2000000 INFO @ Sat, 15 Jan 2022 21:48:52: 3000000 INFO @ Sat, 15 Jan 2022 21:48:52: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:48:52: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:48:52: #1 total tags in treatment: 1058948 INFO @ Sat, 15 Jan 2022 21:48:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:48:52: #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 21:48:52: #1 tags after filtering in treatment: 697166 INFO @ Sat, 15 Jan 2022 21:48:52: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 21:48:52: #1 finished! INFO @ Sat, 15 Jan 2022 21:48:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:48:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:48:52: #2 number of paired peaks: 531 WARNING @ Sat, 15 Jan 2022 21:48:52: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Sat, 15 Jan 2022 21:48:52: start model_add_line... INFO @ Sat, 15 Jan 2022 21:48:52: start X-correlation... INFO @ Sat, 15 Jan 2022 21:48:52: end of X-cor INFO @ Sat, 15 Jan 2022 21:48:52: #2 finished! INFO @ Sat, 15 Jan 2022 21:48:52: #2 predicted fragment length is 149 bps INFO @ Sat, 15 Jan 2022 21:48:52: #2 alternative fragment length(s) may be 149 bps INFO @ Sat, 15 Jan 2022 21:48:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.10_model.r WARNING @ Sat, 15 Jan 2022 21:48:52: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:48:52: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Sat, 15 Jan 2022 21:48:52: #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 21:48:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:48:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:48:55: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:48:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:48:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:48:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.10_summits.bed INFO @ Sat, 15 Jan 2022 21:48:55: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (704 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 21:49:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.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 21:49:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:49:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:49:07: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:49:15: 2000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:49:21: 3000000 INFO @ Sat, 15 Jan 2022 21:49:21: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:49:21: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:49:21: #1 total tags in treatment: 1058948 INFO @ Sat, 15 Jan 2022 21:49:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:49:21: #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 21:49:21: #1 tags after filtering in treatment: 697166 INFO @ Sat, 15 Jan 2022 21:49:21: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 21:49:21: #1 finished! INFO @ Sat, 15 Jan 2022 21:49:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:49:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:49:21: #2 number of paired peaks: 531 WARNING @ Sat, 15 Jan 2022 21:49:21: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Sat, 15 Jan 2022 21:49:21: start model_add_line... INFO @ Sat, 15 Jan 2022 21:49:21: start X-correlation... INFO @ Sat, 15 Jan 2022 21:49:21: end of X-cor INFO @ Sat, 15 Jan 2022 21:49:21: #2 finished! INFO @ Sat, 15 Jan 2022 21:49:21: #2 predicted fragment length is 149 bps INFO @ Sat, 15 Jan 2022 21:49:21: #2 alternative fragment length(s) may be 149 bps INFO @ Sat, 15 Jan 2022 21:49:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.20_model.r WARNING @ Sat, 15 Jan 2022 21:49:21: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:49:21: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Sat, 15 Jan 2022 21:49:21: #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 21:49:21: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:49:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:49:23: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:49:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:49:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:49:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439552/ERX4439552.20_summits.bed INFO @ Sat, 15 Jan 2022 21:49:24: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (569 records, 4 fields): 2 millis CompletedMACS2peakCalling