Job ID = 6508739 SRX = SRX467061 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:08:00 prefetch.2.10.7: 1) Downloading 'SRR1164485'... 2020-06-26T15:08:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:09:12 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:09:13 prefetch.2.10.7: 'SRR1164485' is valid 2020-06-26T15:09:13 prefetch.2.10.7: 1) 'SRR1164485' was downloaded successfully Read 10522386 spots for SRR1164485/SRR1164485.sra Written 10522386 spots for SRR1164485/SRR1164485.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:19 10522386 reads; of these: 10522386 (100.00%) were unpaired; of these: 721547 (6.86%) aligned 0 times 6145768 (58.41%) aligned exactly 1 time 3655071 (34.74%) aligned >1 times 93.14% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 2970263 / 9800839 = 0.3031 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 27 Jun 2020 00:16:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 27 Jun 2020 00:16:38: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:16:38: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:16:44: 1000000 INFO @ Sat, 27 Jun 2020 00:16:50: 2000000 INFO @ Sat, 27 Jun 2020 00:16:55: 3000000 INFO @ Sat, 27 Jun 2020 00:17:01: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 27 Jun 2020 00:17:07: 5000000 INFO @ Sat, 27 Jun 2020 00:17:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 27 Jun 2020 00:17:08: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:17:08: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:17:14: 6000000 INFO @ Sat, 27 Jun 2020 00:17:14: 1000000 INFO @ Sat, 27 Jun 2020 00:17:19: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:17:19: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:17:19: #1 total tags in treatment: 6830576 INFO @ Sat, 27 Jun 2020 00:17:19: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:17:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:17:19: #1 tags after filtering in treatment: 6830519 INFO @ Sat, 27 Jun 2020 00:17:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:17:19: #1 finished! INFO @ Sat, 27 Jun 2020 00:17:19: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:17:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:17:20: #2 number of paired peaks: 979 WARNING @ Sat, 27 Jun 2020 00:17:20: Fewer paired peaks (979) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 979 pairs to build model! INFO @ Sat, 27 Jun 2020 00:17:20: start model_add_line... INFO @ Sat, 27 Jun 2020 00:17:20: start X-correlation... INFO @ Sat, 27 Jun 2020 00:17:20: end of X-cor INFO @ Sat, 27 Jun 2020 00:17:20: #2 finished! INFO @ Sat, 27 Jun 2020 00:17:20: #2 predicted fragment length is 32 bps INFO @ Sat, 27 Jun 2020 00:17:20: #2 alternative fragment length(s) may be 3,13,32,48,567 bps INFO @ Sat, 27 Jun 2020 00:17:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.05_model.r WARNING @ Sat, 27 Jun 2020 00:17:20: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:17:20: #2 You may need to consider one of the other alternative d(s): 3,13,32,48,567 WARNING @ Sat, 27 Jun 2020 00:17:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:17:20: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:17:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:17:20: 2000000 INFO @ Sat, 27 Jun 2020 00:17:27: 3000000 INFO @ Sat, 27 Jun 2020 00:17:33: 4000000 INFO @ Sat, 27 Jun 2020 00:17:35: #3 Call peaks for each chromosome... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 27 Jun 2020 00:17:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 27 Jun 2020 00:17:38: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:17:38: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:17:39: 5000000 INFO @ Sat, 27 Jun 2020 00:17:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:17:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:17:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.05_summits.bed INFO @ Sat, 27 Jun 2020 00:17:42: Done! pass1 - making usageList (484 chroms): 2 millis pass2 - checking and writing primary data (2189 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:17:44: 1000000 INFO @ Sat, 27 Jun 2020 00:17:45: 6000000 INFO @ Sat, 27 Jun 2020 00:17:50: 2000000 INFO @ Sat, 27 Jun 2020 00:17:51: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:17:51: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:17:51: #1 total tags in treatment: 6830576 INFO @ Sat, 27 Jun 2020 00:17:51: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:17:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:17:51: #1 tags after filtering in treatment: 6830519 INFO @ Sat, 27 Jun 2020 00:17:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:17:51: #1 finished! INFO @ Sat, 27 Jun 2020 00:17:51: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:17:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:17:52: #2 number of paired peaks: 979 WARNING @ Sat, 27 Jun 2020 00:17:52: Fewer paired peaks (979) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 979 pairs to build model! INFO @ Sat, 27 Jun 2020 00:17:52: start model_add_line... INFO @ Sat, 27 Jun 2020 00:17:52: start X-correlation... INFO @ Sat, 27 Jun 2020 00:17:52: end of X-cor INFO @ Sat, 27 Jun 2020 00:17:52: #2 finished! INFO @ Sat, 27 Jun 2020 00:17:52: #2 predicted fragment length is 32 bps INFO @ Sat, 27 Jun 2020 00:17:52: #2 alternative fragment length(s) may be 3,13,32,48,567 bps INFO @ Sat, 27 Jun 2020 00:17:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.10_model.r WARNING @ Sat, 27 Jun 2020 00:17:52: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:17:52: #2 You may need to consider one of the other alternative d(s): 3,13,32,48,567 WARNING @ Sat, 27 Jun 2020 00:17:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:17:52: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:17:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:17:56: 3000000 INFO @ Sat, 27 Jun 2020 00:18:02: 4000000 INFO @ Sat, 27 Jun 2020 00:18:06: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:18:08: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:18:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:18:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:18:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.10_summits.bed INFO @ Sat, 27 Jun 2020 00:18:14: Done! pass1 - making usageList (395 chroms): 1 millis pass2 - checking and writing primary data (1528 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:18:14: 6000000 INFO @ Sat, 27 Jun 2020 00:18:19: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:18:19: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:18:19: #1 total tags in treatment: 6830576 INFO @ Sat, 27 Jun 2020 00:18:19: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:18:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:18:20: #1 tags after filtering in treatment: 6830519 INFO @ Sat, 27 Jun 2020 00:18:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:18:20: #1 finished! INFO @ Sat, 27 Jun 2020 00:18:20: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:18:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:18:20: #2 number of paired peaks: 979 WARNING @ Sat, 27 Jun 2020 00:18:20: Fewer paired peaks (979) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 979 pairs to build model! INFO @ Sat, 27 Jun 2020 00:18:20: start model_add_line... INFO @ Sat, 27 Jun 2020 00:18:20: start X-correlation... INFO @ Sat, 27 Jun 2020 00:18:20: end of X-cor INFO @ Sat, 27 Jun 2020 00:18:20: #2 finished! INFO @ Sat, 27 Jun 2020 00:18:20: #2 predicted fragment length is 32 bps INFO @ Sat, 27 Jun 2020 00:18:20: #2 alternative fragment length(s) may be 3,13,32,48,567 bps INFO @ Sat, 27 Jun 2020 00:18:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.20_model.r WARNING @ Sat, 27 Jun 2020 00:18:20: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:18:20: #2 You may need to consider one of the other alternative d(s): 3,13,32,48,567 WARNING @ Sat, 27 Jun 2020 00:18:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:18:20: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:18:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:18:35: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:18:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:18:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:18:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467061/SRX467061.20_summits.bed INFO @ Sat, 27 Jun 2020 00:18:42: Done! pass1 - making usageList (141 chroms): 1 millis pass2 - checking and writing primary data (235 records, 4 fields): 6 millis CompletedMACS2peakCalling