Job ID = 6508841 SRX = SRX495216 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:49:52 prefetch.2.10.7: 1) Downloading 'SRR1198721'... 2020-06-26T14:49:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:51:15 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:51:15 prefetch.2.10.7: 'SRR1198721' is valid 2020-06-26T14:51:15 prefetch.2.10.7: 1) 'SRR1198721' was downloaded successfully Read 13623353 spots for SRR1198721/SRR1198721.sra Written 13623353 spots for SRR1198721/SRR1198721.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: 00:01:53 13623353 reads; of these: 13623353 (100.00%) were unpaired; of these: 8719095 (64.00%) aligned 0 times 4423236 (32.47%) aligned exactly 1 time 481022 (3.53%) aligned >1 times 36.00% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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] 641047 / 4904258 = 0.1307 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 @ Fri, 26 Jun 2020 23:55:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.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 @ Fri, 26 Jun 2020 23:55:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:55:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:55:32: 1000000 INFO @ Fri, 26 Jun 2020 23:55:38: 2000000 INFO @ Fri, 26 Jun 2020 23:55:43: 3000000 INFO @ Fri, 26 Jun 2020 23:55:50: 4000000 INFO @ Fri, 26 Jun 2020 23:55:51: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 23:55:51: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 23:55:51: #1 total tags in treatment: 4263211 INFO @ Fri, 26 Jun 2020 23:55:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:55:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:55:52: #1 tags after filtering in treatment: 4262962 INFO @ Fri, 26 Jun 2020 23:55:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:55:52: #1 finished! INFO @ Fri, 26 Jun 2020 23:55:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:55:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:55:52: #2 number of paired peaks: 983 WARNING @ Fri, 26 Jun 2020 23:55:52: Fewer paired peaks (983) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 983 pairs to build model! INFO @ Fri, 26 Jun 2020 23:55:52: start model_add_line... INFO @ Fri, 26 Jun 2020 23:55:52: start X-correlation... INFO @ Fri, 26 Jun 2020 23:55:52: end of X-cor INFO @ Fri, 26 Jun 2020 23:55:52: #2 finished! INFO @ Fri, 26 Jun 2020 23:55:52: #2 predicted fragment length is 64 bps INFO @ Fri, 26 Jun 2020 23:55:52: #2 alternative fragment length(s) may be 3,11,35,64,563,584 bps INFO @ Fri, 26 Jun 2020 23:55:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.05_model.r WARNING @ Fri, 26 Jun 2020 23:55:52: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:55:52: #2 You may need to consider one of the other alternative d(s): 3,11,35,64,563,584 WARNING @ Fri, 26 Jun 2020 23:55:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:55:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:55:52: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 23:55:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.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 @ Fri, 26 Jun 2020 23:55:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:55:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:56:01: 1000000 INFO @ Fri, 26 Jun 2020 23:56:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:56:06: 2000000 INFO @ Fri, 26 Jun 2020 23:56:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:56:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:56:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.05_summits.bed INFO @ Fri, 26 Jun 2020 23:56:06: Done! pass1 - making usageList (60 chroms): 1 millis pass2 - checking and writing primary data (217 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:56:11: 3000000 INFO @ Fri, 26 Jun 2020 23:56:16: 4000000 INFO @ Fri, 26 Jun 2020 23:56:18: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 23:56:18: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 23:56:18: #1 total tags in treatment: 4263211 INFO @ Fri, 26 Jun 2020 23:56:18: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:56:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:56:18: #1 tags after filtering in treatment: 4262962 INFO @ Fri, 26 Jun 2020 23:56:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:56:18: #1 finished! INFO @ Fri, 26 Jun 2020 23:56:18: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:56:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:56:18: #2 number of paired peaks: 983 WARNING @ Fri, 26 Jun 2020 23:56:18: Fewer paired peaks (983) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 983 pairs to build model! INFO @ Fri, 26 Jun 2020 23:56:18: start model_add_line... INFO @ Fri, 26 Jun 2020 23:56:18: start X-correlation... INFO @ Fri, 26 Jun 2020 23:56:18: end of X-cor INFO @ Fri, 26 Jun 2020 23:56:18: #2 finished! INFO @ Fri, 26 Jun 2020 23:56:18: #2 predicted fragment length is 64 bps INFO @ Fri, 26 Jun 2020 23:56:18: #2 alternative fragment length(s) may be 3,11,35,64,563,584 bps INFO @ Fri, 26 Jun 2020 23:56:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.10_model.r WARNING @ Fri, 26 Jun 2020 23:56:18: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:56:18: #2 You may need to consider one of the other alternative d(s): 3,11,35,64,563,584 WARNING @ Fri, 26 Jun 2020 23:56:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:56:18: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:56:18: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 23:56:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.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 @ Fri, 26 Jun 2020 23:56:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:56:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:56:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:56:32: 1000000 INFO @ Fri, 26 Jun 2020 23:56:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:56:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:56:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.10_summits.bed INFO @ Fri, 26 Jun 2020 23:56:33: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (55 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:56:38: 2000000 INFO @ Fri, 26 Jun 2020 23:56:44: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:56:50: 4000000 INFO @ Fri, 26 Jun 2020 23:56:52: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 23:56:52: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 23:56:52: #1 total tags in treatment: 4263211 INFO @ Fri, 26 Jun 2020 23:56:52: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:56:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:56:52: #1 tags after filtering in treatment: 4262962 INFO @ Fri, 26 Jun 2020 23:56:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:56:52: #1 finished! INFO @ Fri, 26 Jun 2020 23:56:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:56:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:56:52: #2 number of paired peaks: 983 WARNING @ Fri, 26 Jun 2020 23:56:52: Fewer paired peaks (983) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 983 pairs to build model! INFO @ Fri, 26 Jun 2020 23:56:52: start model_add_line... INFO @ Fri, 26 Jun 2020 23:56:52: start X-correlation... INFO @ Fri, 26 Jun 2020 23:56:52: end of X-cor INFO @ Fri, 26 Jun 2020 23:56:52: #2 finished! INFO @ Fri, 26 Jun 2020 23:56:52: #2 predicted fragment length is 64 bps INFO @ Fri, 26 Jun 2020 23:56:52: #2 alternative fragment length(s) may be 3,11,35,64,563,584 bps INFO @ Fri, 26 Jun 2020 23:56:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.20_model.r WARNING @ Fri, 26 Jun 2020 23:56:52: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:56:52: #2 You may need to consider one of the other alternative d(s): 3,11,35,64,563,584 WARNING @ Fri, 26 Jun 2020 23:56:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:56:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:56:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:57:02: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:57:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:57:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:57:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495216/SRX495216.20_summits.bed INFO @ Fri, 26 Jun 2020 23:57:06: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (33 records, 4 fields): 1 millis CompletedMACS2peakCalling