Job ID = 6459014 SRX = SRX5931376 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:01:04 prefetch.2.10.7: 1) Downloading 'SRR9158298'... 2020-06-21T13:01:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:05:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:05:14 prefetch.2.10.7: 'SRR9158298' is valid 2020-06-21T13:05:14 prefetch.2.10.7: 1) 'SRR9158298' was downloaded successfully 2020-06-21T13:05:14 prefetch.2.10.7: 'SRR9158298' has 0 unresolved dependencies Read 3661038 spots for SRR9158298/SRR9158298.sra Written 3661038 spots for SRR9158298/SRR9158298.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: 00:03:24 3661038 reads; of these: 3661038 (100.00%) were unpaired; of these: 826224 (22.57%) aligned 0 times 2067509 (56.47%) aligned exactly 1 time 767305 (20.96%) aligned >1 times 77.43% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 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] 136284 / 2834814 = 0.0481 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 @ Sun, 21 Jun 2020 22:10:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.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 @ Sun, 21 Jun 2020 22:10:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:10:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:10:58: 1000000 INFO @ Sun, 21 Jun 2020 22:11:05: 2000000 INFO @ Sun, 21 Jun 2020 22:11:11: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 22:11:11: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 22:11:11: #1 total tags in treatment: 2698530 INFO @ Sun, 21 Jun 2020 22:11:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:11:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:11:11: #1 tags after filtering in treatment: 2698251 INFO @ Sun, 21 Jun 2020 22:11:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:11:11: #1 finished! INFO @ Sun, 21 Jun 2020 22:11:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:11:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:11:11: #2 number of paired peaks: 963 WARNING @ Sun, 21 Jun 2020 22:11:11: Fewer paired peaks (963) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 963 pairs to build model! INFO @ Sun, 21 Jun 2020 22:11:11: start model_add_line... INFO @ Sun, 21 Jun 2020 22:11:11: start X-correlation... INFO @ Sun, 21 Jun 2020 22:11:11: end of X-cor INFO @ Sun, 21 Jun 2020 22:11:11: #2 finished! INFO @ Sun, 21 Jun 2020 22:11:11: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 22:11:11: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 22:11:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.05_model.r WARNING @ Sun, 21 Jun 2020 22:11:11: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:11:11: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Sun, 21 Jun 2020 22:11:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:11:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:11:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:11:18: #3 Call peaks for each chromosome... 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 @ Sun, 21 Jun 2020 22:11:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.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 @ Sun, 21 Jun 2020 22:11:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:11:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:11:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:11:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:11:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.05_summits.bed INFO @ Sun, 21 Jun 2020 22:11:21: Done! pass1 - making usageList (518 chroms): 1 millis pass2 - checking and writing primary data (1105 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:11:27: 1000000 INFO @ Sun, 21 Jun 2020 22:11:35: 2000000 INFO @ Sun, 21 Jun 2020 22:11:40: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 22:11:40: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 22:11:40: #1 total tags in treatment: 2698530 INFO @ Sun, 21 Jun 2020 22:11:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:11:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:11:40: #1 tags after filtering in treatment: 2698251 INFO @ Sun, 21 Jun 2020 22:11:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:11:40: #1 finished! INFO @ Sun, 21 Jun 2020 22:11:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:11:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:11:41: #2 number of paired peaks: 963 WARNING @ Sun, 21 Jun 2020 22:11:41: Fewer paired peaks (963) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 963 pairs to build model! INFO @ Sun, 21 Jun 2020 22:11:41: start model_add_line... INFO @ Sun, 21 Jun 2020 22:11:41: start X-correlation... INFO @ Sun, 21 Jun 2020 22:11:41: end of X-cor INFO @ Sun, 21 Jun 2020 22:11:41: #2 finished! INFO @ Sun, 21 Jun 2020 22:11:41: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 22:11:41: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 22:11:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.10_model.r WARNING @ Sun, 21 Jun 2020 22:11:41: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:11:41: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Sun, 21 Jun 2020 22:11:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:11:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:11:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:11:48: #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 @ Sun, 21 Jun 2020 22:11:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.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 @ Sun, 21 Jun 2020 22:11:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:11:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:11:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:11:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:11:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.10_summits.bed INFO @ Sun, 21 Jun 2020 22:11:51: Done! pass1 - making usageList (436 chroms): 1 millis pass2 - checking and writing primary data (773 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:11:58: 1000000 INFO @ Sun, 21 Jun 2020 22:12:06: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:12:12: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 22:12:12: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 22:12:12: #1 total tags in treatment: 2698530 INFO @ Sun, 21 Jun 2020 22:12:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:12:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:12:12: #1 tags after filtering in treatment: 2698251 INFO @ Sun, 21 Jun 2020 22:12:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:12:12: #1 finished! INFO @ Sun, 21 Jun 2020 22:12:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:12:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:12:12: #2 number of paired peaks: 963 WARNING @ Sun, 21 Jun 2020 22:12:12: Fewer paired peaks (963) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 963 pairs to build model! INFO @ Sun, 21 Jun 2020 22:12:12: start model_add_line... INFO @ Sun, 21 Jun 2020 22:12:12: start X-correlation... INFO @ Sun, 21 Jun 2020 22:12:12: end of X-cor INFO @ Sun, 21 Jun 2020 22:12:12: #2 finished! INFO @ Sun, 21 Jun 2020 22:12:12: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 22:12:12: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 22:12:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.20_model.r WARNING @ Sun, 21 Jun 2020 22:12:12: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:12:12: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Sun, 21 Jun 2020 22:12:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:12:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:12:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:12:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:12:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:12:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:12:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5931376/SRX5931376.20_summits.bed INFO @ Sun, 21 Jun 2020 22:12:23: Done! pass1 - making usageList (311 chroms): 1 millis pass2 - checking and writing primary data (470 records, 4 fields): 10 millis CompletedMACS2peakCalling