Job ID = 6453461 SRX = SRX1158167 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:25:42 prefetch.2.10.7: 1) Downloading 'SRR2173466'... 2020-06-21T08:25:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:29:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:29:46 prefetch.2.10.7: 1) 'SRR2173466' was downloaded successfully Read 8989038 spots for SRR2173466/SRR2173466.sra Written 8989038 spots for SRR2173466/SRR2173466.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: 00:04:00 8989038 reads; of these: 8989038 (100.00%) were unpaired; of these: 2391183 (26.60%) aligned 0 times 4907163 (54.59%) aligned exactly 1 time 1690692 (18.81%) aligned >1 times 73.40% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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] 2361086 / 6597855 = 0.3579 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 17:37:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.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 17:37:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:37:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:37:11: 1000000 INFO @ Sun, 21 Jun 2020 17:37:21: 2000000 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 17:37:30: 3000000 INFO @ Sun, 21 Jun 2020 17:37:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.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 17:37:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:37:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:37:41: 4000000 INFO @ Sun, 21 Jun 2020 17:37:42: 1000000 INFO @ Sun, 21 Jun 2020 17:37:43: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 17:37:43: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 17:37:43: #1 total tags in treatment: 4236769 INFO @ Sun, 21 Jun 2020 17:37:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:37:43: #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 17:37:44: #1 tags after filtering in treatment: 4236511 INFO @ Sun, 21 Jun 2020 17:37:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:37:44: #1 finished! INFO @ Sun, 21 Jun 2020 17:37:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:37:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:37:44: #2 number of paired peaks: 3470 INFO @ Sun, 21 Jun 2020 17:37:44: start model_add_line... INFO @ Sun, 21 Jun 2020 17:37:44: start X-correlation... INFO @ Sun, 21 Jun 2020 17:37:44: end of X-cor INFO @ Sun, 21 Jun 2020 17:37:44: #2 finished! INFO @ Sun, 21 Jun 2020 17:37:44: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 17:37:44: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sun, 21 Jun 2020 17:37:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.05_model.r WARNING @ Sun, 21 Jun 2020 17:37:44: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:37:44: #2 You may need to consider one of the other alternative d(s): 4,148 WARNING @ Sun, 21 Jun 2020 17:37:44: #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 17:37:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:37:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:37:51: 2000000 INFO @ Sun, 21 Jun 2020 17:37:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:37:59: 3000000 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 17:38:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:38:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:38:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.05_summits.bed INFO @ Sun, 21 Jun 2020 17:38:01: Done! pass1 - making usageList (431 chroms): 2 millis pass2 - checking and writing primary data (4667 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:38:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.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 17:38:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:38:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:38:07: 4000000 INFO @ Sun, 21 Jun 2020 17:38:10: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 17:38:10: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 17:38:10: #1 total tags in treatment: 4236769 INFO @ Sun, 21 Jun 2020 17:38:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:38:10: #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 17:38:10: #1 tags after filtering in treatment: 4236511 INFO @ Sun, 21 Jun 2020 17:38:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:38:10: #1 finished! INFO @ Sun, 21 Jun 2020 17:38:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:38:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:38:10: #2 number of paired peaks: 3470 INFO @ Sun, 21 Jun 2020 17:38:10: start model_add_line... INFO @ Sun, 21 Jun 2020 17:38:10: start X-correlation... INFO @ Sun, 21 Jun 2020 17:38:10: end of X-cor INFO @ Sun, 21 Jun 2020 17:38:10: #2 finished! INFO @ Sun, 21 Jun 2020 17:38:10: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 17:38:10: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sun, 21 Jun 2020 17:38:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.10_model.r WARNING @ Sun, 21 Jun 2020 17:38:10: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:38:10: #2 You may need to consider one of the other alternative d(s): 4,148 WARNING @ Sun, 21 Jun 2020 17:38:10: #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 17:38:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:38:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:38:11: 1000000 INFO @ Sun, 21 Jun 2020 17:38:19: 2000000 INFO @ Sun, 21 Jun 2020 17:38:21: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:38:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:38:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:38:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.10_summits.bed INFO @ Sun, 21 Jun 2020 17:38:26: Done! pass1 - making usageList (287 chroms): 3 millis pass2 - checking and writing primary data (1749 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:38:27: 3000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:38:35: 4000000 INFO @ Sun, 21 Jun 2020 17:38:37: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 17:38:37: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 17:38:37: #1 total tags in treatment: 4236769 INFO @ Sun, 21 Jun 2020 17:38:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:38:37: #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 17:38:37: #1 tags after filtering in treatment: 4236511 INFO @ Sun, 21 Jun 2020 17:38:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:38:37: #1 finished! INFO @ Sun, 21 Jun 2020 17:38:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:38:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:38:37: #2 number of paired peaks: 3470 INFO @ Sun, 21 Jun 2020 17:38:37: start model_add_line... INFO @ Sun, 21 Jun 2020 17:38:37: start X-correlation... INFO @ Sun, 21 Jun 2020 17:38:37: end of X-cor INFO @ Sun, 21 Jun 2020 17:38:37: #2 finished! INFO @ Sun, 21 Jun 2020 17:38:37: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 17:38:37: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sun, 21 Jun 2020 17:38:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.20_model.r WARNING @ Sun, 21 Jun 2020 17:38:37: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:38:37: #2 You may need to consider one of the other alternative d(s): 4,148 WARNING @ Sun, 21 Jun 2020 17:38:37: #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 17:38:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:38:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:38:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:38:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:38:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:38:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1158167/SRX1158167.20_summits.bed INFO @ Sun, 21 Jun 2020 17:38:53: Done! pass1 - making usageList (137 chroms): 1 millis pass2 - checking and writing primary data (425 records, 4 fields): 6 millis CompletedMACS2peakCalling