Job ID = 6455308 SRX = SRX287682 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:56:55 prefetch.2.10.7: 1) Downloading 'SRR869870'... 2020-06-21T09:56:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:59:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:59:35 prefetch.2.10.7: 1) 'SRR869870' was downloaded successfully Read 16621255 spots for SRR869870/SRR869870.sra Written 16621255 spots for SRR869870/SRR869870.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: 00:04:31 16621255 reads; of these: 16621255 (100.00%) were unpaired; of these: 1117392 (6.72%) aligned 0 times 11968643 (72.01%) aligned exactly 1 time 3535220 (21.27%) aligned >1 times 93.28% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1581277 / 15503863 = 0.1020 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 19:09:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.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 19:09:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:10: 1000000 INFO @ Sun, 21 Jun 2020 19:09:15: 2000000 INFO @ Sun, 21 Jun 2020 19:09:20: 3000000 INFO @ Sun, 21 Jun 2020 19:09:26: 4000000 INFO @ Sun, 21 Jun 2020 19:09:31: 5000000 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 19:09:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.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 19:09:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:36: 6000000 INFO @ Sun, 21 Jun 2020 19:09:40: 1000000 INFO @ Sun, 21 Jun 2020 19:09:42: 7000000 INFO @ Sun, 21 Jun 2020 19:09:45: 2000000 INFO @ Sun, 21 Jun 2020 19:09:47: 8000000 INFO @ Sun, 21 Jun 2020 19:09:51: 3000000 INFO @ Sun, 21 Jun 2020 19:09:53: 9000000 INFO @ Sun, 21 Jun 2020 19:09:56: 4000000 INFO @ Sun, 21 Jun 2020 19:09:58: 10000000 INFO @ Sun, 21 Jun 2020 19:10:01: 5000000 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 19:10:04: 11000000 INFO @ Sun, 21 Jun 2020 19:10:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.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 19:10:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:10:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:10:06: 6000000 INFO @ Sun, 21 Jun 2020 19:10:09: 1000000 INFO @ Sun, 21 Jun 2020 19:10:10: 12000000 INFO @ Sun, 21 Jun 2020 19:10:11: 7000000 INFO @ Sun, 21 Jun 2020 19:10:14: 2000000 INFO @ Sun, 21 Jun 2020 19:10:15: 13000000 INFO @ Sun, 21 Jun 2020 19:10:17: 8000000 INFO @ Sun, 21 Jun 2020 19:10:18: 3000000 INFO @ Sun, 21 Jun 2020 19:10:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:10:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:10:21: #1 total tags in treatment: 13922586 INFO @ Sun, 21 Jun 2020 19:10:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:21: #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 19:10:21: #1 tags after filtering in treatment: 13922586 INFO @ Sun, 21 Jun 2020 19:10:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:22: 9000000 INFO @ Sun, 21 Jun 2020 19:10:22: #2 number of paired peaks: 257 WARNING @ Sun, 21 Jun 2020 19:10:22: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Sun, 21 Jun 2020 19:10:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:22: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:10:22: #2 alternative fragment length(s) may be 4,39 bps INFO @ Sun, 21 Jun 2020 19:10:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.05_model.r WARNING @ Sun, 21 Jun 2020 19:10:22: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:10:22: #2 You may need to consider one of the other alternative d(s): 4,39 WARNING @ Sun, 21 Jun 2020 19:10:22: #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 19:10:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:23: 4000000 INFO @ Sun, 21 Jun 2020 19:10:27: 10000000 INFO @ Sun, 21 Jun 2020 19:10:28: 5000000 INFO @ Sun, 21 Jun 2020 19:10:32: 11000000 INFO @ Sun, 21 Jun 2020 19:10:33: 6000000 INFO @ Sun, 21 Jun 2020 19:10:37: 12000000 INFO @ Sun, 21 Jun 2020 19:10:37: 7000000 INFO @ Sun, 21 Jun 2020 19:10:42: 13000000 INFO @ Sun, 21 Jun 2020 19:10:42: 8000000 INFO @ Sun, 21 Jun 2020 19:10:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:10:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:10:47: #1 total tags in treatment: 13922586 INFO @ Sun, 21 Jun 2020 19:10:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:47: #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 19:10:47: 9000000 INFO @ Sun, 21 Jun 2020 19:10:47: #1 tags after filtering in treatment: 13922586 INFO @ Sun, 21 Jun 2020 19:10:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:47: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:48: #2 number of paired peaks: 257 WARNING @ Sun, 21 Jun 2020 19:10:48: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Sun, 21 Jun 2020 19:10:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:48: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:48: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:48: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:48: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:10:48: #2 alternative fragment length(s) may be 4,39 bps INFO @ Sun, 21 Jun 2020 19:10:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.10_model.r WARNING @ Sun, 21 Jun 2020 19:10:48: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:10:48: #2 You may need to consider one of the other alternative d(s): 4,39 WARNING @ Sun, 21 Jun 2020 19:10:48: #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 19:10:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:52: 10000000 INFO @ Sun, 21 Jun 2020 19:10:56: 11000000 INFO @ Sun, 21 Jun 2020 19:11:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.05_summits.bed INFO @ Sun, 21 Jun 2020 19:11:00: Done! pass1 - making usageList (497 chroms): 1 millis pass2 - checking and writing primary data (2086 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:11:01: 12000000 INFO @ Sun, 21 Jun 2020 19:11:06: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:11:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:11:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:11:11: #1 total tags in treatment: 13922586 INFO @ Sun, 21 Jun 2020 19:11:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:11:11: #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 19:11:11: #1 tags after filtering in treatment: 13922586 INFO @ Sun, 21 Jun 2020 19:11:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:11:11: #1 finished! INFO @ Sun, 21 Jun 2020 19:11:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:11:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:11:12: #2 number of paired peaks: 257 WARNING @ Sun, 21 Jun 2020 19:11:12: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Sun, 21 Jun 2020 19:11:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:11:12: start X-correlation... INFO @ Sun, 21 Jun 2020 19:11:12: end of X-cor INFO @ Sun, 21 Jun 2020 19:11:12: #2 finished! INFO @ Sun, 21 Jun 2020 19:11:12: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:11:12: #2 alternative fragment length(s) may be 4,39 bps INFO @ Sun, 21 Jun 2020 19:11:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.20_model.r WARNING @ Sun, 21 Jun 2020 19:11:12: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:11:12: #2 You may need to consider one of the other alternative d(s): 4,39 WARNING @ Sun, 21 Jun 2020 19:11:12: #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 19:11:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:11:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:11:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:11:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.10_summits.bed INFO @ Sun, 21 Jun 2020 19:11:28: Done! pass1 - making usageList (352 chroms): 1 millis pass2 - checking and writing primary data (893 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:11:39: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:11:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287682/SRX287682.20_summits.bed INFO @ Sun, 21 Jun 2020 19:11:51: Done! pass1 - making usageList (167 chroms): 0 millis pass2 - checking and writing primary data (370 records, 4 fields): 6 millis CompletedMACS2peakCalling