Job ID = 6455432 SRX = SRX287783 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:03:10 prefetch.2.10.7: 1) Downloading 'SRR869972'... 2020-06-21T10:03:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:05:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:05:09 prefetch.2.10.7: 1) 'SRR869972' was downloaded successfully Read 18336520 spots for SRR869972/SRR869972.sra Written 18336520 spots for SRR869972/SRR869972.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: 00:05:26 18336520 reads; of these: 18336520 (100.00%) were unpaired; of these: 1109227 (6.05%) aligned 0 times 12156025 (66.29%) aligned exactly 1 time 5071268 (27.66%) aligned >1 times 93.95% overall alignment rate Time searching: 00:05:26 Overall time: 00:05:26 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] 2639333 / 17227293 = 0.1532 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 19:16:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.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 19:16:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:16:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:16:22: 1000000 INFO @ Sun, 21 Jun 2020 19:16:28: 2000000 INFO @ Sun, 21 Jun 2020 19:16:34: 3000000 INFO @ Sun, 21 Jun 2020 19:16:40: 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 @ Sun, 21 Jun 2020 19:16:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.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 19:16:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:16:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:16:46: 5000000 INFO @ Sun, 21 Jun 2020 19:16:52: 1000000 INFO @ Sun, 21 Jun 2020 19:16:53: 6000000 INFO @ Sun, 21 Jun 2020 19:16:59: 2000000 INFO @ Sun, 21 Jun 2020 19:16:59: 7000000 INFO @ Sun, 21 Jun 2020 19:17:06: 3000000 INFO @ Sun, 21 Jun 2020 19:17:06: 8000000 INFO @ Sun, 21 Jun 2020 19:17:12: 4000000 INFO @ Sun, 21 Jun 2020 19:17:12: 9000000 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 19:17:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.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 19:17:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:17:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:17:19: 10000000 INFO @ Sun, 21 Jun 2020 19:17:19: 5000000 INFO @ Sun, 21 Jun 2020 19:17:24: 1000000 INFO @ Sun, 21 Jun 2020 19:17:27: 11000000 INFO @ Sun, 21 Jun 2020 19:17:27: 6000000 INFO @ Sun, 21 Jun 2020 19:17:33: 2000000 INFO @ Sun, 21 Jun 2020 19:17:34: 7000000 INFO @ Sun, 21 Jun 2020 19:17:34: 12000000 INFO @ Sun, 21 Jun 2020 19:17:41: 3000000 INFO @ Sun, 21 Jun 2020 19:17:42: 8000000 INFO @ Sun, 21 Jun 2020 19:17:42: 13000000 INFO @ Sun, 21 Jun 2020 19:17:49: 9000000 INFO @ Sun, 21 Jun 2020 19:17:49: 14000000 INFO @ Sun, 21 Jun 2020 19:17:50: 4000000 INFO @ Sun, 21 Jun 2020 19:17:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:17:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:17:54: #1 total tags in treatment: 14587960 INFO @ Sun, 21 Jun 2020 19:17:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:17:54: #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 19:17:55: #1 tags after filtering in treatment: 14587960 INFO @ Sun, 21 Jun 2020 19:17:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:17:55: #1 finished! INFO @ Sun, 21 Jun 2020 19:17:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:17:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:17:56: #2 number of paired peaks: 359 WARNING @ Sun, 21 Jun 2020 19:17:56: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Sun, 21 Jun 2020 19:17:56: start model_add_line... INFO @ Sun, 21 Jun 2020 19:17:56: start X-correlation... INFO @ Sun, 21 Jun 2020 19:17:56: end of X-cor INFO @ Sun, 21 Jun 2020 19:17:56: #2 finished! INFO @ Sun, 21 Jun 2020 19:17:56: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 19:17:56: #2 alternative fragment length(s) may be 4,45 bps INFO @ Sun, 21 Jun 2020 19:17:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.05_model.r WARNING @ Sun, 21 Jun 2020 19:17:56: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:17:56: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Sun, 21 Jun 2020 19:17:56: #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 19:17:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:17:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:17:57: 10000000 INFO @ Sun, 21 Jun 2020 19:17:58: 5000000 INFO @ Sun, 21 Jun 2020 19:18:04: 11000000 INFO @ Sun, 21 Jun 2020 19:18:06: 6000000 INFO @ Sun, 21 Jun 2020 19:18:12: 12000000 INFO @ Sun, 21 Jun 2020 19:18:14: 7000000 INFO @ Sun, 21 Jun 2020 19:18:20: 13000000 INFO @ Sun, 21 Jun 2020 19:18:22: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:18:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:18:27: 14000000 INFO @ Sun, 21 Jun 2020 19:18:30: 9000000 INFO @ Sun, 21 Jun 2020 19:18:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:18:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:18:32: #1 total tags in treatment: 14587960 INFO @ Sun, 21 Jun 2020 19:18:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:18:32: #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 19:18:32: #1 tags after filtering in treatment: 14587960 INFO @ Sun, 21 Jun 2020 19:18:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:18:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:18:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:18:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:18:33: #2 number of paired peaks: 359 WARNING @ Sun, 21 Jun 2020 19:18:33: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Sun, 21 Jun 2020 19:18:33: start model_add_line... INFO @ Sun, 21 Jun 2020 19:18:34: start X-correlation... INFO @ Sun, 21 Jun 2020 19:18:34: end of X-cor INFO @ Sun, 21 Jun 2020 19:18:34: #2 finished! INFO @ Sun, 21 Jun 2020 19:18:34: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 19:18:34: #2 alternative fragment length(s) may be 4,45 bps INFO @ Sun, 21 Jun 2020 19:18:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.10_model.r WARNING @ Sun, 21 Jun 2020 19:18:34: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:18:34: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Sun, 21 Jun 2020 19:18:34: #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 19:18:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:18:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:18:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:18:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:18:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.05_summits.bed INFO @ Sun, 21 Jun 2020 19:18:38: Done! INFO @ Sun, 21 Jun 2020 19:18:38: 10000000 pass1 - making usageList (648 chroms): 1 millis pass2 - checking and writing primary data (2329 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:18:45: 11000000 INFO @ Sun, 21 Jun 2020 19:18:53: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:19:00: 13000000 INFO @ Sun, 21 Jun 2020 19:19:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:19:07: 14000000 INFO @ Sun, 21 Jun 2020 19:19:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:19:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:19:12: #1 total tags in treatment: 14587960 INFO @ Sun, 21 Jun 2020 19:19:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:19:12: #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 19:19:12: #1 tags after filtering in treatment: 14587960 INFO @ Sun, 21 Jun 2020 19:19:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:19:12: #1 finished! INFO @ Sun, 21 Jun 2020 19:19:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:19:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:19:13: #2 number of paired peaks: 359 WARNING @ Sun, 21 Jun 2020 19:19:13: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Sun, 21 Jun 2020 19:19:13: start model_add_line... INFO @ Sun, 21 Jun 2020 19:19:13: start X-correlation... INFO @ Sun, 21 Jun 2020 19:19:13: end of X-cor INFO @ Sun, 21 Jun 2020 19:19:13: #2 finished! INFO @ Sun, 21 Jun 2020 19:19:13: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 19:19:13: #2 alternative fragment length(s) may be 4,45 bps INFO @ Sun, 21 Jun 2020 19:19:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.20_model.r WARNING @ Sun, 21 Jun 2020 19:19:13: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:19:13: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Sun, 21 Jun 2020 19:19:13: #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 19:19:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:19:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:19:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:19:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:19:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.10_summits.bed INFO @ Sun, 21 Jun 2020 19:19:16: Done! pass1 - making usageList (504 chroms): 1 millis pass2 - checking and writing primary data (1714 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:19:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:19:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:19:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:19:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287783/SRX287783.20_summits.bed INFO @ Sun, 21 Jun 2020 19:19:55: Done! pass1 - making usageList (289 chroms): 1 millis pass2 - checking and writing primary data (569 records, 4 fields): 9 millis CompletedMACS2peakCalling