Job ID = 6458421 SRX = SRX5226980 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:36:26 prefetch.2.10.7: 1) Downloading 'SRR8417895'... 2020-06-21T12:36:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:40:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:40:26 prefetch.2.10.7: 1) 'SRR8417895' was downloaded successfully 2020-06-21T12:40:26 prefetch.2.10.7: 'SRR8417895' has 0 unresolved dependencies Read 22124699 spots for SRR8417895/SRR8417895.sra Written 22124699 spots for SRR8417895/SRR8417895.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: 00:07:39 22124699 reads; of these: 22124699 (100.00%) were unpaired; of these: 915263 (4.14%) aligned 0 times 15859363 (71.68%) aligned exactly 1 time 5350073 (24.18%) aligned >1 times 95.86% overall alignment rate Time searching: 00:07:39 Overall time: 00:07:39 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 12 files... [bam_rmdupse_core] 2770105 / 21209436 = 0.1306 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 21:56:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.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 21:56:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:56:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:56:26: 1000000 INFO @ Sun, 21 Jun 2020 21:56:32: 2000000 INFO @ Sun, 21 Jun 2020 21:56:37: 3000000 INFO @ Sun, 21 Jun 2020 21:56:43: 4000000 INFO @ Sun, 21 Jun 2020 21:56:48: 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 21:56:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.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 21:56:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:56:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:56:54: 6000000 INFO @ Sun, 21 Jun 2020 21:56:58: 1000000 INFO @ Sun, 21 Jun 2020 21:57:01: 7000000 INFO @ Sun, 21 Jun 2020 21:57:05: 2000000 INFO @ Sun, 21 Jun 2020 21:57:07: 8000000 INFO @ Sun, 21 Jun 2020 21:57:12: 3000000 INFO @ Sun, 21 Jun 2020 21:57:13: 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 21:57:19: 10000000 INFO @ Sun, 21 Jun 2020 21:57:20: 4000000 INFO @ Sun, 21 Jun 2020 21:57:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.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 21:57:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:57:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:57:26: 11000000 INFO @ Sun, 21 Jun 2020 21:57:27: 1000000 INFO @ Sun, 21 Jun 2020 21:57:27: 5000000 INFO @ Sun, 21 Jun 2020 21:57:33: 12000000 INFO @ Sun, 21 Jun 2020 21:57:33: 2000000 INFO @ Sun, 21 Jun 2020 21:57:34: 6000000 INFO @ Sun, 21 Jun 2020 21:57:39: 13000000 INFO @ Sun, 21 Jun 2020 21:57:40: 3000000 INFO @ Sun, 21 Jun 2020 21:57:42: 7000000 INFO @ Sun, 21 Jun 2020 21:57:45: 14000000 INFO @ Sun, 21 Jun 2020 21:57:46: 4000000 INFO @ Sun, 21 Jun 2020 21:57:49: 8000000 INFO @ Sun, 21 Jun 2020 21:57:52: 15000000 INFO @ Sun, 21 Jun 2020 21:57:53: 5000000 INFO @ Sun, 21 Jun 2020 21:57:56: 9000000 INFO @ Sun, 21 Jun 2020 21:57:59: 16000000 INFO @ Sun, 21 Jun 2020 21:58:00: 6000000 INFO @ Sun, 21 Jun 2020 21:58:03: 10000000 INFO @ Sun, 21 Jun 2020 21:58:05: 17000000 INFO @ Sun, 21 Jun 2020 21:58:06: 7000000 INFO @ Sun, 21 Jun 2020 21:58:11: 11000000 INFO @ Sun, 21 Jun 2020 21:58:12: 18000000 INFO @ Sun, 21 Jun 2020 21:58:13: 8000000 INFO @ Sun, 21 Jun 2020 21:58:15: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:58:15: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:58:15: #1 total tags in treatment: 18439331 INFO @ Sun, 21 Jun 2020 21:58:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:58:15: #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 21:58:15: #1 tags after filtering in treatment: 18439190 INFO @ Sun, 21 Jun 2020 21:58:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:58:15: #1 finished! INFO @ Sun, 21 Jun 2020 21:58:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:58:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:58:17: #2 number of paired peaks: 852 WARNING @ Sun, 21 Jun 2020 21:58:17: Fewer paired peaks (852) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 852 pairs to build model! INFO @ Sun, 21 Jun 2020 21:58:17: start model_add_line... INFO @ Sun, 21 Jun 2020 21:58:17: start X-correlation... INFO @ Sun, 21 Jun 2020 21:58:17: end of X-cor INFO @ Sun, 21 Jun 2020 21:58:17: #2 finished! INFO @ Sun, 21 Jun 2020 21:58:17: #2 predicted fragment length is 94 bps INFO @ Sun, 21 Jun 2020 21:58:17: #2 alternative fragment length(s) may be 4,94 bps INFO @ Sun, 21 Jun 2020 21:58:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.05_model.r WARNING @ Sun, 21 Jun 2020 21:58:17: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:58:17: #2 You may need to consider one of the other alternative d(s): 4,94 WARNING @ Sun, 21 Jun 2020 21:58:17: #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 21:58:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:58:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:58:18: 12000000 INFO @ Sun, 21 Jun 2020 21:58:19: 9000000 INFO @ Sun, 21 Jun 2020 21:58:25: 13000000 INFO @ Sun, 21 Jun 2020 21:58:26: 10000000 INFO @ Sun, 21 Jun 2020 21:58:32: 11000000 INFO @ Sun, 21 Jun 2020 21:58:33: 14000000 INFO @ Sun, 21 Jun 2020 21:58:39: 12000000 INFO @ Sun, 21 Jun 2020 21:58:40: 15000000 INFO @ Sun, 21 Jun 2020 21:58:45: 13000000 INFO @ Sun, 21 Jun 2020 21:58:48: 16000000 INFO @ Sun, 21 Jun 2020 21:58:51: 14000000 INFO @ Sun, 21 Jun 2020 21:58:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:58:55: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:58:58: 15000000 INFO @ Sun, 21 Jun 2020 21:59:02: 18000000 INFO @ Sun, 21 Jun 2020 21:59:05: 16000000 INFO @ Sun, 21 Jun 2020 21:59:05: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:59:05: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:59:05: #1 total tags in treatment: 18439331 INFO @ Sun, 21 Jun 2020 21:59:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:59:05: #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 21:59:06: #1 tags after filtering in treatment: 18439190 INFO @ Sun, 21 Jun 2020 21:59:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:59:06: #1 finished! INFO @ Sun, 21 Jun 2020 21:59:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:59:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:59:07: #2 number of paired peaks: 852 WARNING @ Sun, 21 Jun 2020 21:59:07: Fewer paired peaks (852) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 852 pairs to build model! INFO @ Sun, 21 Jun 2020 21:59:07: start model_add_line... INFO @ Sun, 21 Jun 2020 21:59:07: start X-correlation... INFO @ Sun, 21 Jun 2020 21:59:07: end of X-cor INFO @ Sun, 21 Jun 2020 21:59:07: #2 finished! INFO @ Sun, 21 Jun 2020 21:59:07: #2 predicted fragment length is 94 bps INFO @ Sun, 21 Jun 2020 21:59:07: #2 alternative fragment length(s) may be 4,94 bps INFO @ Sun, 21 Jun 2020 21:59:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.10_model.r WARNING @ Sun, 21 Jun 2020 21:59:07: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:59:07: #2 You may need to consider one of the other alternative d(s): 4,94 WARNING @ Sun, 21 Jun 2020 21:59:07: #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 21:59:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:59:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:59:11: 17000000 INFO @ Sun, 21 Jun 2020 21:59:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:59:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:59:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.05_summits.bed INFO @ Sun, 21 Jun 2020 21:59:13: Done! pass1 - making usageList (458 chroms): 1 millis pass2 - checking and writing primary data (6802 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:59:16: 18000000 INFO @ Sun, 21 Jun 2020 21:59:19: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:59:19: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:59:19: #1 total tags in treatment: 18439331 INFO @ Sun, 21 Jun 2020 21:59:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:59:19: #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 21:59:20: #1 tags after filtering in treatment: 18439190 INFO @ Sun, 21 Jun 2020 21:59:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:59:20: #1 finished! INFO @ Sun, 21 Jun 2020 21:59:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:59:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:59:21: #2 number of paired peaks: 852 WARNING @ Sun, 21 Jun 2020 21:59:21: Fewer paired peaks (852) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 852 pairs to build model! INFO @ Sun, 21 Jun 2020 21:59:21: start model_add_line... INFO @ Sun, 21 Jun 2020 21:59:21: start X-correlation... INFO @ Sun, 21 Jun 2020 21:59:21: end of X-cor INFO @ Sun, 21 Jun 2020 21:59:21: #2 finished! INFO @ Sun, 21 Jun 2020 21:59:21: #2 predicted fragment length is 94 bps INFO @ Sun, 21 Jun 2020 21:59:21: #2 alternative fragment length(s) may be 4,94 bps INFO @ Sun, 21 Jun 2020 21:59:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.20_model.r WARNING @ Sun, 21 Jun 2020 21:59:21: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:59:21: #2 You may need to consider one of the other alternative d(s): 4,94 WARNING @ Sun, 21 Jun 2020 21:59:21: #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 21:59:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:59:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:59:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:00:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:00:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.10_summits.bed INFO @ Sun, 21 Jun 2020 22:00:04: Done! pass1 - making usageList (392 chroms): 1 millis pass2 - checking and writing primary data (3034 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:00:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226980/SRX5226980.20_summits.bed INFO @ Sun, 21 Jun 2020 22:00:19: Done! pass1 - making usageList (282 chroms): 1 millis pass2 - checking and writing primary data (1169 records, 4 fields): 9 millis CompletedMACS2peakCalling