Job ID = 6458942 SRX = SRX5775942 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:50:26 prefetch.2.10.7: 1) Downloading 'SRR8997145'... 2020-06-21T12:50:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:52:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:52:21 prefetch.2.10.7: 'SRR8997145' is valid 2020-06-21T12:52:21 prefetch.2.10.7: 1) 'SRR8997145' was downloaded successfully 2020-06-21T12:52:21 prefetch.2.10.7: 'SRR8997145' has 0 unresolved dependencies Read 9426294 spots for SRR8997145/SRR8997145.sra Written 9426294 spots for SRR8997145/SRR8997145.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: 00:03:30 9426294 reads; of these: 9426294 (100.00%) were unpaired; of these: 361541 (3.84%) aligned 0 times 6384716 (67.73%) aligned exactly 1 time 2680037 (28.43%) aligned >1 times 96.16% overall alignment rate Time searching: 00:03:30 Overall time: 00:03:30 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] 1351993 / 9064753 = 0.1491 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 21:59:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.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 21:59:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:17: 1000000 INFO @ Sun, 21 Jun 2020 21:59:23: 2000000 INFO @ Sun, 21 Jun 2020 21:59:29: 3000000 INFO @ Sun, 21 Jun 2020 21:59:36: 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 21:59:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.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 21:59:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:42: 5000000 INFO @ Sun, 21 Jun 2020 21:59:46: 1000000 INFO @ Sun, 21 Jun 2020 21:59:48: 6000000 INFO @ Sun, 21 Jun 2020 21:59:52: 2000000 INFO @ Sun, 21 Jun 2020 21:59:55: 7000000 INFO @ Sun, 21 Jun 2020 21:59:57: 3000000 INFO @ Sun, 21 Jun 2020 22:00:00: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:00:00: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:00:00: #1 total tags in treatment: 7712760 INFO @ Sun, 21 Jun 2020 22:00:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:00:00: #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 22:00:00: #1 tags after filtering in treatment: 7712758 INFO @ Sun, 21 Jun 2020 22:00:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:00:00: #1 finished! INFO @ Sun, 21 Jun 2020 22:00:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:00:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:00:01: #2 number of paired peaks: 860 WARNING @ Sun, 21 Jun 2020 22:00:01: Fewer paired peaks (860) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 860 pairs to build model! INFO @ Sun, 21 Jun 2020 22:00:01: start model_add_line... INFO @ Sun, 21 Jun 2020 22:00:01: start X-correlation... INFO @ Sun, 21 Jun 2020 22:00:01: end of X-cor INFO @ Sun, 21 Jun 2020 22:00:01: #2 finished! INFO @ Sun, 21 Jun 2020 22:00:01: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 22:00:01: #2 alternative fragment length(s) may be 71 bps INFO @ Sun, 21 Jun 2020 22:00:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.05_model.r WARNING @ Sun, 21 Jun 2020 22:00:01: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:00:01: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sun, 21 Jun 2020 22:00:01: #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 22:00:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:00:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:00:03: 4000000 INFO @ Sun, 21 Jun 2020 22:00:08: 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 22:00:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.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 22:00:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:13: 6000000 INFO @ Sun, 21 Jun 2020 22:00:17: 1000000 INFO @ Sun, 21 Jun 2020 22:00:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:00:19: 7000000 INFO @ Sun, 21 Jun 2020 22:00:23: 2000000 INFO @ Sun, 21 Jun 2020 22:00:23: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:00:23: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:00:23: #1 total tags in treatment: 7712760 INFO @ Sun, 21 Jun 2020 22:00:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:00:23: #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 22:00:24: #1 tags after filtering in treatment: 7712758 INFO @ Sun, 21 Jun 2020 22:00:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:00:24: #1 finished! INFO @ Sun, 21 Jun 2020 22:00:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:00:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:00:24: #2 number of paired peaks: 860 WARNING @ Sun, 21 Jun 2020 22:00:24: Fewer paired peaks (860) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 860 pairs to build model! INFO @ Sun, 21 Jun 2020 22:00:24: start model_add_line... INFO @ Sun, 21 Jun 2020 22:00:24: start X-correlation... INFO @ Sun, 21 Jun 2020 22:00:24: end of X-cor INFO @ Sun, 21 Jun 2020 22:00:24: #2 finished! INFO @ Sun, 21 Jun 2020 22:00:24: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 22:00:24: #2 alternative fragment length(s) may be 71 bps INFO @ Sun, 21 Jun 2020 22:00:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.10_model.r WARNING @ Sun, 21 Jun 2020 22:00:24: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:00:24: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sun, 21 Jun 2020 22:00:24: #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 22:00:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:00:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:00:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.05_summits.bed INFO @ Sun, 21 Jun 2020 22:00:25: Done! pass1 - making usageList (595 chroms): 1 millis pass2 - checking and writing primary data (1755 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:00:29: 3000000 INFO @ Sun, 21 Jun 2020 22:00:36: 4000000 INFO @ Sun, 21 Jun 2020 22:00:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:00:42: 5000000 INFO @ Sun, 21 Jun 2020 22:00:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.10_summits.bed INFO @ Sun, 21 Jun 2020 22:00:48: Done! INFO @ Sun, 21 Jun 2020 22:00:48: 6000000 pass1 - making usageList (498 chroms): 1 millis pass2 - checking and writing primary data (1366 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:00:54: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:00:59: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:00:59: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:00:59: #1 total tags in treatment: 7712760 INFO @ Sun, 21 Jun 2020 22:00:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:00:59: #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 22:01:00: #1 tags after filtering in treatment: 7712758 INFO @ Sun, 21 Jun 2020 22:01:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:01:00: #1 finished! INFO @ Sun, 21 Jun 2020 22:01:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:01:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:01:00: #2 number of paired peaks: 860 WARNING @ Sun, 21 Jun 2020 22:01:00: Fewer paired peaks (860) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 860 pairs to build model! INFO @ Sun, 21 Jun 2020 22:01:00: start model_add_line... INFO @ Sun, 21 Jun 2020 22:01:00: start X-correlation... INFO @ Sun, 21 Jun 2020 22:01:00: end of X-cor INFO @ Sun, 21 Jun 2020 22:01:00: #2 finished! INFO @ Sun, 21 Jun 2020 22:01:00: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 22:01:00: #2 alternative fragment length(s) may be 71 bps INFO @ Sun, 21 Jun 2020 22:01:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.20_model.r WARNING @ Sun, 21 Jun 2020 22:01:00: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:01:00: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sun, 21 Jun 2020 22:01:00: #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 22:01:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:01:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:01:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:01:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:01:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:01:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775942/SRX5775942.20_summits.bed INFO @ Sun, 21 Jun 2020 22:01:25: Done! pass1 - making usageList (402 chroms): 1 millis pass2 - checking and writing primary data (894 records, 4 fields): 12 millis CompletedMACS2peakCalling