Job ID = 6458798 SRX = SRX5535370 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:52:37 prefetch.2.10.7: 1) Downloading 'SRR8743298'... 2020-06-21T12:52:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:58:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:58:46 prefetch.2.10.7: 1) 'SRR8743298' was downloaded successfully 2020-06-21T12:58:46 prefetch.2.10.7: 'SRR8743298' has 0 unresolved dependencies Read 48005801 spots for SRR8743298/SRR8743298.sra Written 48005801 spots for SRR8743298/SRR8743298.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: 00:11:46 48005801 reads; of these: 48005801 (100.00%) were unpaired; of these: 752677 (1.57%) aligned 0 times 39009012 (81.26%) aligned exactly 1 time 8244112 (17.17%) aligned >1 times 98.43% overall alignment rate Time searching: 00:11:46 Overall time: 00:11:46 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 20 files... [bam_rmdupse_core] 27619523 / 47253124 = 0.5845 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 22:20:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.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 22:20:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:20:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:20:09: 1000000 INFO @ Sun, 21 Jun 2020 22:20:15: 2000000 INFO @ Sun, 21 Jun 2020 22:20:20: 3000000 INFO @ Sun, 21 Jun 2020 22:20:26: 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 22:20:32: 5000000 INFO @ Sun, 21 Jun 2020 22:20:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.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 22:20:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:20:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:20:38: 6000000 INFO @ Sun, 21 Jun 2020 22:20:39: 1000000 INFO @ Sun, 21 Jun 2020 22:20:44: 7000000 INFO @ Sun, 21 Jun 2020 22:20:45: 2000000 INFO @ Sun, 21 Jun 2020 22:20:50: 8000000 INFO @ Sun, 21 Jun 2020 22:20:51: 3000000 INFO @ Sun, 21 Jun 2020 22:20:56: 9000000 INFO @ Sun, 21 Jun 2020 22:20:57: 4000000 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 22:21:02: 10000000 INFO @ Sun, 21 Jun 2020 22:21:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.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 22:21:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:21:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:21:03: 5000000 INFO @ Sun, 21 Jun 2020 22:21:08: 11000000 INFO @ Sun, 21 Jun 2020 22:21:09: 1000000 INFO @ Sun, 21 Jun 2020 22:21:09: 6000000 INFO @ Sun, 21 Jun 2020 22:21:15: 12000000 INFO @ Sun, 21 Jun 2020 22:21:15: 2000000 INFO @ Sun, 21 Jun 2020 22:21:15: 7000000 INFO @ Sun, 21 Jun 2020 22:21:21: 13000000 INFO @ Sun, 21 Jun 2020 22:21:21: 3000000 INFO @ Sun, 21 Jun 2020 22:21:22: 8000000 INFO @ Sun, 21 Jun 2020 22:21:27: 14000000 INFO @ Sun, 21 Jun 2020 22:21:27: 4000000 INFO @ Sun, 21 Jun 2020 22:21:28: 9000000 INFO @ Sun, 21 Jun 2020 22:21:33: 5000000 INFO @ Sun, 21 Jun 2020 22:21:33: 15000000 INFO @ Sun, 21 Jun 2020 22:21:34: 10000000 INFO @ Sun, 21 Jun 2020 22:21:39: 6000000 INFO @ Sun, 21 Jun 2020 22:21:39: 16000000 INFO @ Sun, 21 Jun 2020 22:21:40: 11000000 INFO @ Sun, 21 Jun 2020 22:21:45: 7000000 INFO @ Sun, 21 Jun 2020 22:21:46: 17000000 INFO @ Sun, 21 Jun 2020 22:21:47: 12000000 INFO @ Sun, 21 Jun 2020 22:21:52: 8000000 INFO @ Sun, 21 Jun 2020 22:21:52: 18000000 INFO @ Sun, 21 Jun 2020 22:21:53: 13000000 INFO @ Sun, 21 Jun 2020 22:21:58: 9000000 INFO @ Sun, 21 Jun 2020 22:21:58: 19000000 INFO @ Sun, 21 Jun 2020 22:21:59: 14000000 INFO @ Sun, 21 Jun 2020 22:22:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:22:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:22:03: #1 total tags in treatment: 19633601 INFO @ Sun, 21 Jun 2020 22:22:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:22:03: #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 22:22:03: #1 tags after filtering in treatment: 19633529 INFO @ Sun, 21 Jun 2020 22:22:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:22:03: #1 finished! INFO @ Sun, 21 Jun 2020 22:22:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:22:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:22:04: 10000000 INFO @ Sun, 21 Jun 2020 22:22:05: #2 number of paired peaks: 416 WARNING @ Sun, 21 Jun 2020 22:22:05: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Sun, 21 Jun 2020 22:22:05: start model_add_line... INFO @ Sun, 21 Jun 2020 22:22:05: start X-correlation... INFO @ Sun, 21 Jun 2020 22:22:05: end of X-cor INFO @ Sun, 21 Jun 2020 22:22:05: #2 finished! INFO @ Sun, 21 Jun 2020 22:22:05: #2 predicted fragment length is 28 bps INFO @ Sun, 21 Jun 2020 22:22:05: #2 alternative fragment length(s) may be 15,28,56,77,115,244 bps INFO @ Sun, 21 Jun 2020 22:22:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.05_model.r WARNING @ Sun, 21 Jun 2020 22:22:05: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:22:05: #2 You may need to consider one of the other alternative d(s): 15,28,56,77,115,244 WARNING @ Sun, 21 Jun 2020 22:22:05: #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 22:22:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:22:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:22:05: 15000000 INFO @ Sun, 21 Jun 2020 22:22:10: 11000000 INFO @ Sun, 21 Jun 2020 22:22:11: 16000000 INFO @ Sun, 21 Jun 2020 22:22:16: 12000000 INFO @ Sun, 21 Jun 2020 22:22:18: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:22:22: 13000000 INFO @ Sun, 21 Jun 2020 22:22:24: 18000000 INFO @ Sun, 21 Jun 2020 22:22:28: 14000000 INFO @ Sun, 21 Jun 2020 22:22:30: 19000000 INFO @ Sun, 21 Jun 2020 22:22:35: 15000000 INFO @ Sun, 21 Jun 2020 22:22:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:22:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:22:35: #1 total tags in treatment: 19633601 INFO @ Sun, 21 Jun 2020 22:22:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:22:35: #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 22:22:35: #1 tags after filtering in treatment: 19633529 INFO @ Sun, 21 Jun 2020 22:22:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:22:35: #1 finished! INFO @ Sun, 21 Jun 2020 22:22:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:22:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:22:37: #2 number of paired peaks: 416 WARNING @ Sun, 21 Jun 2020 22:22:37: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Sun, 21 Jun 2020 22:22:37: start model_add_line... INFO @ Sun, 21 Jun 2020 22:22:37: start X-correlation... INFO @ Sun, 21 Jun 2020 22:22:37: end of X-cor INFO @ Sun, 21 Jun 2020 22:22:37: #2 finished! INFO @ Sun, 21 Jun 2020 22:22:37: #2 predicted fragment length is 28 bps INFO @ Sun, 21 Jun 2020 22:22:37: #2 alternative fragment length(s) may be 15,28,56,77,115,244 bps INFO @ Sun, 21 Jun 2020 22:22:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.10_model.r WARNING @ Sun, 21 Jun 2020 22:22:37: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:22:37: #2 You may need to consider one of the other alternative d(s): 15,28,56,77,115,244 WARNING @ Sun, 21 Jun 2020 22:22:37: #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 22:22:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:22:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:22:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:22:40: 16000000 INFO @ Sun, 21 Jun 2020 22:22:47: 17000000 INFO @ Sun, 21 Jun 2020 22:22:53: 18000000 INFO @ Sun, 21 Jun 2020 22:22:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:22:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:22:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.05_summits.bed INFO @ Sun, 21 Jun 2020 22:22:55: Done! pass1 - making usageList (128 chroms): 1 millis pass2 - checking and writing primary data (1590 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:22:59: 19000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:23:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:23:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:23:03: #1 total tags in treatment: 19633601 INFO @ Sun, 21 Jun 2020 22:23:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:23:03: #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 22:23:04: #1 tags after filtering in treatment: 19633529 INFO @ Sun, 21 Jun 2020 22:23:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:23:04: #1 finished! INFO @ Sun, 21 Jun 2020 22:23:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:23:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:23:05: #2 number of paired peaks: 416 WARNING @ Sun, 21 Jun 2020 22:23:05: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Sun, 21 Jun 2020 22:23:05: start model_add_line... INFO @ Sun, 21 Jun 2020 22:23:05: start X-correlation... INFO @ Sun, 21 Jun 2020 22:23:05: end of X-cor INFO @ Sun, 21 Jun 2020 22:23:05: #2 finished! INFO @ Sun, 21 Jun 2020 22:23:05: #2 predicted fragment length is 28 bps INFO @ Sun, 21 Jun 2020 22:23:05: #2 alternative fragment length(s) may be 15,28,56,77,115,244 bps INFO @ Sun, 21 Jun 2020 22:23:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.20_model.r WARNING @ Sun, 21 Jun 2020 22:23:05: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:23:05: #2 You may need to consider one of the other alternative d(s): 15,28,56,77,115,244 WARNING @ Sun, 21 Jun 2020 22:23:05: #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 22:23:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:23:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:23:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:23:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:23:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:23:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.10_summits.bed INFO @ Sun, 21 Jun 2020 22:23:29: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (102 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:23:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:23:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:23:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:23:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5535370/SRX5535370.20_summits.bed INFO @ Sun, 21 Jun 2020 22:23:58: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (17 records, 4 fields): 1 millis CompletedMACS2peakCalling