Job ID = 6458980 SRX = SRX5827844 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:39:14 prefetch.2.10.7: 1) Downloading 'SRR9051595'... 2020-06-21T12:39:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:44:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:44:16 prefetch.2.10.7: 1) 'SRR9051595' was downloaded successfully 2020-06-21T12:44:16 prefetch.2.10.7: 'SRR9051595' has 0 unresolved dependencies Read 49997396 spots for SRR9051595/SRR9051595.sra Written 49997396 spots for SRR9051595/SRR9051595.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: 00:12:21 49997396 reads; of these: 49997396 (100.00%) were unpaired; of these: 5863068 (11.73%) aligned 0 times 35525820 (71.06%) aligned exactly 1 time 8608508 (17.22%) aligned >1 times 88.27% overall alignment rate Time searching: 00:12:21 Overall time: 00:12:21 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] 23614613 / 44134328 = 0.5351 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 22:09:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.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 22:09:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:09:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:09:06: 1000000 INFO @ Sun, 21 Jun 2020 22:09:10: 2000000 INFO @ Sun, 21 Jun 2020 22:09:15: 3000000 INFO @ Sun, 21 Jun 2020 22:09:20: 4000000 INFO @ Sun, 21 Jun 2020 22:09:25: 5000000 INFO @ Sun, 21 Jun 2020 22:09:29: 6000000 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 22:09:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.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 22:09:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:09:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:09:34: 7000000 INFO @ Sun, 21 Jun 2020 22:09:36: 1000000 INFO @ Sun, 21 Jun 2020 22:09:39: 8000000 INFO @ Sun, 21 Jun 2020 22:09:40: 2000000 INFO @ Sun, 21 Jun 2020 22:09:44: 9000000 INFO @ Sun, 21 Jun 2020 22:09:45: 3000000 INFO @ Sun, 21 Jun 2020 22:09:50: 4000000 INFO @ Sun, 21 Jun 2020 22:09:50: 10000000 INFO @ Sun, 21 Jun 2020 22:09:54: 5000000 INFO @ Sun, 21 Jun 2020 22:09:55: 11000000 INFO @ Sun, 21 Jun 2020 22:09:59: 6000000 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 22:10:00: 12000000 INFO @ Sun, 21 Jun 2020 22:10:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.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 22:10:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:10:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:10:03: 7000000 INFO @ Sun, 21 Jun 2020 22:10:05: 13000000 INFO @ Sun, 21 Jun 2020 22:10:06: 1000000 INFO @ Sun, 21 Jun 2020 22:10:08: 8000000 INFO @ Sun, 21 Jun 2020 22:10:10: 14000000 INFO @ Sun, 21 Jun 2020 22:10:12: 2000000 INFO @ Sun, 21 Jun 2020 22:10:13: 9000000 INFO @ Sun, 21 Jun 2020 22:10:16: 15000000 INFO @ Sun, 21 Jun 2020 22:10:17: 3000000 INFO @ Sun, 21 Jun 2020 22:10:17: 10000000 INFO @ Sun, 21 Jun 2020 22:10:21: 16000000 INFO @ Sun, 21 Jun 2020 22:10:22: 4000000 INFO @ Sun, 21 Jun 2020 22:10:22: 11000000 INFO @ Sun, 21 Jun 2020 22:10:27: 12000000 INFO @ Sun, 21 Jun 2020 22:10:27: 17000000 INFO @ Sun, 21 Jun 2020 22:10:27: 5000000 INFO @ Sun, 21 Jun 2020 22:10:31: 13000000 INFO @ Sun, 21 Jun 2020 22:10:32: 18000000 INFO @ Sun, 21 Jun 2020 22:10:33: 6000000 INFO @ Sun, 21 Jun 2020 22:10:36: 14000000 INFO @ Sun, 21 Jun 2020 22:10:37: 19000000 INFO @ Sun, 21 Jun 2020 22:10:38: 7000000 INFO @ Sun, 21 Jun 2020 22:10:41: 15000000 INFO @ Sun, 21 Jun 2020 22:10:43: 20000000 INFO @ Sun, 21 Jun 2020 22:10:43: 8000000 INFO @ Sun, 21 Jun 2020 22:10:45: 16000000 INFO @ Sun, 21 Jun 2020 22:10:46: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:10:46: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:10:46: #1 total tags in treatment: 20519715 INFO @ Sun, 21 Jun 2020 22:10:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:10:46: #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 22:10:46: #1 tags after filtering in treatment: 20519713 INFO @ Sun, 21 Jun 2020 22:10:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:10:46: #1 finished! INFO @ Sun, 21 Jun 2020 22:10:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:10:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:10:48: #2 number of paired peaks: 449 WARNING @ Sun, 21 Jun 2020 22:10:48: Fewer paired peaks (449) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 449 pairs to build model! INFO @ Sun, 21 Jun 2020 22:10:48: start model_add_line... INFO @ Sun, 21 Jun 2020 22:10:48: start X-correlation... INFO @ Sun, 21 Jun 2020 22:10:48: end of X-cor INFO @ Sun, 21 Jun 2020 22:10:48: #2 finished! INFO @ Sun, 21 Jun 2020 22:10:48: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 22:10:48: #2 alternative fragment length(s) may be 2,49,575 bps INFO @ Sun, 21 Jun 2020 22:10:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.05_model.r WARNING @ Sun, 21 Jun 2020 22:10:48: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:10:48: #2 You may need to consider one of the other alternative d(s): 2,49,575 WARNING @ Sun, 21 Jun 2020 22:10:48: #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 22:10:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:10:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:10:49: 9000000 INFO @ Sun, 21 Jun 2020 22:10:50: 17000000 INFO @ Sun, 21 Jun 2020 22:10:54: 10000000 INFO @ Sun, 21 Jun 2020 22:10:55: 18000000 INFO @ Sun, 21 Jun 2020 22:10:59: 11000000 INFO @ Sun, 21 Jun 2020 22:11:00: 19000000 INFO @ Sun, 21 Jun 2020 22:11:04: 20000000 INFO @ Sun, 21 Jun 2020 22:11:05: 12000000 INFO @ Sun, 21 Jun 2020 22:11:07: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:11:07: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:11:07: #1 total tags in treatment: 20519715 INFO @ Sun, 21 Jun 2020 22:11:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:11:07: #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 22:11:07: #1 tags after filtering in treatment: 20519713 INFO @ Sun, 21 Jun 2020 22:11:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:11:07: #1 finished! INFO @ Sun, 21 Jun 2020 22:11:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:11:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:11:09: #2 number of paired peaks: 449 WARNING @ Sun, 21 Jun 2020 22:11:09: Fewer paired peaks (449) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 449 pairs to build model! INFO @ Sun, 21 Jun 2020 22:11:09: start model_add_line... INFO @ Sun, 21 Jun 2020 22:11:09: start X-correlation... INFO @ Sun, 21 Jun 2020 22:11:09: end of X-cor INFO @ Sun, 21 Jun 2020 22:11:09: #2 finished! INFO @ Sun, 21 Jun 2020 22:11:09: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 22:11:09: #2 alternative fragment length(s) may be 2,49,575 bps INFO @ Sun, 21 Jun 2020 22:11:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.10_model.r WARNING @ Sun, 21 Jun 2020 22:11:09: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:11:09: #2 You may need to consider one of the other alternative d(s): 2,49,575 WARNING @ Sun, 21 Jun 2020 22:11:09: #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 22:11:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:11:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:11:10: 13000000 INFO @ Sun, 21 Jun 2020 22:11:15: 14000000 INFO @ Sun, 21 Jun 2020 22:11:20: 15000000 INFO @ Sun, 21 Jun 2020 22:11:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:11:25: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:11:31: 17000000 INFO @ Sun, 21 Jun 2020 22:11:36: 18000000 INFO @ Sun, 21 Jun 2020 22:11:42: 19000000 INFO @ Sun, 21 Jun 2020 22:11:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:11:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:11:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.05_summits.bed INFO @ Sun, 21 Jun 2020 22:11:43: Done! pass1 - making usageList (684 chroms): 1 millis pass2 - checking and writing primary data (2912 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:11:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:11:47: 20000000 INFO @ Sun, 21 Jun 2020 22:11:50: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:11:50: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:11:50: #1 total tags in treatment: 20519715 INFO @ Sun, 21 Jun 2020 22:11:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:11:50: #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 22:11:50: #1 tags after filtering in treatment: 20519713 INFO @ Sun, 21 Jun 2020 22:11:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:11:50: #1 finished! INFO @ Sun, 21 Jun 2020 22:11:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:11:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:11:52: #2 number of paired peaks: 449 WARNING @ Sun, 21 Jun 2020 22:11:52: Fewer paired peaks (449) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 449 pairs to build model! INFO @ Sun, 21 Jun 2020 22:11:52: start model_add_line... INFO @ Sun, 21 Jun 2020 22:11:52: start X-correlation... INFO @ Sun, 21 Jun 2020 22:11:52: end of X-cor INFO @ Sun, 21 Jun 2020 22:11:52: #2 finished! INFO @ Sun, 21 Jun 2020 22:11:52: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 22:11:52: #2 alternative fragment length(s) may be 2,49,575 bps INFO @ Sun, 21 Jun 2020 22:11:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.20_model.r WARNING @ Sun, 21 Jun 2020 22:11:52: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:11:52: #2 You may need to consider one of the other alternative d(s): 2,49,575 WARNING @ Sun, 21 Jun 2020 22:11:52: #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 22:11:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:11:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:12:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:12:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:12:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.10_summits.bed INFO @ Sun, 21 Jun 2020 22:12:03: Done! pass1 - making usageList (536 chroms): 2 millis pass2 - checking and writing primary data (1941 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:12:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:12:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:12:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:12:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827844/SRX5827844.20_summits.bed INFO @ Sun, 21 Jun 2020 22:12:47: Done! pass1 - making usageList (377 chroms): 1 millis pass2 - checking and writing primary data (1014 records, 4 fields): 11 millis CompletedMACS2peakCalling