Job ID = 6455251 SRX = SRX287593 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:58:55 prefetch.2.10.7: 1) Downloading 'SRR869736'... 2020-06-21T09:58:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:02:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:02:43 prefetch.2.10.7: 1) 'SRR869736' was downloaded successfully Read 25893315 spots for SRR869736/SRR869736.sra Written 25893315 spots for SRR869736/SRR869736.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: 00:07:19 25893315 reads; of these: 25893315 (100.00%) were unpaired; of these: 1817570 (7.02%) aligned 0 times 17091631 (66.01%) aligned exactly 1 time 6984114 (26.97%) aligned >1 times 92.98% overall alignment rate Time searching: 00:07:19 Overall time: 00:07:19 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] 4632334 / 24075745 = 0.1924 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 19:17:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.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 19:17:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:17:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:17:20: 1000000 INFO @ Sun, 21 Jun 2020 19:17:25: 2000000 INFO @ Sun, 21 Jun 2020 19:17:30: 3000000 INFO @ Sun, 21 Jun 2020 19:17:36: 4000000 INFO @ Sun, 21 Jun 2020 19:17:41: 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 19:17:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.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 19:17:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:17:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:17:46: 6000000 INFO @ Sun, 21 Jun 2020 19:17:51: 1000000 INFO @ Sun, 21 Jun 2020 19:17:52: 7000000 INFO @ Sun, 21 Jun 2020 19:17:57: 2000000 INFO @ Sun, 21 Jun 2020 19:17:58: 8000000 INFO @ Sun, 21 Jun 2020 19:18:03: 3000000 INFO @ Sun, 21 Jun 2020 19:18:04: 9000000 INFO @ Sun, 21 Jun 2020 19:18:09: 4000000 INFO @ Sun, 21 Jun 2020 19:18:10: 10000000 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 19:18:14: 5000000 INFO @ Sun, 21 Jun 2020 19:18:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.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 19:18:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:18:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:18:16: 11000000 INFO @ Sun, 21 Jun 2020 19:18:20: 6000000 INFO @ Sun, 21 Jun 2020 19:18:20: 1000000 INFO @ Sun, 21 Jun 2020 19:18:21: 12000000 INFO @ Sun, 21 Jun 2020 19:18:26: 7000000 INFO @ Sun, 21 Jun 2020 19:18:26: 2000000 INFO @ Sun, 21 Jun 2020 19:18:27: 13000000 INFO @ Sun, 21 Jun 2020 19:18:32: 8000000 INFO @ Sun, 21 Jun 2020 19:18:32: 3000000 INFO @ Sun, 21 Jun 2020 19:18:33: 14000000 INFO @ Sun, 21 Jun 2020 19:18:38: 9000000 INFO @ Sun, 21 Jun 2020 19:18:38: 4000000 INFO @ Sun, 21 Jun 2020 19:18:39: 15000000 INFO @ Sun, 21 Jun 2020 19:18:44: 10000000 INFO @ Sun, 21 Jun 2020 19:18:44: 5000000 INFO @ Sun, 21 Jun 2020 19:18:45: 16000000 INFO @ Sun, 21 Jun 2020 19:18:50: 11000000 INFO @ Sun, 21 Jun 2020 19:18:50: 6000000 INFO @ Sun, 21 Jun 2020 19:18:51: 17000000 INFO @ Sun, 21 Jun 2020 19:18:56: 7000000 INFO @ Sun, 21 Jun 2020 19:18:56: 12000000 INFO @ Sun, 21 Jun 2020 19:18:57: 18000000 INFO @ Sun, 21 Jun 2020 19:19:01: 8000000 INFO @ Sun, 21 Jun 2020 19:19:01: 13000000 INFO @ Sun, 21 Jun 2020 19:19:03: 19000000 INFO @ Sun, 21 Jun 2020 19:19:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:19:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:19:05: #1 total tags in treatment: 19443411 INFO @ Sun, 21 Jun 2020 19:19:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:19:05: #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 19:19:06: #1 tags after filtering in treatment: 19443411 INFO @ Sun, 21 Jun 2020 19:19:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:19:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:19:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:19:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:19:07: 9000000 INFO @ Sun, 21 Jun 2020 19:19:07: 14000000 INFO @ Sun, 21 Jun 2020 19:19:07: #2 number of paired peaks: 657 WARNING @ Sun, 21 Jun 2020 19:19:07: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Sun, 21 Jun 2020 19:19:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:19:07: start X-correlation... INFO @ Sun, 21 Jun 2020 19:19:07: end of X-cor INFO @ Sun, 21 Jun 2020 19:19:07: #2 finished! INFO @ Sun, 21 Jun 2020 19:19:07: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:19:07: #2 alternative fragment length(s) may be 4,54 bps INFO @ Sun, 21 Jun 2020 19:19:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.05_model.r WARNING @ Sun, 21 Jun 2020 19:19:07: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:19:07: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Sun, 21 Jun 2020 19:19:07: #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 19:19:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:19:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:19:13: 10000000 INFO @ Sun, 21 Jun 2020 19:19:13: 15000000 INFO @ Sun, 21 Jun 2020 19:19:19: 11000000 INFO @ Sun, 21 Jun 2020 19:19:19: 16000000 INFO @ Sun, 21 Jun 2020 19:19:24: 12000000 INFO @ Sun, 21 Jun 2020 19:19:25: 17000000 INFO @ Sun, 21 Jun 2020 19:19:30: 13000000 INFO @ Sun, 21 Jun 2020 19:19:30: 18000000 INFO @ Sun, 21 Jun 2020 19:19:36: 14000000 INFO @ Sun, 21 Jun 2020 19:19:36: 19000000 INFO @ Sun, 21 Jun 2020 19:19:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:19:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:19:39: #1 total tags in treatment: 19443411 INFO @ Sun, 21 Jun 2020 19:19:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:19:39: #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 19:19:39: #1 tags after filtering in treatment: 19443411 INFO @ Sun, 21 Jun 2020 19:19:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:19:39: #1 finished! INFO @ Sun, 21 Jun 2020 19:19:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:19:39: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:19:41: #2 number of paired peaks: 657 WARNING @ Sun, 21 Jun 2020 19:19:41: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Sun, 21 Jun 2020 19:19:41: start model_add_line... INFO @ Sun, 21 Jun 2020 19:19:41: start X-correlation... INFO @ Sun, 21 Jun 2020 19:19:41: end of X-cor INFO @ Sun, 21 Jun 2020 19:19:41: #2 finished! INFO @ Sun, 21 Jun 2020 19:19:41: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:19:41: #2 alternative fragment length(s) may be 4,54 bps INFO @ Sun, 21 Jun 2020 19:19:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.10_model.r WARNING @ Sun, 21 Jun 2020 19:19:41: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:19:41: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Sun, 21 Jun 2020 19:19:41: #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 19:19:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:19:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:19:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:19:41: 15000000 INFO @ Sun, 21 Jun 2020 19:19:47: 16000000 INFO @ Sun, 21 Jun 2020 19:19:52: 17000000 INFO @ Sun, 21 Jun 2020 19:19:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:19:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:19:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.05_summits.bed INFO @ Sun, 21 Jun 2020 19:19:57: Done! pass1 - making usageList (698 chroms): 1 millis pass2 - checking and writing primary data (3089 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:19:58: 18000000 INFO @ Sun, 21 Jun 2020 19:20:03: 19000000 INFO @ Sun, 21 Jun 2020 19:20:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:20:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:20:06: #1 total tags in treatment: 19443411 INFO @ Sun, 21 Jun 2020 19:20:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:20:06: #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 19:20:06: #1 tags after filtering in treatment: 19443411 INFO @ Sun, 21 Jun 2020 19:20:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:20:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:20:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:20:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:20:08: #2 number of paired peaks: 657 WARNING @ Sun, 21 Jun 2020 19:20:08: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Sun, 21 Jun 2020 19:20:08: start model_add_line... INFO @ Sun, 21 Jun 2020 19:20:08: start X-correlation... INFO @ Sun, 21 Jun 2020 19:20:08: end of X-cor INFO @ Sun, 21 Jun 2020 19:20:08: #2 finished! INFO @ Sun, 21 Jun 2020 19:20:08: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:20:08: #2 alternative fragment length(s) may be 4,54 bps INFO @ Sun, 21 Jun 2020 19:20:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.20_model.r WARNING @ Sun, 21 Jun 2020 19:20:08: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:20:08: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Sun, 21 Jun 2020 19:20:08: #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 19:20:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:20:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:20:16: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:20:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:20:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:20:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.10_summits.bed INFO @ Sun, 21 Jun 2020 19:20:33: Done! pass1 - making usageList (598 chroms): 1 millis pass2 - checking and writing primary data (2309 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:20:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:20:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:20:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:20:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287593/SRX287593.20_summits.bed INFO @ Sun, 21 Jun 2020 19:20:58: Done! pass1 - making usageList (455 chroms): 1 millis pass2 - checking and writing primary data (1508 records, 4 fields): 13 millis CompletedMACS2peakCalling