Job ID = 6454128 SRX = SRX1837980 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:50:49 prefetch.2.10.7: 1) Downloading 'SRR3658921'... 2020-06-21T08:50:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:57:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:57:06 prefetch.2.10.7: 1) 'SRR3658921' was downloaded successfully 2020-06-21T08:57:06 prefetch.2.10.7: 'SRR3658921' has 0 unresolved dependencies Read 17562043 spots for SRR3658921/SRR3658921.sra Written 17562043 spots for SRR3658921/SRR3658921.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: 00:13:08 17562043 reads; of these: 17562043 (100.00%) were unpaired; of these: 592751 (3.38%) aligned 0 times 13731041 (78.19%) aligned exactly 1 time 3238251 (18.44%) aligned >1 times 96.62% overall alignment rate Time searching: 00:13:08 Overall time: 00:13:08 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 16 files... [bam_rmdupse_core] 2515906 / 16969292 = 0.1483 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 18:18:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.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 18:18:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:49: 1000000 INFO @ Sun, 21 Jun 2020 18:18:56: 2000000 INFO @ Sun, 21 Jun 2020 18:19:03: 3000000 INFO @ Sun, 21 Jun 2020 18:19:10: 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 18:19:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.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 18:19:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:17: 5000000 INFO @ Sun, 21 Jun 2020 18:19:19: 1000000 INFO @ Sun, 21 Jun 2020 18:19:25: 6000000 INFO @ Sun, 21 Jun 2020 18:19:27: 2000000 INFO @ Sun, 21 Jun 2020 18:19:32: 7000000 INFO @ Sun, 21 Jun 2020 18:19:35: 3000000 INFO @ Sun, 21 Jun 2020 18:19:40: 8000000 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 18:19:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.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 18:19:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:42: 4000000 INFO @ Sun, 21 Jun 2020 18:19:48: 9000000 INFO @ Sun, 21 Jun 2020 18:19:50: 1000000 INFO @ Sun, 21 Jun 2020 18:19:50: 5000000 INFO @ Sun, 21 Jun 2020 18:19:55: 10000000 INFO @ Sun, 21 Jun 2020 18:19:58: 2000000 INFO @ Sun, 21 Jun 2020 18:19:58: 6000000 INFO @ Sun, 21 Jun 2020 18:20:03: 11000000 INFO @ Sun, 21 Jun 2020 18:20:06: 3000000 INFO @ Sun, 21 Jun 2020 18:20:06: 7000000 INFO @ Sun, 21 Jun 2020 18:20:11: 12000000 INFO @ Sun, 21 Jun 2020 18:20:14: 4000000 INFO @ Sun, 21 Jun 2020 18:20:14: 8000000 INFO @ Sun, 21 Jun 2020 18:20:20: 13000000 INFO @ Sun, 21 Jun 2020 18:20:22: 5000000 INFO @ Sun, 21 Jun 2020 18:20:22: 9000000 INFO @ Sun, 21 Jun 2020 18:20:28: 14000000 INFO @ Sun, 21 Jun 2020 18:20:30: 6000000 INFO @ Sun, 21 Jun 2020 18:20:30: 10000000 INFO @ Sun, 21 Jun 2020 18:20:32: #1 tag size is determined as 150 bps INFO @ Sun, 21 Jun 2020 18:20:32: #1 tag size = 150 INFO @ Sun, 21 Jun 2020 18:20:32: #1 total tags in treatment: 14453386 INFO @ Sun, 21 Jun 2020 18:20:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:32: #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 18:20:33: #1 tags after filtering in treatment: 14453258 INFO @ Sun, 21 Jun 2020 18:20:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:33: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:34: #2 number of paired peaks: 464 WARNING @ Sun, 21 Jun 2020 18:20:34: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Sun, 21 Jun 2020 18:20:34: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:34: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:34: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:34: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:34: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 18:20:34: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 18:20:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.05_model.r WARNING @ Sun, 21 Jun 2020 18:20:34: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:34: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sun, 21 Jun 2020 18:20:34: #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 18:20:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:38: 7000000 INFO @ Sun, 21 Jun 2020 18:20:38: 11000000 INFO @ Sun, 21 Jun 2020 18:20:46: 8000000 INFO @ Sun, 21 Jun 2020 18:20:47: 12000000 INFO @ Sun, 21 Jun 2020 18:20:55: 9000000 INFO @ Sun, 21 Jun 2020 18:20:55: 13000000 INFO @ Sun, 21 Jun 2020 18:21:03: 10000000 INFO @ Sun, 21 Jun 2020 18:21:03: 14000000 INFO @ Sun, 21 Jun 2020 18:21:07: #1 tag size is determined as 150 bps INFO @ Sun, 21 Jun 2020 18:21:07: #1 tag size = 150 INFO @ Sun, 21 Jun 2020 18:21:07: #1 total tags in treatment: 14453386 INFO @ Sun, 21 Jun 2020 18:21:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:07: #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 18:21:08: #1 tags after filtering in treatment: 14453258 INFO @ Sun, 21 Jun 2020 18:21:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:08: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:09: #2 number of paired peaks: 464 WARNING @ Sun, 21 Jun 2020 18:21:09: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Sun, 21 Jun 2020 18:21:09: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:09: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:09: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:09: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:09: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 18:21:09: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 18:21:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.10_model.r WARNING @ Sun, 21 Jun 2020 18:21:09: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:21:09: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sun, 21 Jun 2020 18:21:09: #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 18:21:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:10: 11000000 INFO @ Sun, 21 Jun 2020 18:21:18: 12000000 INFO @ Sun, 21 Jun 2020 18:21:26: 13000000 INFO @ Sun, 21 Jun 2020 18:21:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.05_summits.bed INFO @ Sun, 21 Jun 2020 18:21:27: Done! pass1 - making usageList (436 chroms): 3 millis pass2 - checking and writing primary data (18954 records, 4 fields): 30 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:21:34: 14000000 INFO @ Sun, 21 Jun 2020 18:21:38: #1 tag size is determined as 150 bps INFO @ Sun, 21 Jun 2020 18:21:38: #1 tag size = 150 INFO @ Sun, 21 Jun 2020 18:21:38: #1 total tags in treatment: 14453386 INFO @ Sun, 21 Jun 2020 18:21:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:38: #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 18:21:38: #1 tags after filtering in treatment: 14453258 INFO @ Sun, 21 Jun 2020 18:21:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:39: #2 number of paired peaks: 464 WARNING @ Sun, 21 Jun 2020 18:21:39: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Sun, 21 Jun 2020 18:21:39: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:39: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:39: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:39: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:39: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 18:21:39: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 18:21:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.20_model.r WARNING @ Sun, 21 Jun 2020 18:21:39: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:21:39: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sun, 21 Jun 2020 18:21:39: #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 18:21:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.10_summits.bed INFO @ Sun, 21 Jun 2020 18:22:01: Done! pass1 - making usageList (354 chroms): 2 millis pass2 - checking and writing primary data (6857 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:22:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837980/SRX1837980.20_summits.bed INFO @ Sun, 21 Jun 2020 18:22:32: Done! pass1 - making usageList (271 chroms): 1 millis pass2 - checking and writing primary data (1627 records, 4 fields): 11 millis CompletedMACS2peakCalling