Job ID = 6454126 SRX = SRX1837978 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:00:49 prefetch.2.10.7: 1) Downloading 'SRR3658919'... 2020-06-21T09:00:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:03:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:03:30 prefetch.2.10.7: 1) 'SRR3658919' was downloaded successfully 2020-06-21T09:03:30 prefetch.2.10.7: 'SRR3658919' has 0 unresolved dependencies Read 9027732 spots for SRR3658919/SRR3658919.sra Written 9027732 spots for SRR3658919/SRR3658919.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: 00:12:47 9027732 reads; of these: 9027732 (100.00%) were unpaired; of these: 1393184 (15.43%) aligned 0 times 4326939 (47.93%) aligned exactly 1 time 3307609 (36.64%) aligned >1 times 84.57% overall alignment rate Time searching: 00:12:47 Overall time: 00:12:47 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 8 files... [bam_rmdupse_core] 2989630 / 7634548 = 0.3916 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 18:20:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.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 18:20:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:20:35: 1000000 INFO @ Sun, 21 Jun 2020 18:20:43: 2000000 INFO @ Sun, 21 Jun 2020 18:20:51: 3000000 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 18:20:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.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 18:20:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:21:00: 4000000 INFO @ Sun, 21 Jun 2020 18:21:03: 1000000 INFO @ Sun, 21 Jun 2020 18:21:06: #1 tag size is determined as 142 bps INFO @ Sun, 21 Jun 2020 18:21:06: #1 tag size = 142 INFO @ Sun, 21 Jun 2020 18:21:06: #1 total tags in treatment: 4644918 INFO @ Sun, 21 Jun 2020 18:21:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:06: #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 18:21:06: #1 tags after filtering in treatment: 4644820 INFO @ Sun, 21 Jun 2020 18:21:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:06: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:07: #2 number of paired peaks: 3292 INFO @ Sun, 21 Jun 2020 18:21:07: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:07: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:07: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:07: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:07: #2 predicted fragment length is 179 bps INFO @ Sun, 21 Jun 2020 18:21:07: #2 alternative fragment length(s) may be 179 bps INFO @ Sun, 21 Jun 2020 18:21:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.05_model.r WARNING @ Sun, 21 Jun 2020 18:21:07: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:21:07: #2 You may need to consider one of the other alternative d(s): 179 WARNING @ Sun, 21 Jun 2020 18:21:07: #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 18:21:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:10: 2000000 INFO @ Sun, 21 Jun 2020 18:21:17: 3000000 INFO @ Sun, 21 Jun 2020 18:21:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.05_peaks.narrowPeak BedGraph に変換中... INFO @ Sun, 21 Jun 2020 18:21:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.05_summits.bed 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 18:21:24: Done! INFO @ Sun, 21 Jun 2020 18:21:25: 4000000 pass1 - making usageList (497 chroms): 2 millis pass2 - checking and writing primary data (9812 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.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 18:21:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:21:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:21:29: #1 tag size is determined as 142 bps INFO @ Sun, 21 Jun 2020 18:21:29: #1 tag size = 142 INFO @ Sun, 21 Jun 2020 18:21:29: #1 total tags in treatment: 4644918 INFO @ Sun, 21 Jun 2020 18:21:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:29: #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 18:21:30: #1 tags after filtering in treatment: 4644820 INFO @ Sun, 21 Jun 2020 18:21:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:30: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:30: #2 number of paired peaks: 3292 INFO @ Sun, 21 Jun 2020 18:21:30: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:30: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:30: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:30: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:30: #2 predicted fragment length is 179 bps INFO @ Sun, 21 Jun 2020 18:21:30: #2 alternative fragment length(s) may be 179 bps INFO @ Sun, 21 Jun 2020 18:21:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.10_model.r WARNING @ Sun, 21 Jun 2020 18:21:30: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:21:30: #2 You may need to consider one of the other alternative d(s): 179 WARNING @ Sun, 21 Jun 2020 18:21:30: #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 18:21:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:34: 1000000 INFO @ Sun, 21 Jun 2020 18:21:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:42: 2000000 INFO @ Sun, 21 Jun 2020 18:21:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.10_summits.bed INFO @ Sun, 21 Jun 2020 18:21:46: Done! pass1 - making usageList (376 chroms): 1 millis pass2 - checking and writing primary data (6162 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:50: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:21:58: 4000000 INFO @ Sun, 21 Jun 2020 18:22:04: #1 tag size is determined as 142 bps INFO @ Sun, 21 Jun 2020 18:22:04: #1 tag size = 142 INFO @ Sun, 21 Jun 2020 18:22:04: #1 total tags in treatment: 4644918 INFO @ Sun, 21 Jun 2020 18:22:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:22:04: #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 18:22:04: #1 tags after filtering in treatment: 4644820 INFO @ Sun, 21 Jun 2020 18:22:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:22:04: #1 finished! INFO @ Sun, 21 Jun 2020 18:22:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:22:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:22:05: #2 number of paired peaks: 3292 INFO @ Sun, 21 Jun 2020 18:22:05: start model_add_line... INFO @ Sun, 21 Jun 2020 18:22:05: start X-correlation... INFO @ Sun, 21 Jun 2020 18:22:05: end of X-cor INFO @ Sun, 21 Jun 2020 18:22:05: #2 finished! INFO @ Sun, 21 Jun 2020 18:22:05: #2 predicted fragment length is 179 bps INFO @ Sun, 21 Jun 2020 18:22:05: #2 alternative fragment length(s) may be 179 bps INFO @ Sun, 21 Jun 2020 18:22:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.20_model.r WARNING @ Sun, 21 Jun 2020 18:22:05: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:22:05: #2 You may need to consider one of the other alternative d(s): 179 WARNING @ Sun, 21 Jun 2020 18:22:05: #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 18:22:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:22:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:22:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837978/SRX1837978.20_summits.bed INFO @ Sun, 21 Jun 2020 18:22:23: Done! pass1 - making usageList (227 chroms): 1 millis pass2 - checking and writing primary data (3050 records, 4 fields): 10 millis CompletedMACS2peakCalling