Job ID = 6455148 SRX = SRX2788646 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:48:25 prefetch.2.10.7: 1) Downloading 'SRR5515266'... 2020-06-21T09:48:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:53:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:53:09 prefetch.2.10.7: 1) 'SRR5515266' was downloaded successfully 2020-06-21T09:53:09 prefetch.2.10.7: 'SRR5515266' has 0 unresolved dependencies Read 14693698 spots for SRR5515266/SRR5515266.sra Written 14693698 spots for SRR5515266/SRR5515266.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: 00:05:08 14693698 reads; of these: 14693698 (100.00%) were unpaired; of these: 2201224 (14.98%) aligned 0 times 10913877 (74.28%) aligned exactly 1 time 1578597 (10.74%) aligned >1 times 85.02% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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] 7494716 / 12492474 = 0.5999 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 19:03:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.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 19:03:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:43: 1000000 INFO @ Sun, 21 Jun 2020 19:03:51: 2000000 INFO @ Sun, 21 Jun 2020 19:03:59: 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 19:04:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.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 19:04:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:04:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:04:08: 4000000 INFO @ Sun, 21 Jun 2020 19:04:13: 1000000 INFO @ Sun, 21 Jun 2020 19:04:17: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 19:04:17: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 19:04:17: #1 total tags in treatment: 4997758 INFO @ Sun, 21 Jun 2020 19:04:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:17: #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 19:04:18: #1 tags after filtering in treatment: 4997505 INFO @ Sun, 21 Jun 2020 19:04:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:18: #2 number of paired peaks: 6257 INFO @ Sun, 21 Jun 2020 19:04:18: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:18: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:18: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:18: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:18: #2 predicted fragment length is 185 bps INFO @ Sun, 21 Jun 2020 19:04:18: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 21 Jun 2020 19:04:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.05_model.r WARNING @ Sun, 21 Jun 2020 19:04:18: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:04:18: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Sun, 21 Jun 2020 19:04:18: #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 19:04:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:04:20: 2000000 INFO @ Sun, 21 Jun 2020 19:04:28: 3000000 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 19:04:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.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 19:04:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:04:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:04:35: 4000000 INFO @ Sun, 21 Jun 2020 19:04:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:04:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:04:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.05_summits.bed INFO @ Sun, 21 Jun 2020 19:04:41: Done! pass1 - making usageList (165 chroms): 2 millis pass2 - checking and writing primary data (5906 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:04:43: 1000000 INFO @ Sun, 21 Jun 2020 19:04:43: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 19:04:43: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 19:04:43: #1 total tags in treatment: 4997758 INFO @ Sun, 21 Jun 2020 19:04:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:43: #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 19:04:43: #1 tags after filtering in treatment: 4997505 INFO @ Sun, 21 Jun 2020 19:04:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:43: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:44: #2 number of paired peaks: 6257 INFO @ Sun, 21 Jun 2020 19:04:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:44: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:44: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:44: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:44: #2 predicted fragment length is 185 bps INFO @ Sun, 21 Jun 2020 19:04:44: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 21 Jun 2020 19:04:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.10_model.r WARNING @ Sun, 21 Jun 2020 19:04:44: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:04:44: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Sun, 21 Jun 2020 19:04:44: #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 19:04:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:04:50: 2000000 INFO @ Sun, 21 Jun 2020 19:04:57: 3000000 INFO @ Sun, 21 Jun 2020 19:04:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:05:05: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:05:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.10_summits.bed INFO @ Sun, 21 Jun 2020 19:05:07: Done! pass1 - making usageList (108 chroms): 1 millis pass2 - checking and writing primary data (4793 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:05:12: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 19:05:12: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 19:05:12: #1 total tags in treatment: 4997758 INFO @ Sun, 21 Jun 2020 19:05:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:05:12: #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 19:05:13: #1 tags after filtering in treatment: 4997505 INFO @ Sun, 21 Jun 2020 19:05:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:05:13: #1 finished! INFO @ Sun, 21 Jun 2020 19:05:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:05:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:05:13: #2 number of paired peaks: 6257 INFO @ Sun, 21 Jun 2020 19:05:13: start model_add_line... INFO @ Sun, 21 Jun 2020 19:05:14: start X-correlation... INFO @ Sun, 21 Jun 2020 19:05:14: end of X-cor INFO @ Sun, 21 Jun 2020 19:05:14: #2 finished! INFO @ Sun, 21 Jun 2020 19:05:14: #2 predicted fragment length is 185 bps INFO @ Sun, 21 Jun 2020 19:05:14: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 21 Jun 2020 19:05:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.20_model.r WARNING @ Sun, 21 Jun 2020 19:05:14: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:05:14: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Sun, 21 Jun 2020 19:05:14: #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 19:05:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:05:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:05:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:05:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2788646/SRX2788646.20_summits.bed INFO @ Sun, 21 Jun 2020 19:05:36: Done! pass1 - making usageList (77 chroms): 2 millis pass2 - checking and writing primary data (3528 records, 4 fields): 8 millis CompletedMACS2peakCalling