Job ID = 6455138 SRX = SRX2788639 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:05:55 prefetch.2.10.7: 1) Downloading 'SRR5515259'... 2020-06-21T10:05:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:33:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:33:01 prefetch.2.10.7: 1) 'SRR5515259' was downloaded successfully 2020-06-21T10:33:01 prefetch.2.10.7: 'SRR5515259' has 0 unresolved dependencies Read 83847447 spots for SRR5515259/SRR5515259.sra Written 83847447 spots for SRR5515259/SRR5515259.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: 00:23:04 83847447 reads; of these: 83847447 (100.00%) were unpaired; of these: 51677628 (61.63%) aligned 0 times 27197722 (32.44%) aligned exactly 1 time 4972097 (5.93%) aligned >1 times 38.37% overall alignment rate Time searching: 00:23:04 Overall time: 00:23:04 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] 29757306 / 32169819 = 0.9250 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 20:11:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.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 20:11:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:11:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:11:57: 1000000 INFO @ Sun, 21 Jun 2020 20:12:06: 2000000 INFO @ Sun, 21 Jun 2020 20:12:10: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:12:10: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:12:10: #1 total tags in treatment: 2412513 INFO @ Sun, 21 Jun 2020 20:12:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:12:10: #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 20:12:10: #1 tags after filtering in treatment: 2412301 INFO @ Sun, 21 Jun 2020 20:12:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:12:10: #1 finished! INFO @ Sun, 21 Jun 2020 20:12:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:12:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:12:10: #2 number of paired peaks: 3492 INFO @ Sun, 21 Jun 2020 20:12:10: start model_add_line... INFO @ Sun, 21 Jun 2020 20:12:10: start X-correlation... INFO @ Sun, 21 Jun 2020 20:12:10: end of X-cor INFO @ Sun, 21 Jun 2020 20:12:10: #2 finished! INFO @ Sun, 21 Jun 2020 20:12:10: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 20:12:10: #2 alternative fragment length(s) may be 104 bps INFO @ Sun, 21 Jun 2020 20:12:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.05_model.r WARNING @ Sun, 21 Jun 2020 20:12:10: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:12:10: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Sun, 21 Jun 2020 20:12:10: #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 20:12:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:12:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:12:17: #3 Call peaks for each chromosome... 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 20:12:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.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 20:12:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:12:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:12:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:12:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:12:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.05_summits.bed INFO @ Sun, 21 Jun 2020 20:12:19: Done! pass1 - making usageList (525 chroms): 1 millis pass2 - checking and writing primary data (1815 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:12:28: 1000000 INFO @ Sun, 21 Jun 2020 20:12:37: 2000000 INFO @ Sun, 21 Jun 2020 20:12:41: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:12:41: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:12:41: #1 total tags in treatment: 2412513 INFO @ Sun, 21 Jun 2020 20:12:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:12:41: #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 20:12:41: #1 tags after filtering in treatment: 2412301 INFO @ Sun, 21 Jun 2020 20:12:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:12:41: #1 finished! INFO @ Sun, 21 Jun 2020 20:12:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:12:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:12:41: #2 number of paired peaks: 3492 INFO @ Sun, 21 Jun 2020 20:12:41: start model_add_line... INFO @ Sun, 21 Jun 2020 20:12:42: start X-correlation... INFO @ Sun, 21 Jun 2020 20:12:42: end of X-cor INFO @ Sun, 21 Jun 2020 20:12:42: #2 finished! INFO @ Sun, 21 Jun 2020 20:12:42: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 20:12:42: #2 alternative fragment length(s) may be 104 bps INFO @ Sun, 21 Jun 2020 20:12:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.10_model.r WARNING @ Sun, 21 Jun 2020 20:12:42: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:12:42: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Sun, 21 Jun 2020 20:12:42: #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 20:12:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:12:42: #3 Pre-compute pvalue-qvalue table... 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 20:12:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:12:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.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 20:12:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:12:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:12:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:12:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:12:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.10_summits.bed INFO @ Sun, 21 Jun 2020 20:12:51: Done! pass1 - making usageList (330 chroms): 1 millis pass2 - checking and writing primary data (835 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:12:57: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:13:06: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:13:10: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:13:10: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:13:10: #1 total tags in treatment: 2412513 INFO @ Sun, 21 Jun 2020 20:13:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:13:10: #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 20:13:10: #1 tags after filtering in treatment: 2412301 INFO @ Sun, 21 Jun 2020 20:13:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:13:10: #1 finished! INFO @ Sun, 21 Jun 2020 20:13:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:13:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:13:11: #2 number of paired peaks: 3492 INFO @ Sun, 21 Jun 2020 20:13:11: start model_add_line... INFO @ Sun, 21 Jun 2020 20:13:11: start X-correlation... INFO @ Sun, 21 Jun 2020 20:13:11: end of X-cor INFO @ Sun, 21 Jun 2020 20:13:11: #2 finished! INFO @ Sun, 21 Jun 2020 20:13:11: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 20:13:11: #2 alternative fragment length(s) may be 104 bps INFO @ Sun, 21 Jun 2020 20:13:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.20_model.r WARNING @ Sun, 21 Jun 2020 20:13:11: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:13:11: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Sun, 21 Jun 2020 20:13:11: #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 20:13:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:13:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:13:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:13:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:13:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:13:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2788639/SRX2788639.20_summits.bed INFO @ Sun, 21 Jun 2020 20:13:20: Done! pass1 - making usageList (185 chroms): 1 millis pass2 - checking and writing primary data (382 records, 4 fields): 7 millis CompletedMACS2peakCalling