Job ID = 6458934 SRX = SRX5775934 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:43:40 prefetch.2.10.7: 1) Downloading 'SRR8997137'... 2020-06-21T12:43:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:49:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:49:10 prefetch.2.10.7: 1) 'SRR8997137' was downloaded successfully Read 31653361 spots for SRR8997137/SRR8997137.sra Written 31653361 spots for SRR8997137/SRR8997137.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: 00:08:09 31653361 reads; of these: 31653361 (100.00%) were unpaired; of these: 17201974 (54.34%) aligned 0 times 10285108 (32.49%) aligned exactly 1 time 4166279 (13.16%) aligned >1 times 45.66% overall alignment rate Time searching: 00:08:09 Overall time: 00:08:09 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] 10611013 / 14451387 = 0.7343 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 22:02:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.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 22:02:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:02:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:02:18: 1000000 INFO @ Sun, 21 Jun 2020 22:02:24: 2000000 INFO @ Sun, 21 Jun 2020 22:02:30: 3000000 INFO @ Sun, 21 Jun 2020 22:02:35: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:02:35: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:02:35: #1 total tags in treatment: 3840374 INFO @ Sun, 21 Jun 2020 22:02:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:02:35: #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 22:02:36: #1 tags after filtering in treatment: 3840356 INFO @ Sun, 21 Jun 2020 22:02:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:02:36: #1 finished! INFO @ Sun, 21 Jun 2020 22:02:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:02:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:02:36: #2 number of paired peaks: 1689 INFO @ Sun, 21 Jun 2020 22:02:36: start model_add_line... INFO @ Sun, 21 Jun 2020 22:02:36: start X-correlation... INFO @ Sun, 21 Jun 2020 22:02:36: end of X-cor INFO @ Sun, 21 Jun 2020 22:02:36: #2 finished! INFO @ Sun, 21 Jun 2020 22:02:36: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 22:02:36: #2 alternative fragment length(s) may be 79 bps INFO @ Sun, 21 Jun 2020 22:02:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.05_model.r WARNING @ Sun, 21 Jun 2020 22:02:36: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:02:36: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Sun, 21 Jun 2020 22:02:36: #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 22:02:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:02:36: #3 Pre-compute pvalue-qvalue table... 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 22:02:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.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 22:02:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:02:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:02:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:02:49: 1000000 INFO @ Sun, 21 Jun 2020 22:02:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:02:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:02:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.05_summits.bed INFO @ Sun, 21 Jun 2020 22:02:49: Done! pass1 - making usageList (722 chroms): 1 millis pass2 - checking and writing primary data (2490 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:02:55: 2000000 INFO @ Sun, 21 Jun 2020 22:03:01: 3000000 INFO @ Sun, 21 Jun 2020 22:03:06: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:03:06: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:03:06: #1 total tags in treatment: 3840374 INFO @ Sun, 21 Jun 2020 22:03:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:03:06: #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 22:03:07: #1 tags after filtering in treatment: 3840356 INFO @ Sun, 21 Jun 2020 22:03:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:03:07: #1 finished! INFO @ Sun, 21 Jun 2020 22:03:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:03:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:03:07: #2 number of paired peaks: 1689 INFO @ Sun, 21 Jun 2020 22:03:07: start model_add_line... INFO @ Sun, 21 Jun 2020 22:03:07: start X-correlation... INFO @ Sun, 21 Jun 2020 22:03:07: end of X-cor INFO @ Sun, 21 Jun 2020 22:03:07: #2 finished! INFO @ Sun, 21 Jun 2020 22:03:07: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 22:03:07: #2 alternative fragment length(s) may be 79 bps INFO @ Sun, 21 Jun 2020 22:03:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.10_model.r WARNING @ Sun, 21 Jun 2020 22:03:07: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:03:07: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Sun, 21 Jun 2020 22:03:07: #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 22:03:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:03:07: #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 22:03:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.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 22:03:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:03:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:03:20: 1000000 INFO @ Sun, 21 Jun 2020 22:03:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:03:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:03:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.10_summits.bed INFO @ Sun, 21 Jun 2020 22:03:20: Done! pass1 - making usageList (577 chroms): 1 millis pass2 - checking and writing primary data (1649 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:03:27: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:03:34: 3000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:03:40: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:03:40: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:03:40: #1 total tags in treatment: 3840374 INFO @ Sun, 21 Jun 2020 22:03:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:03:40: #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 22:03:41: #1 tags after filtering in treatment: 3840356 INFO @ Sun, 21 Jun 2020 22:03:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:03:41: #1 finished! INFO @ Sun, 21 Jun 2020 22:03:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:03:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:03:41: #2 number of paired peaks: 1689 INFO @ Sun, 21 Jun 2020 22:03:41: start model_add_line... INFO @ Sun, 21 Jun 2020 22:03:41: start X-correlation... INFO @ Sun, 21 Jun 2020 22:03:41: end of X-cor INFO @ Sun, 21 Jun 2020 22:03:41: #2 finished! INFO @ Sun, 21 Jun 2020 22:03:41: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 22:03:41: #2 alternative fragment length(s) may be 79 bps INFO @ Sun, 21 Jun 2020 22:03:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.20_model.r WARNING @ Sun, 21 Jun 2020 22:03:41: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:03:41: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Sun, 21 Jun 2020 22:03:41: #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 22:03:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:03:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:03:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:03:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:03:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:03:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775934/SRX5775934.20_summits.bed INFO @ Sun, 21 Jun 2020 22:03:54: Done! pass1 - making usageList (442 chroms): 1 millis pass2 - checking and writing primary data (1110 records, 4 fields): 13 millis CompletedMACS2peakCalling