Job ID = 6458424 SRX = SRX5226983 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:30:53 prefetch.2.10.7: 1) Downloading 'SRR8417898'... 2020-06-21T12:30:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:32:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:32:27 prefetch.2.10.7: 'SRR8417898' is valid 2020-06-21T12:32:27 prefetch.2.10.7: 1) 'SRR8417898' was downloaded successfully 2020-06-21T12:32:27 prefetch.2.10.7: 'SRR8417898' has 0 unresolved dependencies Read 9798542 spots for SRR8417898/SRR8417898.sra Written 9798542 spots for SRR8417898/SRR8417898.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: 00:03:20 9798542 reads; of these: 9798542 (100.00%) were unpaired; of these: 2077939 (21.21%) aligned 0 times 5479754 (55.92%) aligned exactly 1 time 2240849 (22.87%) aligned >1 times 78.79% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 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_rmdupse_core] 792449 / 7720603 = 0.1026 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 21:39:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.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 21:39:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:39:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:39:35: 1000000 INFO @ Sun, 21 Jun 2020 21:39:41: 2000000 INFO @ Sun, 21 Jun 2020 21:39:48: 3000000 INFO @ Sun, 21 Jun 2020 21:39:55: 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 21:39:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.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 21:39:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:39:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:02: 5000000 INFO @ Sun, 21 Jun 2020 21:40:06: 1000000 INFO @ Sun, 21 Jun 2020 21:40:09: 6000000 INFO @ Sun, 21 Jun 2020 21:40:13: 2000000 INFO @ Sun, 21 Jun 2020 21:40:16: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:40:16: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:40:16: #1 total tags in treatment: 6928154 INFO @ Sun, 21 Jun 2020 21:40:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:40:16: #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 21:40:17: #1 tags after filtering in treatment: 6927959 INFO @ Sun, 21 Jun 2020 21:40:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:40:17: #1 finished! INFO @ Sun, 21 Jun 2020 21:40:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:40:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:40:17: #2 number of paired peaks: 1514 INFO @ Sun, 21 Jun 2020 21:40:17: start model_add_line... INFO @ Sun, 21 Jun 2020 21:40:17: start X-correlation... INFO @ Sun, 21 Jun 2020 21:40:17: end of X-cor INFO @ Sun, 21 Jun 2020 21:40:17: #2 finished! INFO @ Sun, 21 Jun 2020 21:40:17: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 21:40:17: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 21:40:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.05_model.r WARNING @ Sun, 21 Jun 2020 21:40:17: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:40:17: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sun, 21 Jun 2020 21:40:17: #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 21:40:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:40:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:40:20: 3000000 INFO @ Sun, 21 Jun 2020 21:40:26: 4000000 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 21:40:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.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 21:40:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:33: 5000000 INFO @ Sun, 21 Jun 2020 21:40:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:40:37: 1000000 INFO @ Sun, 21 Jun 2020 21:40:41: 6000000 INFO @ Sun, 21 Jun 2020 21:40:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:40:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:40:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.05_summits.bed INFO @ Sun, 21 Jun 2020 21:40:42: Done! pass1 - making usageList (440 chroms): 1 millis pass2 - checking and writing primary data (3004 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:40:46: 2000000 INFO @ Sun, 21 Jun 2020 21:40:49: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:40:49: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:40:49: #1 total tags in treatment: 6928154 INFO @ Sun, 21 Jun 2020 21:40:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:40:49: #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 21:40:49: #1 tags after filtering in treatment: 6927959 INFO @ Sun, 21 Jun 2020 21:40:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:40:49: #1 finished! INFO @ Sun, 21 Jun 2020 21:40:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:40:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:40:50: #2 number of paired peaks: 1514 INFO @ Sun, 21 Jun 2020 21:40:50: start model_add_line... INFO @ Sun, 21 Jun 2020 21:40:50: start X-correlation... INFO @ Sun, 21 Jun 2020 21:40:50: end of X-cor INFO @ Sun, 21 Jun 2020 21:40:50: #2 finished! INFO @ Sun, 21 Jun 2020 21:40:50: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 21:40:50: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 21:40:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.10_model.r WARNING @ Sun, 21 Jun 2020 21:40:50: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:40:50: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sun, 21 Jun 2020 21:40:50: #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 21:40:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:40:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:40:54: 3000000 INFO @ Sun, 21 Jun 2020 21:41:03: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:41:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:11: 5000000 INFO @ Sun, 21 Jun 2020 21:41:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.10_summits.bed INFO @ Sun, 21 Jun 2020 21:41:13: Done! pass1 - making usageList (304 chroms): 1 millis pass2 - checking and writing primary data (1400 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:41:19: 6000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:41:27: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:41:27: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:41:27: #1 total tags in treatment: 6928154 INFO @ Sun, 21 Jun 2020 21:41:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:27: #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 21:41:27: #1 tags after filtering in treatment: 6927959 INFO @ Sun, 21 Jun 2020 21:41:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:41:27: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:28: #2 number of paired peaks: 1514 INFO @ Sun, 21 Jun 2020 21:41:28: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:28: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:28: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:28: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:28: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 21:41:28: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 21:41:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.20_model.r WARNING @ Sun, 21 Jun 2020 21:41:28: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:41:28: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sun, 21 Jun 2020 21:41:28: #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 21:41:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:41:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226983/SRX5226983.20_summits.bed INFO @ Sun, 21 Jun 2020 21:41:53: Done! pass1 - making usageList (173 chroms): 1 millis pass2 - checking and writing primary data (528 records, 4 fields): 7 millis CompletedMACS2peakCalling