Job ID = 6458437 SRX = SRX5226991 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:30:08 prefetch.2.10.7: 1) Downloading 'SRR8417906'... 2020-06-21T12:30:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:32:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:32:03 prefetch.2.10.7: 'SRR8417906' is valid 2020-06-21T12:32:03 prefetch.2.10.7: 1) 'SRR8417906' was downloaded successfully 2020-06-21T12:32:03 prefetch.2.10.7: 'SRR8417906' has 0 unresolved dependencies Read 10736313 spots for SRR8417906/SRR8417906.sra Written 10736313 spots for SRR8417906/SRR8417906.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: 00:03:41 10736313 reads; of these: 10736313 (100.00%) were unpaired; of these: 898562 (8.37%) aligned 0 times 7304312 (68.03%) aligned exactly 1 time 2533439 (23.60%) aligned >1 times 91.63% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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] 848072 / 9837751 = 0.0862 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 21:39:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.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 21:39:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:39:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:03: 1000000 INFO @ Sun, 21 Jun 2020 21:40:08: 2000000 INFO @ Sun, 21 Jun 2020 21:40:13: 3000000 INFO @ Sun, 21 Jun 2020 21:40:18: 4000000 INFO @ Sun, 21 Jun 2020 21:40:23: 5000000 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 21:40:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.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 21:40:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:28: 6000000 INFO @ Sun, 21 Jun 2020 21:40:33: 1000000 INFO @ Sun, 21 Jun 2020 21:40:33: 7000000 INFO @ Sun, 21 Jun 2020 21:40:38: 2000000 INFO @ Sun, 21 Jun 2020 21:40:39: 8000000 INFO @ Sun, 21 Jun 2020 21:40:43: 3000000 INFO @ Sun, 21 Jun 2020 21:40:44: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:40:44: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:40:44: #1 total tags in treatment: 8989679 INFO @ Sun, 21 Jun 2020 21:40:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:40:44: #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 21:40:45: #1 tags after filtering in treatment: 8989501 INFO @ Sun, 21 Jun 2020 21:40:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:40:45: #1 finished! INFO @ Sun, 21 Jun 2020 21:40:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:40:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:40:45: #2 number of paired peaks: 1204 INFO @ Sun, 21 Jun 2020 21:40:45: start model_add_line... INFO @ Sun, 21 Jun 2020 21:40:45: start X-correlation... INFO @ Sun, 21 Jun 2020 21:40:45: end of X-cor INFO @ Sun, 21 Jun 2020 21:40:45: #2 finished! INFO @ Sun, 21 Jun 2020 21:40:45: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 21:40:45: #2 alternative fragment length(s) may be 96 bps INFO @ Sun, 21 Jun 2020 21:40:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.05_model.r WARNING @ Sun, 21 Jun 2020 21:40:45: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:40:45: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sun, 21 Jun 2020 21:40:45: #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 21:40:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:40:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:40:48: 4000000 INFO @ Sun, 21 Jun 2020 21:40:54: 5000000 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 21:40:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.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 21:40:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:59: 6000000 INFO @ Sun, 21 Jun 2020 21:41:03: 1000000 INFO @ Sun, 21 Jun 2020 21:41:04: 7000000 INFO @ Sun, 21 Jun 2020 21:41:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:08: 2000000 INFO @ Sun, 21 Jun 2020 21:41:10: 8000000 INFO @ Sun, 21 Jun 2020 21:41:14: 3000000 INFO @ Sun, 21 Jun 2020 21:41:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.05_summits.bed INFO @ Sun, 21 Jun 2020 21:41:15: Done! pass1 - making usageList (419 chroms): 1 millis pass2 - checking and writing primary data (3701 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:41:16: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:41:16: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:41:16: #1 total tags in treatment: 8989679 INFO @ Sun, 21 Jun 2020 21:41:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:16: #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 21:41:16: #1 tags after filtering in treatment: 8989501 INFO @ Sun, 21 Jun 2020 21:41:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:41:16: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:17: #2 number of paired peaks: 1204 INFO @ Sun, 21 Jun 2020 21:41:17: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:17: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:17: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:17: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:17: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 21:41:17: #2 alternative fragment length(s) may be 96 bps INFO @ Sun, 21 Jun 2020 21:41:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.10_model.r WARNING @ Sun, 21 Jun 2020 21:41:17: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:41:17: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sun, 21 Jun 2020 21:41:17: #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 21:41:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:41:19: 4000000 INFO @ Sun, 21 Jun 2020 21:41:25: 5000000 INFO @ Sun, 21 Jun 2020 21:41:30: 6000000 INFO @ Sun, 21 Jun 2020 21:41:36: 7000000 INFO @ Sun, 21 Jun 2020 21:41:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:42: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:41:47: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:41:47: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:41:47: #1 total tags in treatment: 8989679 INFO @ Sun, 21 Jun 2020 21:41:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:47: #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 21:41:48: #1 tags after filtering in treatment: 8989501 INFO @ Sun, 21 Jun 2020 21:41:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:41:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.10_summits.bed INFO @ Sun, 21 Jun 2020 21:41:48: Done! INFO @ Sun, 21 Jun 2020 21:41:49: #2 number of paired peaks: 1204 INFO @ Sun, 21 Jun 2020 21:41:49: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:49: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:49: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:49: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:49: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 21:41:49: #2 alternative fragment length(s) may be 96 bps INFO @ Sun, 21 Jun 2020 21:41:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.20_model.r WARNING @ Sun, 21 Jun 2020 21:41:49: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:41:49: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sun, 21 Jun 2020 21:41:49: #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 21:41:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:49: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (314 chroms): 1 millis pass2 - checking and writing primary data (1581 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:42:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:42:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:42:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:42:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226991/SRX5226991.20_summits.bed INFO @ Sun, 21 Jun 2020 21:42:18: Done! pass1 - making usageList (199 chroms): 1 millis pass2 - checking and writing primary data (598 records, 4 fields): 8 millis CompletedMACS2peakCalling