Job ID = 6458830 SRX = SRX5661477 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:55:40 prefetch.2.10.7: 1) Downloading 'SRR8874484'... 2020-06-21T12:55:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:00:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:00:03 prefetch.2.10.7: 1) 'SRR8874484' was downloaded successfully 2020-06-21T13:00:03 prefetch.2.10.7: 'SRR8874484' has 0 unresolved dependencies Read 34877874 spots for SRR8874484/SRR8874484.sra Written 34877874 spots for SRR8874484/SRR8874484.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: 00:10:22 34877874 reads; of these: 34877874 (100.00%) were unpaired; of these: 6878868 (19.72%) aligned 0 times 20133585 (57.73%) aligned exactly 1 time 7865421 (22.55%) aligned >1 times 80.28% overall alignment rate Time searching: 00:10:22 Overall time: 00:10:22 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 12 files... [bam_rmdupse_core] 19555306 / 27999006 = 0.6984 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 22:16:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.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 22:16:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:16:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:03: 1000000 INFO @ Sun, 21 Jun 2020 22:17:09: 2000000 INFO @ Sun, 21 Jun 2020 22:17:15: 3000000 INFO @ Sun, 21 Jun 2020 22:17:21: 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 22:17:27: 5000000 INFO @ Sun, 21 Jun 2020 22:17:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.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 22:17:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:17:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:33: 6000000 INFO @ Sun, 21 Jun 2020 22:17:34: 1000000 INFO @ Sun, 21 Jun 2020 22:17:40: 7000000 INFO @ Sun, 21 Jun 2020 22:17:40: 2000000 INFO @ Sun, 21 Jun 2020 22:17:46: 8000000 INFO @ Sun, 21 Jun 2020 22:17:47: 3000000 INFO @ Sun, 21 Jun 2020 22:17:49: #1 tag size is determined as 62 bps INFO @ Sun, 21 Jun 2020 22:17:49: #1 tag size = 62 INFO @ Sun, 21 Jun 2020 22:17:49: #1 total tags in treatment: 8443700 INFO @ Sun, 21 Jun 2020 22:17:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:17:49: #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 22:17:49: #1 tags after filtering in treatment: 8443689 INFO @ Sun, 21 Jun 2020 22:17:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:17:49: #1 finished! INFO @ Sun, 21 Jun 2020 22:17:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:17:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:17:50: #2 number of paired peaks: 1659 INFO @ Sun, 21 Jun 2020 22:17:50: start model_add_line... INFO @ Sun, 21 Jun 2020 22:17:50: start X-correlation... INFO @ Sun, 21 Jun 2020 22:17:50: end of X-cor INFO @ Sun, 21 Jun 2020 22:17:50: #2 finished! INFO @ Sun, 21 Jun 2020 22:17:50: #2 predicted fragment length is 67 bps INFO @ Sun, 21 Jun 2020 22:17:50: #2 alternative fragment length(s) may be 4,67 bps INFO @ Sun, 21 Jun 2020 22:17:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.05_model.r WARNING @ Sun, 21 Jun 2020 22:17:50: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:17:50: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Sun, 21 Jun 2020 22:17:50: #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 22:17:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:17:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:17:53: 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 22:17:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.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 22:17:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:17:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:59: 5000000 INFO @ Sun, 21 Jun 2020 22:18:04: 1000000 INFO @ Sun, 21 Jun 2020 22:18:06: 6000000 INFO @ Sun, 21 Jun 2020 22:18:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:18:10: 2000000 INFO @ Sun, 21 Jun 2020 22:18:12: 7000000 INFO @ Sun, 21 Jun 2020 22:18:17: 3000000 INFO @ Sun, 21 Jun 2020 22:18:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:18:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:18:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.05_summits.bed INFO @ Sun, 21 Jun 2020 22:18:18: Done! pass1 - making usageList (925 chroms): 2 millis pass2 - checking and writing primary data (3889 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:18:19: 8000000 INFO @ Sun, 21 Jun 2020 22:18:22: #1 tag size is determined as 62 bps INFO @ Sun, 21 Jun 2020 22:18:22: #1 tag size = 62 INFO @ Sun, 21 Jun 2020 22:18:22: #1 total tags in treatment: 8443700 INFO @ Sun, 21 Jun 2020 22:18:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:18:22: #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 22:18:22: #1 tags after filtering in treatment: 8443689 INFO @ Sun, 21 Jun 2020 22:18:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:18:22: #1 finished! INFO @ Sun, 21 Jun 2020 22:18:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:18:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:18:23: #2 number of paired peaks: 1659 INFO @ Sun, 21 Jun 2020 22:18:23: start model_add_line... INFO @ Sun, 21 Jun 2020 22:18:23: start X-correlation... INFO @ Sun, 21 Jun 2020 22:18:23: end of X-cor INFO @ Sun, 21 Jun 2020 22:18:23: #2 finished! INFO @ Sun, 21 Jun 2020 22:18:23: #2 predicted fragment length is 67 bps INFO @ Sun, 21 Jun 2020 22:18:23: #2 alternative fragment length(s) may be 4,67 bps INFO @ Sun, 21 Jun 2020 22:18:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.10_model.r WARNING @ Sun, 21 Jun 2020 22:18:23: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:18:23: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Sun, 21 Jun 2020 22:18:23: #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 22:18:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:18:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:18:23: 4000000 INFO @ Sun, 21 Jun 2020 22:18:29: 5000000 INFO @ Sun, 21 Jun 2020 22:18:35: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:18:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:18:42: 7000000 INFO @ Sun, 21 Jun 2020 22:18:48: 8000000 INFO @ Sun, 21 Jun 2020 22:18:51: #1 tag size is determined as 62 bps INFO @ Sun, 21 Jun 2020 22:18:51: #1 tag size = 62 INFO @ Sun, 21 Jun 2020 22:18:51: #1 total tags in treatment: 8443700 INFO @ Sun, 21 Jun 2020 22:18:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:18:51: #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 22:18:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:18:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:18:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.10_summits.bed INFO @ Sun, 21 Jun 2020 22:18:51: Done! INFO @ Sun, 21 Jun 2020 22:18:51: #1 tags after filtering in treatment: 8443689 INFO @ Sun, 21 Jun 2020 22:18:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:18:51: #1 finished! INFO @ Sun, 21 Jun 2020 22:18:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:18:51: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (698 chroms): 1 millis pass2 - checking and writing primary data (2357 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:18:52: #2 number of paired peaks: 1659 INFO @ Sun, 21 Jun 2020 22:18:52: start model_add_line... INFO @ Sun, 21 Jun 2020 22:18:52: start X-correlation... INFO @ Sun, 21 Jun 2020 22:18:52: end of X-cor INFO @ Sun, 21 Jun 2020 22:18:52: #2 finished! INFO @ Sun, 21 Jun 2020 22:18:52: #2 predicted fragment length is 67 bps INFO @ Sun, 21 Jun 2020 22:18:52: #2 alternative fragment length(s) may be 4,67 bps INFO @ Sun, 21 Jun 2020 22:18:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.20_model.r WARNING @ Sun, 21 Jun 2020 22:18:52: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:18:52: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Sun, 21 Jun 2020 22:18:52: #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 22:18:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:18:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:19:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:19:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:19:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:19:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661477/SRX5661477.20_summits.bed INFO @ Sun, 21 Jun 2020 22:19:20: Done! pass1 - making usageList (546 chroms): 3 millis pass2 - checking and writing primary data (1528 records, 4 fields): 17 millis CompletedMACS2peakCalling