Job ID = 6459417 SRX = SRX6747983 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:13:49 prefetch.2.10.7: 1) Downloading 'SRR10009758'... 2020-06-21T13:13:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:20:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:20:51 prefetch.2.10.7: 1) 'SRR10009758' was downloaded successfully 2020-06-21T13:20:51 prefetch.2.10.7: 'SRR10009758' has 0 unresolved dependencies Read 36915668 spots for SRR10009758/SRR10009758.sra Written 36915668 spots for SRR10009758/SRR10009758.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: 00:08:57 36915668 reads; of these: 36915668 (100.00%) were unpaired; of these: 22285747 (60.37%) aligned 0 times 9684505 (26.23%) aligned exactly 1 time 4945416 (13.40%) aligned >1 times 39.63% overall alignment rate Time searching: 00:08:57 Overall time: 00:08:57 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] 3180926 / 14629921 = 0.2174 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 22:36:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.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 22:36:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:36:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:36:14: 1000000 INFO @ Sun, 21 Jun 2020 22:36:20: 2000000 INFO @ Sun, 21 Jun 2020 22:36:26: 3000000 INFO @ Sun, 21 Jun 2020 22:36:31: 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 22:36:37: 5000000 INFO @ Sun, 21 Jun 2020 22:36:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.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 22:36:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:36:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:36:43: 6000000 INFO @ Sun, 21 Jun 2020 22:36:44: 1000000 INFO @ Sun, 21 Jun 2020 22:36:49: 7000000 INFO @ Sun, 21 Jun 2020 22:36:50: 2000000 INFO @ Sun, 21 Jun 2020 22:36:55: 8000000 INFO @ Sun, 21 Jun 2020 22:36:57: 3000000 INFO @ Sun, 21 Jun 2020 22:37:01: 9000000 INFO @ Sun, 21 Jun 2020 22:37:03: 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 22:37:08: 10000000 INFO @ Sun, 21 Jun 2020 22:37:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.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 22:37:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:37:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:37:09: 5000000 INFO @ Sun, 21 Jun 2020 22:37:14: 11000000 INFO @ Sun, 21 Jun 2020 22:37:15: 1000000 INFO @ Sun, 21 Jun 2020 22:37:16: 6000000 INFO @ Sun, 21 Jun 2020 22:37:17: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:37:17: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:37:17: #1 total tags in treatment: 11448995 INFO @ Sun, 21 Jun 2020 22:37:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:37:17: #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 22:37:18: #1 tags after filtering in treatment: 11448889 INFO @ Sun, 21 Jun 2020 22:37:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:37:18: #1 finished! INFO @ Sun, 21 Jun 2020 22:37:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:37:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:37:19: #2 number of paired peaks: 2087 INFO @ Sun, 21 Jun 2020 22:37:19: start model_add_line... INFO @ Sun, 21 Jun 2020 22:37:19: start X-correlation... INFO @ Sun, 21 Jun 2020 22:37:19: end of X-cor INFO @ Sun, 21 Jun 2020 22:37:19: #2 finished! INFO @ Sun, 21 Jun 2020 22:37:19: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 22:37:19: #2 alternative fragment length(s) may be 3,77 bps INFO @ Sun, 21 Jun 2020 22:37:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.05_model.r WARNING @ Sun, 21 Jun 2020 22:37:19: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:37:19: #2 You may need to consider one of the other alternative d(s): 3,77 WARNING @ Sun, 21 Jun 2020 22:37:19: #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 22:37:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:37:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:37:21: 2000000 INFO @ Sun, 21 Jun 2020 22:37:22: 7000000 INFO @ Sun, 21 Jun 2020 22:37:27: 3000000 INFO @ Sun, 21 Jun 2020 22:37:28: 8000000 INFO @ Sun, 21 Jun 2020 22:37:33: 4000000 INFO @ Sun, 21 Jun 2020 22:37:34: 9000000 INFO @ Sun, 21 Jun 2020 22:37:39: 5000000 INFO @ Sun, 21 Jun 2020 22:37:41: 10000000 INFO @ Sun, 21 Jun 2020 22:37:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:37:45: 6000000 INFO @ Sun, 21 Jun 2020 22:37:47: 11000000 INFO @ Sun, 21 Jun 2020 22:37:50: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:37:50: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:37:50: #1 total tags in treatment: 11448995 INFO @ Sun, 21 Jun 2020 22:37:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:37:50: #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 22:37:51: #1 tags after filtering in treatment: 11448889 INFO @ Sun, 21 Jun 2020 22:37:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:37:51: #1 finished! INFO @ Sun, 21 Jun 2020 22:37:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:37:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:37:52: 7000000 INFO @ Sun, 21 Jun 2020 22:37:52: #2 number of paired peaks: 2087 INFO @ Sun, 21 Jun 2020 22:37:52: start model_add_line... INFO @ Sun, 21 Jun 2020 22:37:52: start X-correlation... INFO @ Sun, 21 Jun 2020 22:37:52: end of X-cor INFO @ Sun, 21 Jun 2020 22:37:52: #2 finished! INFO @ Sun, 21 Jun 2020 22:37:52: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 22:37:52: #2 alternative fragment length(s) may be 3,77 bps INFO @ Sun, 21 Jun 2020 22:37:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.10_model.r WARNING @ Sun, 21 Jun 2020 22:37:52: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:37:52: #2 You may need to consider one of the other alternative d(s): 3,77 WARNING @ Sun, 21 Jun 2020 22:37:52: #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 22:37:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:37:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:37:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:37:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:37:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.05_summits.bed INFO @ Sun, 21 Jun 2020 22:37:56: Done! pass1 - making usageList (636 chroms): 1 millis pass2 - checking and writing primary data (2704 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:37:58: 8000000 INFO @ Sun, 21 Jun 2020 22:38:04: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:38:10: 10000000 INFO @ Sun, 21 Jun 2020 22:38:16: 11000000 INFO @ Sun, 21 Jun 2020 22:38:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:38:19: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:38:19: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:38:19: #1 total tags in treatment: 11448995 INFO @ Sun, 21 Jun 2020 22:38:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:38:19: #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 22:38:19: #1 tags after filtering in treatment: 11448889 INFO @ Sun, 21 Jun 2020 22:38:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:38:19: #1 finished! INFO @ Sun, 21 Jun 2020 22:38:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:38:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:38:20: #2 number of paired peaks: 2087 INFO @ Sun, 21 Jun 2020 22:38:20: start model_add_line... INFO @ Sun, 21 Jun 2020 22:38:20: start X-correlation... INFO @ Sun, 21 Jun 2020 22:38:20: end of X-cor INFO @ Sun, 21 Jun 2020 22:38:20: #2 finished! INFO @ Sun, 21 Jun 2020 22:38:20: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 22:38:20: #2 alternative fragment length(s) may be 3,77 bps INFO @ Sun, 21 Jun 2020 22:38:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.20_model.r WARNING @ Sun, 21 Jun 2020 22:38:20: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:38:20: #2 You may need to consider one of the other alternative d(s): 3,77 WARNING @ Sun, 21 Jun 2020 22:38:20: #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 22:38:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:38:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:38:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:38:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:38:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.10_summits.bed INFO @ Sun, 21 Jun 2020 22:38:28: Done! pass1 - making usageList (542 chroms): 1 millis pass2 - checking and writing primary data (1801 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:38:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:38:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:38:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:38:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6747983/SRX6747983.20_summits.bed INFO @ Sun, 21 Jun 2020 22:38:56: Done! pass1 - making usageList (451 chroms): 1 millis pass2 - checking and writing primary data (1209 records, 4 fields): 14 millis CompletedMACS2peakCalling