Job ID = 6458247 SRX = SRX5011014 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:20:07 prefetch.2.10.7: 1) Downloading 'SRR8191463'... 2020-06-21T12:20:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:22:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:22:23 prefetch.2.10.7: 'SRR8191463' is valid 2020-06-21T12:22:23 prefetch.2.10.7: 1) 'SRR8191463' was downloaded successfully 2020-06-21T12:22:23 prefetch.2.10.7: 'SRR8191463' has 0 unresolved dependencies Read 23240584 spots for SRR8191463/SRR8191463.sra Written 23240584 spots for SRR8191463/SRR8191463.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: 00:06:03 23240584 reads; of these: 23240584 (100.00%) were unpaired; of these: 568093 (2.44%) aligned 0 times 16231335 (69.84%) aligned exactly 1 time 6441156 (27.72%) aligned >1 times 97.56% overall alignment rate Time searching: 00:06:03 Overall time: 00:06:03 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] 9588377 / 22672491 = 0.4229 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 21:33:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.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 21:33:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:33:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:33:33: 1000000 INFO @ Sun, 21 Jun 2020 21:33:39: 2000000 INFO @ Sun, 21 Jun 2020 21:33:45: 3000000 INFO @ Sun, 21 Jun 2020 21:33:51: 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 21:33:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.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 21:33:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:33:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:33:57: 5000000 INFO @ Sun, 21 Jun 2020 21:34:03: 6000000 INFO @ Sun, 21 Jun 2020 21:34:03: 1000000 INFO @ Sun, 21 Jun 2020 21:34:10: 7000000 INFO @ Sun, 21 Jun 2020 21:34:10: 2000000 INFO @ Sun, 21 Jun 2020 21:34:16: 8000000 INFO @ Sun, 21 Jun 2020 21:34:17: 3000000 INFO @ Sun, 21 Jun 2020 21:34:23: 9000000 INFO @ Sun, 21 Jun 2020 21:34:24: 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 21:34:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.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 21:34:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:34:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:34:29: 10000000 INFO @ Sun, 21 Jun 2020 21:34:30: 5000000 INFO @ Sun, 21 Jun 2020 21:34:33: 1000000 INFO @ Sun, 21 Jun 2020 21:34:36: 11000000 INFO @ Sun, 21 Jun 2020 21:34:37: 6000000 INFO @ Sun, 21 Jun 2020 21:34:39: 2000000 INFO @ Sun, 21 Jun 2020 21:34:42: 12000000 INFO @ Sun, 21 Jun 2020 21:34:43: 7000000 INFO @ Sun, 21 Jun 2020 21:34:45: 3000000 INFO @ Sun, 21 Jun 2020 21:34:49: 13000000 INFO @ Sun, 21 Jun 2020 21:34:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:34:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:34:49: #1 total tags in treatment: 13084114 INFO @ Sun, 21 Jun 2020 21:34:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:34:49: #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 21:34:50: 8000000 INFO @ Sun, 21 Jun 2020 21:34:50: #1 tags after filtering in treatment: 13084063 INFO @ Sun, 21 Jun 2020 21:34:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:34:50: #1 finished! INFO @ Sun, 21 Jun 2020 21:34:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:34:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:34:50: 4000000 INFO @ Sun, 21 Jun 2020 21:34:51: #2 number of paired peaks: 1400 INFO @ Sun, 21 Jun 2020 21:34:51: start model_add_line... INFO @ Sun, 21 Jun 2020 21:34:51: start X-correlation... INFO @ Sun, 21 Jun 2020 21:34:51: end of X-cor INFO @ Sun, 21 Jun 2020 21:34:51: #2 finished! INFO @ Sun, 21 Jun 2020 21:34:51: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 21:34:51: #2 alternative fragment length(s) may be 3,58 bps INFO @ Sun, 21 Jun 2020 21:34:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.05_model.r WARNING @ Sun, 21 Jun 2020 21:34:51: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:34:51: #2 You may need to consider one of the other alternative d(s): 3,58 WARNING @ Sun, 21 Jun 2020 21:34:51: #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 21:34:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:34:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:34:56: 5000000 INFO @ Sun, 21 Jun 2020 21:34:56: 9000000 INFO @ Sun, 21 Jun 2020 21:35:02: 6000000 INFO @ Sun, 21 Jun 2020 21:35:03: 10000000 INFO @ Sun, 21 Jun 2020 21:35:08: 7000000 INFO @ Sun, 21 Jun 2020 21:35:10: 11000000 INFO @ Sun, 21 Jun 2020 21:35:14: 8000000 INFO @ Sun, 21 Jun 2020 21:35:16: 12000000 INFO @ Sun, 21 Jun 2020 21:35:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:35:20: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:35:23: 13000000 INFO @ Sun, 21 Jun 2020 21:35:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:35:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:35:24: #1 total tags in treatment: 13084114 INFO @ Sun, 21 Jun 2020 21:35:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:35:24: #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 21:35:24: #1 tags after filtering in treatment: 13084063 INFO @ Sun, 21 Jun 2020 21:35:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:35:24: #1 finished! INFO @ Sun, 21 Jun 2020 21:35:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:35:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:35:25: #2 number of paired peaks: 1400 INFO @ Sun, 21 Jun 2020 21:35:25: start model_add_line... INFO @ Sun, 21 Jun 2020 21:35:25: start X-correlation... INFO @ Sun, 21 Jun 2020 21:35:25: end of X-cor INFO @ Sun, 21 Jun 2020 21:35:25: #2 finished! INFO @ Sun, 21 Jun 2020 21:35:25: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 21:35:25: #2 alternative fragment length(s) may be 3,58 bps INFO @ Sun, 21 Jun 2020 21:35:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.10_model.r WARNING @ Sun, 21 Jun 2020 21:35:25: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:35:25: #2 You may need to consider one of the other alternative d(s): 3,58 WARNING @ Sun, 21 Jun 2020 21:35:25: #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 21:35:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:35:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:35:26: 10000000 INFO @ Sun, 21 Jun 2020 21:35:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:35:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:35:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.05_summits.bed INFO @ Sun, 21 Jun 2020 21:35:30: Done! pass1 - making usageList (757 chroms): 2 millis pass2 - checking and writing primary data (3975 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:35:31: 11000000 INFO @ Sun, 21 Jun 2020 21:35:36: 12000000 INFO @ Sun, 21 Jun 2020 21:35:42: 13000000 INFO @ Sun, 21 Jun 2020 21:35:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:35:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:35:42: #1 total tags in treatment: 13084114 INFO @ Sun, 21 Jun 2020 21:35:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:35:42: #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 21:35:43: #1 tags after filtering in treatment: 13084063 INFO @ Sun, 21 Jun 2020 21:35:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:35:43: #1 finished! INFO @ Sun, 21 Jun 2020 21:35:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:35:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:35:44: #2 number of paired peaks: 1400 INFO @ Sun, 21 Jun 2020 21:35:44: start model_add_line... INFO @ Sun, 21 Jun 2020 21:35:44: start X-correlation... INFO @ Sun, 21 Jun 2020 21:35:44: end of X-cor INFO @ Sun, 21 Jun 2020 21:35:44: #2 finished! INFO @ Sun, 21 Jun 2020 21:35:44: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 21:35:44: #2 alternative fragment length(s) may be 3,58 bps INFO @ Sun, 21 Jun 2020 21:35:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.20_model.r WARNING @ Sun, 21 Jun 2020 21:35:44: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:35:44: #2 You may need to consider one of the other alternative d(s): 3,58 WARNING @ Sun, 21 Jun 2020 21:35:44: #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 21:35:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:35:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:35:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:36:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.10_summits.bed INFO @ Sun, 21 Jun 2020 21:36:04: Done! pass1 - making usageList (624 chroms): 1 millis pass2 - checking and writing primary data (2386 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:36:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:36:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011014/SRX5011014.20_summits.bed INFO @ Sun, 21 Jun 2020 21:36:23: Done! pass1 - making usageList (339 chroms): 1 millis pass2 - checking and writing primary data (789 records, 4 fields): 10 millis CompletedMACS2peakCalling