Job ID = 6455635 SRX = SRX287944 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:05:40 prefetch.2.10.7: 1) Downloading 'SRR870133'... 2020-06-21T10:05:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:08:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:08:44 prefetch.2.10.7: 1) 'SRR870133' was downloaded successfully Read 19653541 spots for SRR870133/SRR870133.sra Written 19653541 spots for SRR870133/SRR870133.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: 00:07:08 19653541 reads; of these: 19653541 (100.00%) were unpaired; of these: 2242586 (11.41%) aligned 0 times 6761616 (34.40%) aligned exactly 1 time 10649339 (54.19%) aligned >1 times 88.59% overall alignment rate Time searching: 00:07:08 Overall time: 00:07:08 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] 4836085 / 17410955 = 0.2778 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 19:21:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.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 19:21:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:21:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:21:19: 1000000 INFO @ Sun, 21 Jun 2020 19:21:24: 2000000 INFO @ Sun, 21 Jun 2020 19:21:29: 3000000 INFO @ Sun, 21 Jun 2020 19:21:34: 4000000 INFO @ Sun, 21 Jun 2020 19:21:39: 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 19:21:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.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 19:21:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:21:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:21:44: 6000000 INFO @ Sun, 21 Jun 2020 19:21:49: 1000000 INFO @ Sun, 21 Jun 2020 19:21:49: 7000000 INFO @ Sun, 21 Jun 2020 19:21:54: 2000000 INFO @ Sun, 21 Jun 2020 19:21:54: 8000000 INFO @ Sun, 21 Jun 2020 19:21:59: 3000000 INFO @ Sun, 21 Jun 2020 19:22:00: 9000000 INFO @ Sun, 21 Jun 2020 19:22:05: 4000000 INFO @ Sun, 21 Jun 2020 19:22:05: 10000000 INFO @ Sun, 21 Jun 2020 19:22:10: 5000000 INFO @ Sun, 21 Jun 2020 19:22:11: 11000000 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 19:22:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.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 19:22:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:22:15: 6000000 INFO @ Sun, 21 Jun 2020 19:22:16: 12000000 INFO @ Sun, 21 Jun 2020 19:22:19: 1000000 INFO @ Sun, 21 Jun 2020 19:22:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:22:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:22:20: #1 total tags in treatment: 12574870 INFO @ Sun, 21 Jun 2020 19:22:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:22:20: #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 19:22:20: #1 tags after filtering in treatment: 12574870 INFO @ Sun, 21 Jun 2020 19:22:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:22:20: #1 finished! INFO @ Sun, 21 Jun 2020 19:22:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:22:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:22:20: 7000000 INFO @ Sun, 21 Jun 2020 19:22:21: #2 number of paired peaks: 3552 INFO @ Sun, 21 Jun 2020 19:22:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:22:21: start X-correlation... INFO @ Sun, 21 Jun 2020 19:22:21: end of X-cor INFO @ Sun, 21 Jun 2020 19:22:21: #2 finished! INFO @ Sun, 21 Jun 2020 19:22:21: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 19:22:21: #2 alternative fragment length(s) may be 4,62 bps INFO @ Sun, 21 Jun 2020 19:22:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.05_model.r WARNING @ Sun, 21 Jun 2020 19:22:21: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:22:21: #2 You may need to consider one of the other alternative d(s): 4,62 WARNING @ Sun, 21 Jun 2020 19:22:21: #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 19:22:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:22:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:22:24: 2000000 INFO @ Sun, 21 Jun 2020 19:22:26: 8000000 INFO @ Sun, 21 Jun 2020 19:22:30: 3000000 INFO @ Sun, 21 Jun 2020 19:22:31: 9000000 INFO @ Sun, 21 Jun 2020 19:22:35: 4000000 INFO @ Sun, 21 Jun 2020 19:22:37: 10000000 INFO @ Sun, 21 Jun 2020 19:22:40: 5000000 INFO @ Sun, 21 Jun 2020 19:22:43: 11000000 INFO @ Sun, 21 Jun 2020 19:22:46: 6000000 INFO @ Sun, 21 Jun 2020 19:22:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:22:49: 12000000 INFO @ Sun, 21 Jun 2020 19:22:51: 7000000 INFO @ Sun, 21 Jun 2020 19:22:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:22:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:22:52: #1 total tags in treatment: 12574870 INFO @ Sun, 21 Jun 2020 19:22:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:22:52: #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 19:22:53: #1 tags after filtering in treatment: 12574870 INFO @ Sun, 21 Jun 2020 19:22:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:22:53: #1 finished! INFO @ Sun, 21 Jun 2020 19:22:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:22:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:22:54: #2 number of paired peaks: 3552 INFO @ Sun, 21 Jun 2020 19:22:54: start model_add_line... INFO @ Sun, 21 Jun 2020 19:22:54: start X-correlation... INFO @ Sun, 21 Jun 2020 19:22:54: end of X-cor INFO @ Sun, 21 Jun 2020 19:22:54: #2 finished! INFO @ Sun, 21 Jun 2020 19:22:54: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 19:22:54: #2 alternative fragment length(s) may be 4,62 bps INFO @ Sun, 21 Jun 2020 19:22:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.10_model.r WARNING @ Sun, 21 Jun 2020 19:22:54: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:22:54: #2 You may need to consider one of the other alternative d(s): 4,62 WARNING @ Sun, 21 Jun 2020 19:22:54: #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 19:22:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:22:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:22:56: 8000000 INFO @ Sun, 21 Jun 2020 19:23:02: 9000000 INFO @ Sun, 21 Jun 2020 19:23:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:23:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:23:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.05_summits.bed INFO @ Sun, 21 Jun 2020 19:23:03: Done! pass1 - making usageList (1438 chroms): 2 millis pass2 - checking and writing primary data (9611 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:23:07: 10000000 INFO @ Sun, 21 Jun 2020 19:23:13: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:23:18: 12000000 INFO @ Sun, 21 Jun 2020 19:23:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:23:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:23:22: #1 total tags in treatment: 12574870 INFO @ Sun, 21 Jun 2020 19:23:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:23:22: #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 19:23:22: #1 tags after filtering in treatment: 12574870 INFO @ Sun, 21 Jun 2020 19:23:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:23:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:23:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:23:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:23:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:23:23: #2 number of paired peaks: 3552 INFO @ Sun, 21 Jun 2020 19:23:23: start model_add_line... INFO @ Sun, 21 Jun 2020 19:23:23: start X-correlation... INFO @ Sun, 21 Jun 2020 19:23:23: end of X-cor INFO @ Sun, 21 Jun 2020 19:23:23: #2 finished! INFO @ Sun, 21 Jun 2020 19:23:23: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 19:23:23: #2 alternative fragment length(s) may be 4,62 bps INFO @ Sun, 21 Jun 2020 19:23:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.20_model.r WARNING @ Sun, 21 Jun 2020 19:23:23: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:23:23: #2 You may need to consider one of the other alternative d(s): 4,62 WARNING @ Sun, 21 Jun 2020 19:23:23: #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 19:23:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:23:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:23:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:23:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:23:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.10_summits.bed INFO @ Sun, 21 Jun 2020 19:23:37: Done! pass1 - making usageList (1195 chroms): 1 millis pass2 - checking and writing primary data (4758 records, 4 fields): 38 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:23:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:24:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:24:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:24:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287944/SRX287944.20_summits.bed INFO @ Sun, 21 Jun 2020 19:24:04: Done! pass1 - making usageList (914 chroms): 2 millis pass2 - checking and writing primary data (2539 records, 4 fields): 24 millis CompletedMACS2peakCalling