Job ID = 6454231 SRX = SRX193310 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:55:35 prefetch.2.10.7: 1) Downloading 'SRR585043'... 2020-06-21T08:55:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:04:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:04:26 prefetch.2.10.7: 1) 'SRR585043' was downloaded successfully Read 28305986 spots for SRR585043/SRR585043.sra Written 28305986 spots for SRR585043/SRR585043.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: 00:08:46 28305986 reads; of these: 28305986 (100.00%) were unpaired; of these: 1114207 (3.94%) aligned 0 times 17453021 (61.66%) aligned exactly 1 time 9738758 (34.41%) aligned >1 times 96.06% overall alignment rate Time searching: 00:08:46 Overall time: 00:08:46 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] 7749544 / 27191779 = 0.2850 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 18:20:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.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 18:20:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:20:48: 1000000 INFO @ Sun, 21 Jun 2020 18:20:53: 2000000 INFO @ Sun, 21 Jun 2020 18:20:58: 3000000 INFO @ Sun, 21 Jun 2020 18:21:03: 4000000 INFO @ Sun, 21 Jun 2020 18:21:08: 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 18:21:13: 6000000 INFO @ Sun, 21 Jun 2020 18:21:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.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 18:21:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:21:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:21:18: 7000000 INFO @ Sun, 21 Jun 2020 18:21:19: 1000000 INFO @ Sun, 21 Jun 2020 18:21:23: 8000000 INFO @ Sun, 21 Jun 2020 18:21:24: 2000000 INFO @ Sun, 21 Jun 2020 18:21:28: 9000000 INFO @ Sun, 21 Jun 2020 18:21:30: 3000000 INFO @ Sun, 21 Jun 2020 18:21:33: 10000000 INFO @ Sun, 21 Jun 2020 18:21:36: 4000000 INFO @ Sun, 21 Jun 2020 18:21:38: 11000000 INFO @ Sun, 21 Jun 2020 18:21:41: 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 18:21:43: 12000000 INFO @ Sun, 21 Jun 2020 18:21:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.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 18:21:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:21:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:21:47: 6000000 INFO @ Sun, 21 Jun 2020 18:21:48: 13000000 INFO @ Sun, 21 Jun 2020 18:21:49: 1000000 INFO @ Sun, 21 Jun 2020 18:21:52: 7000000 INFO @ Sun, 21 Jun 2020 18:21:53: 14000000 INFO @ Sun, 21 Jun 2020 18:21:54: 2000000 INFO @ Sun, 21 Jun 2020 18:21:58: 8000000 INFO @ Sun, 21 Jun 2020 18:21:58: 15000000 INFO @ Sun, 21 Jun 2020 18:21:59: 3000000 INFO @ Sun, 21 Jun 2020 18:22:03: 16000000 INFO @ Sun, 21 Jun 2020 18:22:03: 9000000 INFO @ Sun, 21 Jun 2020 18:22:04: 4000000 INFO @ Sun, 21 Jun 2020 18:22:08: 17000000 INFO @ Sun, 21 Jun 2020 18:22:09: 10000000 INFO @ Sun, 21 Jun 2020 18:22:09: 5000000 INFO @ Sun, 21 Jun 2020 18:22:13: 18000000 INFO @ Sun, 21 Jun 2020 18:22:15: 6000000 INFO @ Sun, 21 Jun 2020 18:22:15: 11000000 INFO @ Sun, 21 Jun 2020 18:22:19: 19000000 INFO @ Sun, 21 Jun 2020 18:22:20: 7000000 INFO @ Sun, 21 Jun 2020 18:22:20: 12000000 INFO @ Sun, 21 Jun 2020 18:22:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:22:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:22:21: #1 total tags in treatment: 19442235 INFO @ Sun, 21 Jun 2020 18:22:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:22:21: #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 18:22:22: #1 tags after filtering in treatment: 19442173 INFO @ Sun, 21 Jun 2020 18:22:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:22:22: #1 finished! INFO @ Sun, 21 Jun 2020 18:22:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:22:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:22:23: #2 number of paired peaks: 1526 INFO @ Sun, 21 Jun 2020 18:22:23: start model_add_line... INFO @ Sun, 21 Jun 2020 18:22:23: start X-correlation... INFO @ Sun, 21 Jun 2020 18:22:23: end of X-cor INFO @ Sun, 21 Jun 2020 18:22:23: #2 finished! INFO @ Sun, 21 Jun 2020 18:22:23: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 18:22:23: #2 alternative fragment length(s) may be 2,46,585 bps INFO @ Sun, 21 Jun 2020 18:22:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.05_model.r WARNING @ Sun, 21 Jun 2020 18:22:23: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:22:23: #2 You may need to consider one of the other alternative d(s): 2,46,585 WARNING @ Sun, 21 Jun 2020 18:22:23: #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 18:22:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:22:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:22:25: 8000000 INFO @ Sun, 21 Jun 2020 18:22:26: 13000000 INFO @ Sun, 21 Jun 2020 18:22:30: 9000000 INFO @ Sun, 21 Jun 2020 18:22:32: 14000000 INFO @ Sun, 21 Jun 2020 18:22:35: 10000000 INFO @ Sun, 21 Jun 2020 18:22:37: 15000000 INFO @ Sun, 21 Jun 2020 18:22:40: 11000000 INFO @ Sun, 21 Jun 2020 18:22:43: 16000000 INFO @ Sun, 21 Jun 2020 18:22:46: 12000000 INFO @ Sun, 21 Jun 2020 18:22:49: 17000000 INFO @ Sun, 21 Jun 2020 18:22:51: 13000000 INFO @ Sun, 21 Jun 2020 18:22:54: 18000000 INFO @ Sun, 21 Jun 2020 18:22:56: 14000000 INFO @ Sun, 21 Jun 2020 18:23:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:23:00: 19000000 INFO @ Sun, 21 Jun 2020 18:23:01: 15000000 INFO @ Sun, 21 Jun 2020 18:23:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:23:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:23:03: #1 total tags in treatment: 19442235 INFO @ Sun, 21 Jun 2020 18:23:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:03: #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 18:23:03: #1 tags after filtering in treatment: 19442173 INFO @ Sun, 21 Jun 2020 18:23:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:03: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:23:05: #2 number of paired peaks: 1526 INFO @ Sun, 21 Jun 2020 18:23:05: start model_add_line... INFO @ Sun, 21 Jun 2020 18:23:05: start X-correlation... INFO @ Sun, 21 Jun 2020 18:23:05: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:05: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:05: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 18:23:05: #2 alternative fragment length(s) may be 2,46,585 bps INFO @ Sun, 21 Jun 2020 18:23:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.10_model.r WARNING @ Sun, 21 Jun 2020 18:23:05: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:23:05: #2 You may need to consider one of the other alternative d(s): 2,46,585 WARNING @ Sun, 21 Jun 2020 18:23:05: #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 18:23:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:23:06: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:23:11: 17000000 INFO @ Sun, 21 Jun 2020 18:23:16: 18000000 INFO @ Sun, 21 Jun 2020 18:23:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:23:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:23:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.05_summits.bed INFO @ Sun, 21 Jun 2020 18:23:19: Done! pass1 - making usageList (664 chroms): 1 millis pass2 - checking and writing primary data (3044 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:23:21: 19000000 INFO @ Sun, 21 Jun 2020 18:23:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:23:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:23:23: #1 total tags in treatment: 19442235 INFO @ Sun, 21 Jun 2020 18:23:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:23: #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 18:23:24: #1 tags after filtering in treatment: 19442173 INFO @ Sun, 21 Jun 2020 18:23:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:23:25: #2 number of paired peaks: 1526 INFO @ Sun, 21 Jun 2020 18:23:25: start model_add_line... INFO @ Sun, 21 Jun 2020 18:23:25: start X-correlation... INFO @ Sun, 21 Jun 2020 18:23:25: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:25: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:25: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 18:23:25: #2 alternative fragment length(s) may be 2,46,585 bps INFO @ Sun, 21 Jun 2020 18:23:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.20_model.r WARNING @ Sun, 21 Jun 2020 18:23:25: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:23:25: #2 You may need to consider one of the other alternative d(s): 2,46,585 WARNING @ Sun, 21 Jun 2020 18:23:25: #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 18:23:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:23:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:24:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:24:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:24:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.10_summits.bed INFO @ Sun, 21 Jun 2020 18:24:01: Done! pass1 - making usageList (578 chroms): 2 millis pass2 - checking and writing primary data (2366 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:24:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:24:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:24:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:24:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193310/SRX193310.20_summits.bed INFO @ Sun, 21 Jun 2020 18:24:19: Done! pass1 - making usageList (458 chroms): 1 millis pass2 - checking and writing primary data (1509 records, 4 fields): 14 millis CompletedMACS2peakCalling