Job ID = 6455918 SRX = SRX3068958 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:47:24 prefetch.2.10.7: 1) Downloading 'SRR5907434'... 2020-06-21T10:47:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:49:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:49:42 prefetch.2.10.7: 'SRR5907434' is valid 2020-06-21T10:49:42 prefetch.2.10.7: 1) 'SRR5907434' was downloaded successfully Read 13264499 spots for SRR5907434/SRR5907434.sra Written 13264499 spots for SRR5907434/SRR5907434.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: 00:03:39 13264499 reads; of these: 13264499 (100.00%) were unpaired; of these: 1305852 (9.84%) aligned 0 times 10444618 (78.74%) aligned exactly 1 time 1514029 (11.41%) aligned >1 times 90.16% overall alignment rate Time searching: 00:03:39 Overall time: 00:03:39 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] 2981375 / 11958647 = 0.2493 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 19:57:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.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 19:57:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:57:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:57:16: 1000000 INFO @ Sun, 21 Jun 2020 19:57:23: 2000000 INFO @ Sun, 21 Jun 2020 19:57:30: 3000000 INFO @ Sun, 21 Jun 2020 19:57:36: 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 19:57:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.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 19:57:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:57:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:57:43: 5000000 INFO @ Sun, 21 Jun 2020 19:57:46: 1000000 INFO @ Sun, 21 Jun 2020 19:57:50: 6000000 INFO @ Sun, 21 Jun 2020 19:57:53: 2000000 INFO @ Sun, 21 Jun 2020 19:57:57: 7000000 INFO @ Sun, 21 Jun 2020 19:58:00: 3000000 INFO @ Sun, 21 Jun 2020 19:58:04: 8000000 INFO @ Sun, 21 Jun 2020 19:58:07: 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 19:58:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.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 19:58:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:58:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:58:11: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:58:11: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:58:11: #1 total tags in treatment: 8977272 INFO @ Sun, 21 Jun 2020 19:58:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:58:11: #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 19:58:12: #1 tags after filtering in treatment: 8977211 INFO @ Sun, 21 Jun 2020 19:58:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:58:12: #1 finished! INFO @ Sun, 21 Jun 2020 19:58:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:58:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:58:12: #2 number of paired peaks: 4560 INFO @ Sun, 21 Jun 2020 19:58:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:58:13: start X-correlation... INFO @ Sun, 21 Jun 2020 19:58:13: end of X-cor INFO @ Sun, 21 Jun 2020 19:58:13: #2 finished! INFO @ Sun, 21 Jun 2020 19:58:13: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 19:58:13: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 21 Jun 2020 19:58:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.05_model.r INFO @ Sun, 21 Jun 2020 19:58:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:58:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:58:14: 5000000 INFO @ Sun, 21 Jun 2020 19:58:17: 1000000 INFO @ Sun, 21 Jun 2020 19:58:20: 6000000 INFO @ Sun, 21 Jun 2020 19:58:24: 2000000 INFO @ Sun, 21 Jun 2020 19:58:27: 7000000 INFO @ Sun, 21 Jun 2020 19:58:31: 3000000 INFO @ Sun, 21 Jun 2020 19:58:34: 8000000 INFO @ Sun, 21 Jun 2020 19:58:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:58:38: 4000000 INFO @ Sun, 21 Jun 2020 19:58:40: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:58:40: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:58:40: #1 total tags in treatment: 8977272 INFO @ Sun, 21 Jun 2020 19:58:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:58:40: #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 19:58:40: #1 tags after filtering in treatment: 8977211 INFO @ Sun, 21 Jun 2020 19:58:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:58:40: #1 finished! INFO @ Sun, 21 Jun 2020 19:58:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:58:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:58:41: #2 number of paired peaks: 4560 INFO @ Sun, 21 Jun 2020 19:58:41: start model_add_line... INFO @ Sun, 21 Jun 2020 19:58:41: start X-correlation... INFO @ Sun, 21 Jun 2020 19:58:41: end of X-cor INFO @ Sun, 21 Jun 2020 19:58:41: #2 finished! INFO @ Sun, 21 Jun 2020 19:58:41: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 19:58:41: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 21 Jun 2020 19:58:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.10_model.r INFO @ Sun, 21 Jun 2020 19:58:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:58:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:58:45: 5000000 INFO @ Sun, 21 Jun 2020 19:58:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:58:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:58:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.05_summits.bed INFO @ Sun, 21 Jun 2020 19:58:45: Done! pass1 - making usageList (455 chroms): 2 millis pass2 - checking and writing primary data (10970 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:58:52: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:58:58: 7000000 INFO @ Sun, 21 Jun 2020 19:59:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:59:05: 8000000 INFO @ Sun, 21 Jun 2020 19:59:11: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:59:11: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:59:11: #1 total tags in treatment: 8977272 INFO @ Sun, 21 Jun 2020 19:59:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:59:11: #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 19:59:12: #1 tags after filtering in treatment: 8977211 INFO @ Sun, 21 Jun 2020 19:59:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:59:12: #1 finished! INFO @ Sun, 21 Jun 2020 19:59:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:59:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:59:13: #2 number of paired peaks: 4560 INFO @ Sun, 21 Jun 2020 19:59:13: start model_add_line... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:59:13: start X-correlation... INFO @ Sun, 21 Jun 2020 19:59:13: end of X-cor INFO @ Sun, 21 Jun 2020 19:59:13: #2 finished! INFO @ Sun, 21 Jun 2020 19:59:13: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 19:59:13: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 21 Jun 2020 19:59:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.20_model.r INFO @ Sun, 21 Jun 2020 19:59:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:59:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:59:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:59:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:59:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.10_summits.bed INFO @ Sun, 21 Jun 2020 19:59:16: Done! pass1 - making usageList (395 chroms): 2 millis pass2 - checking and writing primary data (8005 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:59:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:59:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:59:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:59:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068958/SRX3068958.20_summits.bed INFO @ Sun, 21 Jun 2020 19:59:46: Done! pass1 - making usageList (245 chroms): 1 millis pass2 - checking and writing primary data (5038 records, 4 fields): 12 millis CompletedMACS2peakCalling