Job ID = 6458505 SRX = SRX5247955 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:26:37 prefetch.2.10.7: 1) Downloading 'SRR8440602'... 2020-06-21T12:26:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:27:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:27:37 prefetch.2.10.7: 'SRR8440602' is valid 2020-06-21T12:27:37 prefetch.2.10.7: 1) 'SRR8440602' was downloaded successfully Read 6533000 spots for SRR8440602/SRR8440602.sra Written 6533000 spots for SRR8440602/SRR8440602.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: 00:02:01 6533000 reads; of these: 6533000 (100.00%) were unpaired; of these: 482961 (7.39%) aligned 0 times 3963256 (60.67%) aligned exactly 1 time 2086783 (31.94%) aligned >1 times 92.61% overall alignment rate Time searching: 00:02:01 Overall time: 00:02:01 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_rmdupse_core] 435481 / 6050039 = 0.0720 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 21:31:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.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 21:31:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:31:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:32:00: 1000000 INFO @ Sun, 21 Jun 2020 21:32:06: 2000000 INFO @ Sun, 21 Jun 2020 21:32:12: 3000000 INFO @ Sun, 21 Jun 2020 21:32:19: 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 21:32:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.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 21:32:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:32:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:32:26: 5000000 INFO @ Sun, 21 Jun 2020 21:32:30: 1000000 INFO @ Sun, 21 Jun 2020 21:32:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:32:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:32:31: #1 total tags in treatment: 5614558 INFO @ Sun, 21 Jun 2020 21:32:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:32:31: #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 21:32:31: #1 tags after filtering in treatment: 5614458 INFO @ Sun, 21 Jun 2020 21:32:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:32:31: #1 finished! INFO @ Sun, 21 Jun 2020 21:32:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:32:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:32:32: #2 number of paired peaks: 1996 INFO @ Sun, 21 Jun 2020 21:32:32: start model_add_line... INFO @ Sun, 21 Jun 2020 21:32:32: start X-correlation... INFO @ Sun, 21 Jun 2020 21:32:32: end of X-cor INFO @ Sun, 21 Jun 2020 21:32:32: #2 finished! INFO @ Sun, 21 Jun 2020 21:32:32: #2 predicted fragment length is 179 bps INFO @ Sun, 21 Jun 2020 21:32:32: #2 alternative fragment length(s) may be 4,179 bps INFO @ Sun, 21 Jun 2020 21:32:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.05_model.r INFO @ Sun, 21 Jun 2020 21:32:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:32:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:32:36: 2000000 INFO @ Sun, 21 Jun 2020 21:32:41: 3000000 INFO @ Sun, 21 Jun 2020 21:32:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:32:47: 4000000 INFO @ Sun, 21 Jun 2020 21:32:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:32:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:32:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.05_summits.bed INFO @ Sun, 21 Jun 2020 21:32:51: Done! 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 pass1 - making usageList (320 chroms): 1 millis pass2 - checking and writing primary data (1775 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:32:53: 5000000 INFO @ Sun, 21 Jun 2020 21:32:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.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 21:32:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:32:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:32:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:32:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:32:57: #1 total tags in treatment: 5614558 INFO @ Sun, 21 Jun 2020 21:32:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:32:57: #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 21:32:57: #1 tags after filtering in treatment: 5614458 INFO @ Sun, 21 Jun 2020 21:32:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:32:57: #1 finished! INFO @ Sun, 21 Jun 2020 21:32:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:32:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:32:58: #2 number of paired peaks: 1996 INFO @ Sun, 21 Jun 2020 21:32:58: start model_add_line... INFO @ Sun, 21 Jun 2020 21:32:58: start X-correlation... INFO @ Sun, 21 Jun 2020 21:32:58: end of X-cor INFO @ Sun, 21 Jun 2020 21:32:58: #2 finished! INFO @ Sun, 21 Jun 2020 21:32:58: #2 predicted fragment length is 179 bps INFO @ Sun, 21 Jun 2020 21:32:58: #2 alternative fragment length(s) may be 4,179 bps INFO @ Sun, 21 Jun 2020 21:32:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.10_model.r INFO @ Sun, 21 Jun 2020 21:32:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:32:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:32:59: 1000000 INFO @ Sun, 21 Jun 2020 21:33:05: 2000000 INFO @ Sun, 21 Jun 2020 21:33:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:33:11: 3000000 INFO @ Sun, 21 Jun 2020 21:33:17: 4000000 INFO @ Sun, 21 Jun 2020 21:33:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:33:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:33:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.10_summits.bed INFO @ Sun, 21 Jun 2020 21:33:17: Done! pass1 - making usageList (152 chroms): 1 millis pass2 - checking and writing primary data (702 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:33:23: 5000000 INFO @ Sun, 21 Jun 2020 21:33:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:33:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:33:26: #1 total tags in treatment: 5614558 INFO @ Sun, 21 Jun 2020 21:33:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:33:26: #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 21:33:27: #1 tags after filtering in treatment: 5614458 INFO @ Sun, 21 Jun 2020 21:33:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:33:27: #1 finished! INFO @ Sun, 21 Jun 2020 21:33:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:33:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:33:27: #2 number of paired peaks: 1996 INFO @ Sun, 21 Jun 2020 21:33:27: start model_add_line... INFO @ Sun, 21 Jun 2020 21:33:27: start X-correlation... INFO @ Sun, 21 Jun 2020 21:33:27: end of X-cor INFO @ Sun, 21 Jun 2020 21:33:27: #2 finished! INFO @ Sun, 21 Jun 2020 21:33:27: #2 predicted fragment length is 179 bps INFO @ Sun, 21 Jun 2020 21:33:27: #2 alternative fragment length(s) may be 4,179 bps INFO @ Sun, 21 Jun 2020 21:33:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.20_model.r INFO @ Sun, 21 Jun 2020 21:33:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:33:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:33:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:33:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:33:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:33:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5247955/SRX5247955.20_summits.bed INFO @ Sun, 21 Jun 2020 21:33:48: Done! pass1 - making usageList (82 chroms): 1 millis pass2 - checking and writing primary data (267 records, 4 fields): 5 millis CompletedMACS2peakCalling