Job ID = 6457827 SRX = SRX4798869 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:13:34 prefetch.2.10.7: 1) Downloading 'SRR7965200'... 2020-06-21T12:13:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:15:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:15:55 prefetch.2.10.7: 'SRR7965200' is valid 2020-06-21T12:15:55 prefetch.2.10.7: 1) 'SRR7965200' was downloaded successfully Read 13756405 spots for SRR7965200/SRR7965200.sra Written 13756405 spots for SRR7965200/SRR7965200.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: 00:02:16 13756405 reads; of these: 13756405 (100.00%) were unpaired; of these: 5267712 (38.29%) aligned 0 times 7843509 (57.02%) aligned exactly 1 time 645184 (4.69%) aligned >1 times 61.71% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 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] 2146024 / 8488693 = 0.2528 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 21:21:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.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 21:21:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:21:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:21:42: 1000000 INFO @ Sun, 21 Jun 2020 21:21:48: 2000000 INFO @ Sun, 21 Jun 2020 21:21:54: 3000000 INFO @ Sun, 21 Jun 2020 21:22:00: 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 21:22:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.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 21:22:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:22:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:22:06: 5000000 INFO @ Sun, 21 Jun 2020 21:22:13: 1000000 INFO @ Sun, 21 Jun 2020 21:22:13: 6000000 INFO @ Sun, 21 Jun 2020 21:22:16: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:22:16: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:22:16: #1 total tags in treatment: 6342669 INFO @ Sun, 21 Jun 2020 21:22:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:22:16: #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 21:22:16: #1 tags after filtering in treatment: 6342474 INFO @ Sun, 21 Jun 2020 21:22:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:22:16: #1 finished! INFO @ Sun, 21 Jun 2020 21:22:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:22:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:22:17: #2 number of paired peaks: 1568 INFO @ Sun, 21 Jun 2020 21:22:17: start model_add_line... INFO @ Sun, 21 Jun 2020 21:22:17: start X-correlation... INFO @ Sun, 21 Jun 2020 21:22:17: end of X-cor INFO @ Sun, 21 Jun 2020 21:22:17: #2 finished! INFO @ Sun, 21 Jun 2020 21:22:17: #2 predicted fragment length is 201 bps INFO @ Sun, 21 Jun 2020 21:22:17: #2 alternative fragment length(s) may be 201 bps INFO @ Sun, 21 Jun 2020 21:22:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.05_model.r INFO @ Sun, 21 Jun 2020 21:22:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:22:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:22:19: 2000000 INFO @ Sun, 21 Jun 2020 21:22:25: 3000000 INFO @ Sun, 21 Jun 2020 21:22:31: 4000000 INFO @ Sun, 21 Jun 2020 21:22:33: #3 Call peaks for each chromosome... 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 21:22:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.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 21:22:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:22:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:22:38: 5000000 INFO @ Sun, 21 Jun 2020 21:22:42: 1000000 INFO @ Sun, 21 Jun 2020 21:22:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:22:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:22:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.05_summits.bed INFO @ Sun, 21 Jun 2020 21:22:43: Done! pass1 - making usageList (55 chroms): 2 millis pass2 - checking and writing primary data (6997 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:22:45: 6000000 INFO @ Sun, 21 Jun 2020 21:22:47: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:22:47: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:22:47: #1 total tags in treatment: 6342669 INFO @ Sun, 21 Jun 2020 21:22:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:22:47: #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 21:22:48: #1 tags after filtering in treatment: 6342474 INFO @ Sun, 21 Jun 2020 21:22:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:22:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:22:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:22:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:22:48: #2 number of paired peaks: 1568 INFO @ Sun, 21 Jun 2020 21:22:48: start model_add_line... INFO @ Sun, 21 Jun 2020 21:22:49: start X-correlation... INFO @ Sun, 21 Jun 2020 21:22:49: end of X-cor INFO @ Sun, 21 Jun 2020 21:22:49: #2 finished! INFO @ Sun, 21 Jun 2020 21:22:49: #2 predicted fragment length is 201 bps INFO @ Sun, 21 Jun 2020 21:22:49: #2 alternative fragment length(s) may be 201 bps INFO @ Sun, 21 Jun 2020 21:22:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.10_model.r INFO @ Sun, 21 Jun 2020 21:22:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:22:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:22:49: 2000000 INFO @ Sun, 21 Jun 2020 21:22:55: 3000000 INFO @ Sun, 21 Jun 2020 21:23:01: 4000000 INFO @ Sun, 21 Jun 2020 21:23:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:23:07: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:23:14: 6000000 INFO @ Sun, 21 Jun 2020 21:23:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:23:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:23:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.10_summits.bed INFO @ Sun, 21 Jun 2020 21:23:15: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (3446 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:23:16: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:23:16: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:23:16: #1 total tags in treatment: 6342669 INFO @ Sun, 21 Jun 2020 21:23:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:23:16: #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 21:23:17: #1 tags after filtering in treatment: 6342474 INFO @ Sun, 21 Jun 2020 21:23:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:23:17: #1 finished! INFO @ Sun, 21 Jun 2020 21:23:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:23:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:23:17: #2 number of paired peaks: 1568 INFO @ Sun, 21 Jun 2020 21:23:17: start model_add_line... INFO @ Sun, 21 Jun 2020 21:23:17: start X-correlation... INFO @ Sun, 21 Jun 2020 21:23:17: end of X-cor INFO @ Sun, 21 Jun 2020 21:23:17: #2 finished! INFO @ Sun, 21 Jun 2020 21:23:17: #2 predicted fragment length is 201 bps INFO @ Sun, 21 Jun 2020 21:23:17: #2 alternative fragment length(s) may be 201 bps INFO @ Sun, 21 Jun 2020 21:23:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.20_model.r INFO @ Sun, 21 Jun 2020 21:23:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:23:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:23:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:23:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:23:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:23:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798869/SRX4798869.20_summits.bed INFO @ Sun, 21 Jun 2020 21:23:42: Done! pass1 - making usageList (19 chroms): 1 millis pass2 - checking and writing primary data (1084 records, 4 fields): 3 millis CompletedMACS2peakCalling