Job ID = 6454908 SRX = SRX2592493 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:47:40 prefetch.2.10.7: 1) Downloading 'SRR5289770'... 2020-06-21T09:47:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:50:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:50:12 prefetch.2.10.7: 1) 'SRR5289770' was downloaded successfully Read 16574731 spots for SRR5289770/SRR5289770.sra Written 16574731 spots for SRR5289770/SRR5289770.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: 00:03:36 16574731 reads; of these: 16574731 (100.00%) were unpaired; of these: 2924410 (17.64%) aligned 0 times 12070791 (72.83%) aligned exactly 1 time 1579530 (9.53%) aligned >1 times 82.36% overall alignment rate Time searching: 00:03:36 Overall time: 00:03:36 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] 5152330 / 13650321 = 0.3775 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 18:58:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.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 18:58:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:10: 1000000 INFO @ Sun, 21 Jun 2020 18:58:15: 2000000 INFO @ Sun, 21 Jun 2020 18:58:21: 3000000 INFO @ Sun, 21 Jun 2020 18:58:26: 4000000 INFO @ Sun, 21 Jun 2020 18:58:32: 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 18:58:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.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 18:58:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:37: 6000000 INFO @ Sun, 21 Jun 2020 18:58:40: 1000000 INFO @ Sun, 21 Jun 2020 18:58:43: 7000000 INFO @ Sun, 21 Jun 2020 18:58:46: 2000000 INFO @ Sun, 21 Jun 2020 18:58:48: 8000000 INFO @ Sun, 21 Jun 2020 18:58:51: 3000000 INFO @ Sun, 21 Jun 2020 18:58:51: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:58:51: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:58:51: #1 total tags in treatment: 8497991 INFO @ Sun, 21 Jun 2020 18:58:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:51: #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 18:58:52: #1 tags after filtering in treatment: 8497785 INFO @ Sun, 21 Jun 2020 18:58:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:52: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:53: #2 number of paired peaks: 7847 INFO @ Sun, 21 Jun 2020 18:58:53: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:53: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:53: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:53: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:53: #2 predicted fragment length is 213 bps INFO @ Sun, 21 Jun 2020 18:58:53: #2 alternative fragment length(s) may be 213 bps INFO @ Sun, 21 Jun 2020 18:58:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.05_model.r INFO @ Sun, 21 Jun 2020 18:58:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:58:57: 4000000 INFO @ Sun, 21 Jun 2020 18:59:02: 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 18:59:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.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 18:59:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:59:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:08: 6000000 INFO @ Sun, 21 Jun 2020 18:59:10: 1000000 INFO @ Sun, 21 Jun 2020 18:59:14: 7000000 INFO @ Sun, 21 Jun 2020 18:59:16: 2000000 INFO @ Sun, 21 Jun 2020 18:59:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:59:19: 8000000 INFO @ Sun, 21 Jun 2020 18:59:21: 3000000 INFO @ Sun, 21 Jun 2020 18:59:22: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:59:22: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:59:22: #1 total tags in treatment: 8497991 INFO @ Sun, 21 Jun 2020 18:59:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:59:22: #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 18:59:23: #1 tags after filtering in treatment: 8497785 INFO @ Sun, 21 Jun 2020 18:59:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:59:23: #1 finished! INFO @ Sun, 21 Jun 2020 18:59:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:59:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:59:24: #2 number of paired peaks: 7847 INFO @ Sun, 21 Jun 2020 18:59:24: start model_add_line... INFO @ Sun, 21 Jun 2020 18:59:24: start X-correlation... INFO @ Sun, 21 Jun 2020 18:59:24: end of X-cor INFO @ Sun, 21 Jun 2020 18:59:24: #2 finished! INFO @ Sun, 21 Jun 2020 18:59:24: #2 predicted fragment length is 213 bps INFO @ Sun, 21 Jun 2020 18:59:24: #2 alternative fragment length(s) may be 213 bps INFO @ Sun, 21 Jun 2020 18:59:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.10_model.r INFO @ Sun, 21 Jun 2020 18:59:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:59:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:59:27: 4000000 INFO @ Sun, 21 Jun 2020 18:59:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:59:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:59:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.05_summits.bed INFO @ Sun, 21 Jun 2020 18:59:31: Done! pass1 - making usageList (105 chroms): 2 millis pass2 - checking and writing primary data (9827 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:59:32: 5000000 INFO @ Sun, 21 Jun 2020 18:59:38: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:59:44: 7000000 INFO @ Sun, 21 Jun 2020 18:59:49: 8000000 INFO @ Sun, 21 Jun 2020 18:59:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:59:52: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:59:52: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:59:52: #1 total tags in treatment: 8497991 INFO @ Sun, 21 Jun 2020 18:59:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:59:52: #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 18:59:52: #1 tags after filtering in treatment: 8497785 INFO @ Sun, 21 Jun 2020 18:59:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:59:52: #1 finished! INFO @ Sun, 21 Jun 2020 18:59:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:59:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:59:53: #2 number of paired peaks: 7847 INFO @ Sun, 21 Jun 2020 18:59:53: start model_add_line... INFO @ Sun, 21 Jun 2020 18:59:53: start X-correlation... INFO @ Sun, 21 Jun 2020 18:59:53: end of X-cor INFO @ Sun, 21 Jun 2020 18:59:53: #2 finished! INFO @ Sun, 21 Jun 2020 18:59:53: #2 predicted fragment length is 213 bps INFO @ Sun, 21 Jun 2020 18:59:53: #2 alternative fragment length(s) may be 213 bps INFO @ Sun, 21 Jun 2020 18:59:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.20_model.r INFO @ Sun, 21 Jun 2020 18:59:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:59:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:00:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:00:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:00:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.10_summits.bed INFO @ Sun, 21 Jun 2020 19:00:01: Done! pass1 - making usageList (79 chroms): 2 millis pass2 - checking and writing primary data (7700 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:00:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:00:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:00:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:00:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592493/SRX2592493.20_summits.bed INFO @ Sun, 21 Jun 2020 19:00:31: Done! pass1 - making usageList (64 chroms): 3 millis pass2 - checking and writing primary data (5447 records, 4 fields): 9 millis CompletedMACS2peakCalling