Job ID = 6454191 SRX = SRX186112 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:17:54 prefetch.2.10.7: 1) Downloading 'SRR567589'... 2020-06-21T09:17:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:22:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:22:51 prefetch.2.10.7: 1) 'SRR567589' was downloaded successfully Read 31079613 spots for SRR567589/SRR567589.sra Written 31079613 spots for SRR567589/SRR567589.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: 00:07:31 31079613 reads; of these: 31079613 (100.00%) were unpaired; of these: 1828795 (5.88%) aligned 0 times 23721359 (76.32%) aligned exactly 1 time 5529459 (17.79%) aligned >1 times 94.12% overall alignment rate Time searching: 00:07:31 Overall time: 00:07:31 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] 20645251 / 29250818 = 0.7058 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 18:39:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.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 18:39:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:22: 1000000 INFO @ Sun, 21 Jun 2020 18:39:27: 2000000 INFO @ Sun, 21 Jun 2020 18:39:33: 3000000 INFO @ Sun, 21 Jun 2020 18:39:39: 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 18:39:45: 5000000 INFO @ Sun, 21 Jun 2020 18:39:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.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 18:39:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:50: 6000000 INFO @ Sun, 21 Jun 2020 18:39:52: 1000000 INFO @ Sun, 21 Jun 2020 18:39:57: 7000000 INFO @ Sun, 21 Jun 2020 18:39:58: 2000000 INFO @ Sun, 21 Jun 2020 18:40:03: 8000000 INFO @ Sun, 21 Jun 2020 18:40:04: 3000000 INFO @ Sun, 21 Jun 2020 18:40:07: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:40:07: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:40:07: #1 total tags in treatment: 8605567 INFO @ Sun, 21 Jun 2020 18:40:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:07: #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 18:40:07: #1 tags after filtering in treatment: 8605563 INFO @ Sun, 21 Jun 2020 18:40:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:07: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:40:08: #2 number of paired peaks: 1332 INFO @ Sun, 21 Jun 2020 18:40:08: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:08: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:08: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:08: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:08: #2 predicted fragment length is 141 bps INFO @ Sun, 21 Jun 2020 18:40:08: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 21 Jun 2020 18:40:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.05_model.r INFO @ Sun, 21 Jun 2020 18:40:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:40:10: 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 18:40:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.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 18:40:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:40:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:40:16: 5000000 INFO @ Sun, 21 Jun 2020 18:40:23: 6000000 INFO @ Sun, 21 Jun 2020 18:40:23: 1000000 INFO @ Sun, 21 Jun 2020 18:40:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:40:29: 2000000 INFO @ Sun, 21 Jun 2020 18:40:30: 7000000 INFO @ Sun, 21 Jun 2020 18:40:35: 3000000 INFO @ Sun, 21 Jun 2020 18:40:37: 8000000 INFO @ Sun, 21 Jun 2020 18:40:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.05_summits.bed INFO @ Sun, 21 Jun 2020 18:40:38: Done! pass1 - making usageList (1029 chroms): 3 millis pass2 - checking and writing primary data (6333 records, 4 fields): 61 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:40:41: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:40:41: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:40:41: #1 total tags in treatment: 8605567 INFO @ Sun, 21 Jun 2020 18:40:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:41: #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 18:40:41: 4000000 INFO @ Sun, 21 Jun 2020 18:40:42: #1 tags after filtering in treatment: 8605563 INFO @ Sun, 21 Jun 2020 18:40:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:42: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:40:43: #2 number of paired peaks: 1332 INFO @ Sun, 21 Jun 2020 18:40:43: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:43: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:43: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:43: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:43: #2 predicted fragment length is 141 bps INFO @ Sun, 21 Jun 2020 18:40:43: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 21 Jun 2020 18:40:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.10_model.r INFO @ Sun, 21 Jun 2020 18:40:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:40:48: 5000000 INFO @ Sun, 21 Jun 2020 18:40:53: 6000000 INFO @ Sun, 21 Jun 2020 18:41:00: 7000000 INFO @ Sun, 21 Jun 2020 18:41:03: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:41:06: 8000000 INFO @ Sun, 21 Jun 2020 18:41:10: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:41:10: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:41:10: #1 total tags in treatment: 8605567 INFO @ Sun, 21 Jun 2020 18:41:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:41:10: #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 18:41:11: #1 tags after filtering in treatment: 8605563 INFO @ Sun, 21 Jun 2020 18:41:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:41:11: #1 finished! INFO @ Sun, 21 Jun 2020 18:41:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:41:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:41:12: #2 number of paired peaks: 1332 INFO @ Sun, 21 Jun 2020 18:41:12: start model_add_line... INFO @ Sun, 21 Jun 2020 18:41:12: start X-correlation... INFO @ Sun, 21 Jun 2020 18:41:12: end of X-cor INFO @ Sun, 21 Jun 2020 18:41:12: #2 finished! INFO @ Sun, 21 Jun 2020 18:41:12: #2 predicted fragment length is 141 bps INFO @ Sun, 21 Jun 2020 18:41:12: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 21 Jun 2020 18:41:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.20_model.r INFO @ Sun, 21 Jun 2020 18:41:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:41:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:41:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:41:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:41:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.10_summits.bed INFO @ Sun, 21 Jun 2020 18:41:13: Done! pass1 - making usageList (799 chroms): 2 millis pass2 - checking and writing primary data (3332 records, 4 fields): 47 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:41:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:41:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:41:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:41:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX186112/SRX186112.20_summits.bed INFO @ Sun, 21 Jun 2020 18:41:41: Done! pass1 - making usageList (500 chroms): 1 millis pass2 - checking and writing primary data (1378 records, 4 fields): 29 millis CompletedMACS2peakCalling