Job ID = 5720418 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,805,923 reads read : 27,805,923 reads written : 27,805,923 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289678.sra.cache’: No such file or directory 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: 00:08:30 27805923 reads; of these: 27805923 (100.00%) were unpaired; of these: 1845750 (6.64%) aligned 0 times 20839641 (74.95%) aligned exactly 1 time 5120532 (18.42%) aligned >1 times 93.36% overall alignment rate Time searching: 00:08:30 Overall time: 00:08:30 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 8935149 / 25960173 = 0.3442 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 @ Thu, 16 Apr 2020 00:39:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.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 @ Thu, 16 Apr 2020 00:39:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:39:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:39:18: 1000000 INFO @ Thu, 16 Apr 2020 00:39:23: 2000000 INFO @ Thu, 16 Apr 2020 00:39:27: 3000000 INFO @ Thu, 16 Apr 2020 00:39:33: 4000000 INFO @ Thu, 16 Apr 2020 00:39:38: 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 @ Thu, 16 Apr 2020 00:39:43: 6000000 INFO @ Thu, 16 Apr 2020 00:39:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.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 @ Thu, 16 Apr 2020 00:39:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:39:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:39:48: 7000000 INFO @ Thu, 16 Apr 2020 00:39:48: 1000000 INFO @ Thu, 16 Apr 2020 00:39:53: 8000000 INFO @ Thu, 16 Apr 2020 00:39:54: 2000000 INFO @ Thu, 16 Apr 2020 00:39:58: 9000000 INFO @ Thu, 16 Apr 2020 00:39:59: 3000000 INFO @ Thu, 16 Apr 2020 00:40:03: 10000000 INFO @ Thu, 16 Apr 2020 00:40:05: 4000000 INFO @ Thu, 16 Apr 2020 00:40:08: 11000000 INFO @ Thu, 16 Apr 2020 00:40:10: 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 @ Thu, 16 Apr 2020 00:40:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.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 @ Thu, 16 Apr 2020 00:40:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:40:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:40:13: 12000000 INFO @ Thu, 16 Apr 2020 00:40:16: 6000000 INFO @ Thu, 16 Apr 2020 00:40:18: 1000000 INFO @ Thu, 16 Apr 2020 00:40:18: 13000000 INFO @ Thu, 16 Apr 2020 00:40:22: 7000000 INFO @ Thu, 16 Apr 2020 00:40:23: 2000000 INFO @ Thu, 16 Apr 2020 00:40:23: 14000000 INFO @ Thu, 16 Apr 2020 00:40:27: 8000000 INFO @ Thu, 16 Apr 2020 00:40:28: 3000000 INFO @ Thu, 16 Apr 2020 00:40:28: 15000000 INFO @ Thu, 16 Apr 2020 00:40:33: 16000000 INFO @ Thu, 16 Apr 2020 00:40:33: 4000000 INFO @ Thu, 16 Apr 2020 00:40:33: 9000000 INFO @ Thu, 16 Apr 2020 00:40:38: 17000000 INFO @ Thu, 16 Apr 2020 00:40:38: 5000000 INFO @ Thu, 16 Apr 2020 00:40:38: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:40:38: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:40:38: #1 total tags in treatment: 17025024 INFO @ Thu, 16 Apr 2020 00:40:38: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:40:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:40:38: #1 tags after filtering in treatment: 17025024 INFO @ Thu, 16 Apr 2020 00:40:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:40:38: #1 finished! INFO @ Thu, 16 Apr 2020 00:40:38: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:40:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:40:39: 10000000 INFO @ Thu, 16 Apr 2020 00:40:40: #2 number of paired peaks: 2647 INFO @ Thu, 16 Apr 2020 00:40:40: start model_add_line... INFO @ Thu, 16 Apr 2020 00:40:40: start X-correlation... INFO @ Thu, 16 Apr 2020 00:40:40: end of X-cor INFO @ Thu, 16 Apr 2020 00:40:40: #2 finished! INFO @ Thu, 16 Apr 2020 00:40:40: #2 predicted fragment length is 181 bps INFO @ Thu, 16 Apr 2020 00:40:40: #2 alternative fragment length(s) may be 181 bps INFO @ Thu, 16 Apr 2020 00:40:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.05_model.r INFO @ Thu, 16 Apr 2020 00:40:40: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:40:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:40:43: 6000000 INFO @ Thu, 16 Apr 2020 00:40:44: 11000000 INFO @ Thu, 16 Apr 2020 00:40:48: 7000000 INFO @ Thu, 16 Apr 2020 00:40:50: 12000000 INFO @ Thu, 16 Apr 2020 00:40:53: 8000000 INFO @ Thu, 16 Apr 2020 00:40:55: 13000000 INFO @ Thu, 16 Apr 2020 00:40:58: 9000000 INFO @ Thu, 16 Apr 2020 00:41:00: 14000000 INFO @ Thu, 16 Apr 2020 00:41:03: 10000000 INFO @ Thu, 16 Apr 2020 00:41:06: 15000000 INFO @ Thu, 16 Apr 2020 00:41:08: 11000000 INFO @ Thu, 16 Apr 2020 00:41:11: 16000000 INFO @ Thu, 16 Apr 2020 00:41:13: 12000000 INFO @ Thu, 16 Apr 2020 00:41:16: 17000000 INFO @ Thu, 16 Apr 2020 00:41:16: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:41:16: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:41:16: #1 total tags in treatment: 17025024 INFO @ Thu, 16 Apr 2020 00:41:16: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:41:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:41:17: #1 tags after filtering in treatment: 17025024 INFO @ Thu, 16 Apr 2020 00:41:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:41:17: #1 finished! INFO @ Thu, 16 Apr 2020 00:41:17: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:41:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:41:18: 13000000 INFO @ Thu, 16 Apr 2020 00:41:18: #2 number of paired peaks: 2647 INFO @ Thu, 16 Apr 2020 00:41:18: start model_add_line... INFO @ Thu, 16 Apr 2020 00:41:18: start X-correlation... INFO @ Thu, 16 Apr 2020 00:41:18: end of X-cor INFO @ Thu, 16 Apr 2020 00:41:18: #2 finished! INFO @ Thu, 16 Apr 2020 00:41:18: #2 predicted fragment length is 181 bps INFO @ Thu, 16 Apr 2020 00:41:18: #2 alternative fragment length(s) may be 181 bps INFO @ Thu, 16 Apr 2020 00:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.10_model.r INFO @ Thu, 16 Apr 2020 00:41:18: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:41:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:41:19: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:41:23: 14000000 INFO @ Thu, 16 Apr 2020 00:41:27: 15000000 INFO @ Thu, 16 Apr 2020 00:41:32: 16000000 INFO @ Thu, 16 Apr 2020 00:41:37: 17000000 INFO @ Thu, 16 Apr 2020 00:41:37: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:41:37: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:41:37: #1 total tags in treatment: 17025024 INFO @ Thu, 16 Apr 2020 00:41:37: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:41:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:41:37: #1 tags after filtering in treatment: 17025024 INFO @ Thu, 16 Apr 2020 00:41:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:41:37: #1 finished! INFO @ Thu, 16 Apr 2020 00:41:37: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:41:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:41:39: #2 number of paired peaks: 2647 INFO @ Thu, 16 Apr 2020 00:41:39: start model_add_line... INFO @ Thu, 16 Apr 2020 00:41:39: start X-correlation... INFO @ Thu, 16 Apr 2020 00:41:39: end of X-cor INFO @ Thu, 16 Apr 2020 00:41:39: #2 finished! INFO @ Thu, 16 Apr 2020 00:41:39: #2 predicted fragment length is 181 bps INFO @ Thu, 16 Apr 2020 00:41:39: #2 alternative fragment length(s) may be 181 bps INFO @ Thu, 16 Apr 2020 00:41:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.20_model.r INFO @ Thu, 16 Apr 2020 00:41:39: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:41:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:41:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:41:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:41:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.05_summits.bed INFO @ Thu, 16 Apr 2020 00:41:39: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (20308 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:41:56: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:42:15: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:42:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:42:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:42:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.10_summits.bed INFO @ Thu, 16 Apr 2020 00:42:15: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (16941 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:42:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:42:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:42:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592401/SRX2592401.20_summits.bed INFO @ Thu, 16 Apr 2020 00:42:33: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (11672 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。