Job ID = 8069472 SRX = SRX7191470 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-08T03:33:11 prefetch.2.10.7: 1) Downloading 'SRR10502454'... 2020-08-08T03:33:11 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:34:11 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:34:12 prefetch.2.10.7: 'SRR10502454' is valid 2020-08-08T03:34:12 prefetch.2.10.7: 1) 'SRR10502454' was downloaded successfully Read 17934749 spots for SRR10502454/SRR10502454.sra Written 17934749 spots for SRR10502454/SRR10502454.sra fastq に変換しました。 bowtie でマッピング中... Your job 8069956 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:45 17934749 reads; of these: 17934749 (100.00%) were unpaired; of these: 848080 (4.73%) aligned 0 times 13221493 (73.72%) aligned exactly 1 time 3865176 (21.55%) aligned >1 times 95.27% overall alignment rate Time searching: 00:05:45 Overall time: 00:05:45 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 8 files... [bam_rmdupse_core] 1577914 / 17086669 = 0.0923 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 @ Sat, 08 Aug 2020 12:44:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.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 @ Sat, 08 Aug 2020 12:44:40: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:44:40: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:44:45: 1000000 INFO @ Sat, 08 Aug 2020 12:44:50: 2000000 INFO @ Sat, 08 Aug 2020 12:44:54: 3000000 INFO @ Sat, 08 Aug 2020 12:44:59: 4000000 INFO @ Sat, 08 Aug 2020 12:45:04: 5000000 INFO @ Sat, 08 Aug 2020 12:45:08: 6000000 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 @ Sat, 08 Aug 2020 12:45:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.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 @ Sat, 08 Aug 2020 12:45:10: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:45:10: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:45:13: 7000000 INFO @ Sat, 08 Aug 2020 12:45:15: 1000000 INFO @ Sat, 08 Aug 2020 12:45:18: 8000000 INFO @ Sat, 08 Aug 2020 12:45:20: 2000000 INFO @ Sat, 08 Aug 2020 12:45:22: 9000000 INFO @ Sat, 08 Aug 2020 12:45:24: 3000000 INFO @ Sat, 08 Aug 2020 12:45:27: 10000000 INFO @ Sat, 08 Aug 2020 12:45:29: 4000000 INFO @ Sat, 08 Aug 2020 12:45:32: 11000000 INFO @ Sat, 08 Aug 2020 12:45:34: 5000000 INFO @ Sat, 08 Aug 2020 12:45:36: 12000000 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 @ Sat, 08 Aug 2020 12:45:38: 6000000 INFO @ Sat, 08 Aug 2020 12:45:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.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 @ Sat, 08 Aug 2020 12:45:40: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:45:40: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:45:41: 13000000 INFO @ Sat, 08 Aug 2020 12:45:43: 7000000 INFO @ Sat, 08 Aug 2020 12:45:45: 1000000 INFO @ Sat, 08 Aug 2020 12:45:46: 14000000 INFO @ Sat, 08 Aug 2020 12:45:48: 8000000 INFO @ Sat, 08 Aug 2020 12:45:50: 2000000 INFO @ Sat, 08 Aug 2020 12:45:50: 15000000 INFO @ Sat, 08 Aug 2020 12:45:52: 9000000 INFO @ Sat, 08 Aug 2020 12:45:53: #1 tag size is determined as 50 bps INFO @ Sat, 08 Aug 2020 12:45:53: #1 tag size = 50 INFO @ Sat, 08 Aug 2020 12:45:53: #1 total tags in treatment: 15508755 INFO @ Sat, 08 Aug 2020 12:45:53: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:45:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:45:53: #1 tags after filtering in treatment: 15508755 INFO @ Sat, 08 Aug 2020 12:45:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Aug 2020 12:45:53: #1 finished! INFO @ Sat, 08 Aug 2020 12:45:53: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:45:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:45:54: #2 number of paired peaks: 966 WARNING @ Sat, 08 Aug 2020 12:45:54: Fewer paired peaks (966) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 966 pairs to build model! INFO @ Sat, 08 Aug 2020 12:45:54: start model_add_line... INFO @ Sat, 08 Aug 2020 12:45:54: 3000000 INFO @ Sat, 08 Aug 2020 12:45:54: start X-correlation... INFO @ Sat, 08 Aug 2020 12:45:54: end of X-cor INFO @ Sat, 08 Aug 2020 12:45:54: #2 finished! INFO @ Sat, 08 Aug 2020 12:45:54: #2 predicted fragment length is 194 bps INFO @ Sat, 08 Aug 2020 12:45:54: #2 alternative fragment length(s) may be 194 bps INFO @ Sat, 08 Aug 2020 12:45:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.05_model.r INFO @ Sat, 08 Aug 2020 12:45:54: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:45:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:45:57: 10000000 INFO @ Sat, 08 Aug 2020 12:45:59: 4000000 INFO @ Sat, 08 Aug 2020 12:46:02: 11000000 INFO @ Sat, 08 Aug 2020 12:46:04: 5000000 INFO @ Sat, 08 Aug 2020 12:46:07: 12000000 INFO @ Sat, 08 Aug 2020 12:46:09: 6000000 INFO @ Sat, 08 Aug 2020 12:46:12: 13000000 INFO @ Sat, 08 Aug 2020 12:46:13: 7000000 INFO @ Sat, 08 Aug 2020 12:46:16: 14000000 INFO @ Sat, 08 Aug 2020 12:46:18: 8000000 INFO @ Sat, 08 Aug 2020 12:46:21: 15000000 INFO @ Sat, 08 Aug 2020 12:46:23: 9000000 INFO @ Sat, 08 Aug 2020 12:46:24: #1 tag size is determined as 50 bps INFO @ Sat, 08 Aug 2020 12:46:24: #1 tag size = 50 INFO @ Sat, 08 Aug 2020 12:46:24: #1 total tags in treatment: 15508755 INFO @ Sat, 08 Aug 2020 12:46:24: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:46:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:46:24: #1 tags after filtering in treatment: 15508755 INFO @ Sat, 08 Aug 2020 12:46:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Aug 2020 12:46:24: #1 finished! INFO @ Sat, 08 Aug 2020 12:46:24: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:46:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:46:25: #2 number of paired peaks: 966 WARNING @ Sat, 08 Aug 2020 12:46:25: Fewer paired peaks (966) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 966 pairs to build model! INFO @ Sat, 08 Aug 2020 12:46:25: start model_add_line... INFO @ Sat, 08 Aug 2020 12:46:25: start X-correlation... INFO @ Sat, 08 Aug 2020 12:46:25: end of X-cor INFO @ Sat, 08 Aug 2020 12:46:25: #2 finished! INFO @ Sat, 08 Aug 2020 12:46:25: #2 predicted fragment length is 194 bps INFO @ Sat, 08 Aug 2020 12:46:25: #2 alternative fragment length(s) may be 194 bps INFO @ Sat, 08 Aug 2020 12:46:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.10_model.r INFO @ Sat, 08 Aug 2020 12:46:25: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:46:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:46:28: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:46:28: 10000000 INFO @ Sat, 08 Aug 2020 12:46:32: 11000000 INFO @ Sat, 08 Aug 2020 12:46:37: 12000000 INFO @ Sat, 08 Aug 2020 12:46:42: 13000000 INFO @ Sat, 08 Aug 2020 12:46:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:46:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:46:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.05_summits.bed INFO @ Sat, 08 Aug 2020 12:46:44: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8732 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:46:47: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:46:51: 15000000 INFO @ Sat, 08 Aug 2020 12:46:54: #1 tag size is determined as 50 bps INFO @ Sat, 08 Aug 2020 12:46:54: #1 tag size = 50 INFO @ Sat, 08 Aug 2020 12:46:54: #1 total tags in treatment: 15508755 INFO @ Sat, 08 Aug 2020 12:46:54: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:46:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:46:54: #1 tags after filtering in treatment: 15508755 INFO @ Sat, 08 Aug 2020 12:46:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Aug 2020 12:46:54: #1 finished! INFO @ Sat, 08 Aug 2020 12:46:54: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:46:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:46:55: #2 number of paired peaks: 966 WARNING @ Sat, 08 Aug 2020 12:46:55: Fewer paired peaks (966) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 966 pairs to build model! INFO @ Sat, 08 Aug 2020 12:46:55: start model_add_line... INFO @ Sat, 08 Aug 2020 12:46:55: start X-correlation... INFO @ Sat, 08 Aug 2020 12:46:55: end of X-cor INFO @ Sat, 08 Aug 2020 12:46:55: #2 finished! INFO @ Sat, 08 Aug 2020 12:46:55: #2 predicted fragment length is 194 bps INFO @ Sat, 08 Aug 2020 12:46:55: #2 alternative fragment length(s) may be 194 bps INFO @ Sat, 08 Aug 2020 12:46:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.20_model.r INFO @ Sat, 08 Aug 2020 12:46:55: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:46:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:46:58: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:47:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:47:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:47:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.10_summits.bed INFO @ Sat, 08 Aug 2020 12:47:15: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6377 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:47:28: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:47:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:47:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:47:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7191470/SRX7191470.20_summits.bed INFO @ Sat, 08 Aug 2020 12:47:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3745 records, 4 fields): 6 millis CompletedMACS2peakCalling