Job ID = 6457816 SRX = SRX4798859 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:00:17 prefetch.2.10.7: 1) Downloading 'SRR7965210'... 2020-06-21T12:00:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:03:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:03:36 prefetch.2.10.7: 'SRR7965210' is valid 2020-06-21T12:03:36 prefetch.2.10.7: 1) 'SRR7965210' was downloaded successfully Read 15563990 spots for SRR7965210/SRR7965210.sra Written 15563990 spots for SRR7965210/SRR7965210.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: 00:03:26 15563990 reads; of these: 15563990 (100.00%) were unpaired; of these: 1581779 (10.16%) aligned 0 times 12738644 (81.85%) aligned exactly 1 time 1243567 (7.99%) aligned >1 times 89.84% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 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] 1815281 / 13982211 = 0.1298 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 21:12:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.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 21:12:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:12:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:12:11: 1000000 INFO @ Sun, 21 Jun 2020 21:12:18: 2000000 INFO @ Sun, 21 Jun 2020 21:12:24: 3000000 INFO @ Sun, 21 Jun 2020 21:12:31: 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 21:12:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.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 21:12:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:12:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:12:38: 5000000 INFO @ Sun, 21 Jun 2020 21:12:41: 1000000 INFO @ Sun, 21 Jun 2020 21:12:45: 6000000 INFO @ Sun, 21 Jun 2020 21:12:48: 2000000 INFO @ Sun, 21 Jun 2020 21:12:52: 7000000 INFO @ Sun, 21 Jun 2020 21:12:55: 3000000 INFO @ Sun, 21 Jun 2020 21:12:59: 8000000 INFO @ Sun, 21 Jun 2020 21:13:02: 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 21:13:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.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 21:13:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:13:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:13:06: 9000000 INFO @ Sun, 21 Jun 2020 21:13:08: 5000000 INFO @ Sun, 21 Jun 2020 21:13:12: 1000000 INFO @ Sun, 21 Jun 2020 21:13:13: 10000000 INFO @ Sun, 21 Jun 2020 21:13:15: 6000000 INFO @ Sun, 21 Jun 2020 21:13:19: 2000000 INFO @ Sun, 21 Jun 2020 21:13:21: 11000000 INFO @ Sun, 21 Jun 2020 21:13:22: 7000000 INFO @ Sun, 21 Jun 2020 21:13:26: 3000000 INFO @ Sun, 21 Jun 2020 21:13:28: 12000000 INFO @ Sun, 21 Jun 2020 21:13:29: 8000000 INFO @ Sun, 21 Jun 2020 21:13:29: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:13:29: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:13:29: #1 total tags in treatment: 12166930 INFO @ Sun, 21 Jun 2020 21:13:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:13:29: #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 21:13:30: #1 tags after filtering in treatment: 12166899 INFO @ Sun, 21 Jun 2020 21:13:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:13:30: #1 finished! INFO @ Sun, 21 Jun 2020 21:13:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:13:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:13:31: #2 number of paired peaks: 730 WARNING @ Sun, 21 Jun 2020 21:13:31: Fewer paired peaks (730) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 730 pairs to build model! INFO @ Sun, 21 Jun 2020 21:13:31: start model_add_line... INFO @ Sun, 21 Jun 2020 21:13:31: start X-correlation... INFO @ Sun, 21 Jun 2020 21:13:31: end of X-cor INFO @ Sun, 21 Jun 2020 21:13:31: #2 finished! INFO @ Sun, 21 Jun 2020 21:13:31: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 21:13:31: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 21:13:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.05_model.r INFO @ Sun, 21 Jun 2020 21:13:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:13:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:13:33: 4000000 INFO @ Sun, 21 Jun 2020 21:13:35: 9000000 INFO @ Sun, 21 Jun 2020 21:13:40: 5000000 INFO @ Sun, 21 Jun 2020 21:13:42: 10000000 INFO @ Sun, 21 Jun 2020 21:13:48: 6000000 INFO @ Sun, 21 Jun 2020 21:13:49: 11000000 INFO @ Sun, 21 Jun 2020 21:13:55: 7000000 INFO @ Sun, 21 Jun 2020 21:13:56: 12000000 INFO @ Sun, 21 Jun 2020 21:13:58: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:13:58: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:13:58: #1 total tags in treatment: 12166930 INFO @ Sun, 21 Jun 2020 21:13:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:13:58: #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 21:13:58: #1 tags after filtering in treatment: 12166899 INFO @ Sun, 21 Jun 2020 21:13:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:13:58: #1 finished! INFO @ Sun, 21 Jun 2020 21:13:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:13:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:13:59: #2 number of paired peaks: 730 WARNING @ Sun, 21 Jun 2020 21:13:59: Fewer paired peaks (730) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 730 pairs to build model! INFO @ Sun, 21 Jun 2020 21:13:59: start model_add_line... INFO @ Sun, 21 Jun 2020 21:13:59: start X-correlation... INFO @ Sun, 21 Jun 2020 21:13:59: end of X-cor INFO @ Sun, 21 Jun 2020 21:13:59: #2 finished! INFO @ Sun, 21 Jun 2020 21:13:59: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 21:13:59: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 21:13:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.10_model.r INFO @ Sun, 21 Jun 2020 21:13:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:13:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:14:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:14:01: 8000000 INFO @ Sun, 21 Jun 2020 21:14:08: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:14:15: 10000000 INFO @ Sun, 21 Jun 2020 21:14:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:14:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:14:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.05_summits.bed INFO @ Sun, 21 Jun 2020 21:14:15: Done! pass1 - making usageList (92 chroms): 2 millis pass2 - checking and writing primary data (8366 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:14:22: 11000000 INFO @ Sun, 21 Jun 2020 21:14:28: 12000000 INFO @ Sun, 21 Jun 2020 21:14:30: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:14:30: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:14:30: #1 total tags in treatment: 12166930 INFO @ Sun, 21 Jun 2020 21:14:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:14:30: #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 21:14:30: #1 tags after filtering in treatment: 12166899 INFO @ Sun, 21 Jun 2020 21:14:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:14:30: #1 finished! INFO @ Sun, 21 Jun 2020 21:14:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:14:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:14:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:14:31: #2 number of paired peaks: 730 WARNING @ Sun, 21 Jun 2020 21:14:31: Fewer paired peaks (730) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 730 pairs to build model! INFO @ Sun, 21 Jun 2020 21:14:31: start model_add_line... INFO @ Sun, 21 Jun 2020 21:14:31: start X-correlation... INFO @ Sun, 21 Jun 2020 21:14:31: end of X-cor INFO @ Sun, 21 Jun 2020 21:14:31: #2 finished! INFO @ Sun, 21 Jun 2020 21:14:31: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 21:14:31: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 21:14:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.20_model.r INFO @ Sun, 21 Jun 2020 21:14:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:14:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:14:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:14:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:14:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.10_summits.bed INFO @ Sun, 21 Jun 2020 21:14:47: Done! pass1 - making usageList (61 chroms): 2 millis pass2 - checking and writing primary data (4149 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:15:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:15:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:15:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:15:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798859/SRX4798859.20_summits.bed INFO @ Sun, 21 Jun 2020 21:15:16: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (1257 records, 4 fields): 3 millis CompletedMACS2peakCalling