Job ID = 6455696 SRX = SRX287997 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:21:06 prefetch.2.10.7: 1) Downloading 'SRR870186'... 2020-06-21T10:21:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:29 prefetch.2.10.7: 'SRR870186' is valid 2020-06-21T10:24:29 prefetch.2.10.7: 1) 'SRR870186' was downloaded successfully Read 10906498 spots for SRR870186/SRR870186.sra Written 10906498 spots for SRR870186/SRR870186.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: 00:02:38 10906498 reads; of these: 10906498 (100.00%) were unpaired; of these: 744734 (6.83%) aligned 0 times 8742923 (80.16%) aligned exactly 1 time 1418841 (13.01%) aligned >1 times 93.17% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 678235 / 10161764 = 0.0667 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 19:30:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.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 19:30:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:31:03: 1000000 INFO @ Sun, 21 Jun 2020 19:31:09: 2000000 INFO @ Sun, 21 Jun 2020 19:31:15: 3000000 INFO @ Sun, 21 Jun 2020 19:31:21: 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 19:31:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.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 19:31:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:31:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:31:28: 5000000 INFO @ Sun, 21 Jun 2020 19:31:33: 1000000 INFO @ Sun, 21 Jun 2020 19:31:34: 6000000 INFO @ Sun, 21 Jun 2020 19:31:39: 2000000 INFO @ Sun, 21 Jun 2020 19:31:41: 7000000 INFO @ Sun, 21 Jun 2020 19:31:44: 3000000 INFO @ Sun, 21 Jun 2020 19:31:47: 8000000 INFO @ Sun, 21 Jun 2020 19:31:50: 4000000 INFO @ Sun, 21 Jun 2020 19:31:54: 9000000 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 19:31:56: 5000000 INFO @ Sun, 21 Jun 2020 19:31:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.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 19:31:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:31:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:31:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:31:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:31:57: #1 total tags in treatment: 9483529 INFO @ Sun, 21 Jun 2020 19:31:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:31:57: #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 19:31:58: #1 tags after filtering in treatment: 9483525 INFO @ Sun, 21 Jun 2020 19:31:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:31:58: #1 finished! INFO @ Sun, 21 Jun 2020 19:31:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:31:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:31:59: #2 number of paired peaks: 817 WARNING @ Sun, 21 Jun 2020 19:31:59: Fewer paired peaks (817) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 817 pairs to build model! INFO @ Sun, 21 Jun 2020 19:31:59: start model_add_line... INFO @ Sun, 21 Jun 2020 19:31:59: start X-correlation... INFO @ Sun, 21 Jun 2020 19:31:59: end of X-cor INFO @ Sun, 21 Jun 2020 19:31:59: #2 finished! INFO @ Sun, 21 Jun 2020 19:31:59: #2 predicted fragment length is 177 bps INFO @ Sun, 21 Jun 2020 19:31:59: #2 alternative fragment length(s) may be 177 bps INFO @ Sun, 21 Jun 2020 19:31:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.05_model.r INFO @ Sun, 21 Jun 2020 19:31:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:31:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:32:02: 6000000 INFO @ Sun, 21 Jun 2020 19:32:02: 1000000 INFO @ Sun, 21 Jun 2020 19:32:07: 7000000 INFO @ Sun, 21 Jun 2020 19:32:08: 2000000 INFO @ Sun, 21 Jun 2020 19:32:13: 8000000 INFO @ Sun, 21 Jun 2020 19:32:13: 3000000 INFO @ Sun, 21 Jun 2020 19:32:19: 9000000 INFO @ Sun, 21 Jun 2020 19:32:19: 4000000 INFO @ Sun, 21 Jun 2020 19:32:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:32:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:32:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:32:22: #1 total tags in treatment: 9483529 INFO @ Sun, 21 Jun 2020 19:32:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:32:22: #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 19:32:22: #1 tags after filtering in treatment: 9483525 INFO @ Sun, 21 Jun 2020 19:32:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:32:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:32:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:32:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:32:23: #2 number of paired peaks: 817 WARNING @ Sun, 21 Jun 2020 19:32:23: Fewer paired peaks (817) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 817 pairs to build model! INFO @ Sun, 21 Jun 2020 19:32:23: start model_add_line... INFO @ Sun, 21 Jun 2020 19:32:23: start X-correlation... INFO @ Sun, 21 Jun 2020 19:32:23: end of X-cor INFO @ Sun, 21 Jun 2020 19:32:23: #2 finished! INFO @ Sun, 21 Jun 2020 19:32:23: #2 predicted fragment length is 177 bps INFO @ Sun, 21 Jun 2020 19:32:23: #2 alternative fragment length(s) may be 177 bps INFO @ Sun, 21 Jun 2020 19:32:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.10_model.r INFO @ Sun, 21 Jun 2020 19:32:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:32:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:32:24: 5000000 INFO @ Sun, 21 Jun 2020 19:32:29: 6000000 INFO @ Sun, 21 Jun 2020 19:32:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:32:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:32:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.05_summits.bed INFO @ Sun, 21 Jun 2020 19:32:31: Done! pass1 - making usageList (388 chroms): 2 millis pass2 - checking and writing primary data (6524 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:32:34: 7000000 INFO @ Sun, 21 Jun 2020 19:32:40: 8000000 INFO @ Sun, 21 Jun 2020 19:32:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:32:45: 9000000 INFO @ Sun, 21 Jun 2020 19:32:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:32:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:32:48: #1 total tags in treatment: 9483529 INFO @ Sun, 21 Jun 2020 19:32:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:32:48: #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 19:32:49: #1 tags after filtering in treatment: 9483525 INFO @ Sun, 21 Jun 2020 19:32:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:32:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:32:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:32:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:32:49: #2 number of paired peaks: 817 WARNING @ Sun, 21 Jun 2020 19:32:49: Fewer paired peaks (817) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 817 pairs to build model! INFO @ Sun, 21 Jun 2020 19:32:49: start model_add_line... INFO @ Sun, 21 Jun 2020 19:32:49: start X-correlation... INFO @ Sun, 21 Jun 2020 19:32:49: end of X-cor INFO @ Sun, 21 Jun 2020 19:32:49: #2 finished! INFO @ Sun, 21 Jun 2020 19:32:49: #2 predicted fragment length is 177 bps INFO @ Sun, 21 Jun 2020 19:32:49: #2 alternative fragment length(s) may be 177 bps INFO @ Sun, 21 Jun 2020 19:32:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.20_model.r INFO @ Sun, 21 Jun 2020 19:32:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:32:49: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:32:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:32:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:32:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.10_summits.bed INFO @ Sun, 21 Jun 2020 19:32:56: Done! pass1 - making usageList (238 chroms): 1 millis pass2 - checking and writing primary data (4148 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:33:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:33:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:33:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:33:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287997/SRX287997.20_summits.bed INFO @ Sun, 21 Jun 2020 19:33:22: Done! pass1 - making usageList (116 chroms): 1 millis pass2 - checking and writing primary data (1711 records, 4 fields): 7 millis CompletedMACS2peakCalling