Job ID = 6455335 SRX = SRX287704 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:55:26 prefetch.2.10.7: 1) Downloading 'SRR869892'... 2020-06-21T09:55:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:57:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:57:43 prefetch.2.10.7: 'SRR869892' is valid 2020-06-21T09:57:43 prefetch.2.10.7: 1) 'SRR869892' was downloaded successfully Read 13702188 spots for SRR869892/SRR869892.sra Written 13702188 spots for SRR869892/SRR869892.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: 00:03:18 13702188 reads; of these: 13702188 (100.00%) were unpaired; of these: 713398 (5.21%) aligned 0 times 11274373 (82.28%) aligned exactly 1 time 1714417 (12.51%) aligned >1 times 94.79% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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] 1395086 / 12988790 = 0.1074 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 19:05:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.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 19:05:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:05:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:05:26: 1000000 INFO @ Sun, 21 Jun 2020 19:05:33: 2000000 INFO @ Sun, 21 Jun 2020 19:05:39: 3000000 INFO @ Sun, 21 Jun 2020 19:05:45: 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 19:05:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.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 19:05:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:05:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:05:52: 5000000 INFO @ Sun, 21 Jun 2020 19:05:58: 1000000 INFO @ Sun, 21 Jun 2020 19:05:59: 6000000 INFO @ Sun, 21 Jun 2020 19:06:06: 2000000 INFO @ Sun, 21 Jun 2020 19:06:06: 7000000 INFO @ Sun, 21 Jun 2020 19:06:14: 8000000 INFO @ Sun, 21 Jun 2020 19:06:14: 3000000 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 19:06:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.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 19:06:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:06:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:06:21: 9000000 INFO @ Sun, 21 Jun 2020 19:06:21: 4000000 INFO @ Sun, 21 Jun 2020 19:06:28: 1000000 INFO @ Sun, 21 Jun 2020 19:06:29: 10000000 INFO @ Sun, 21 Jun 2020 19:06:29: 5000000 INFO @ Sun, 21 Jun 2020 19:06:35: 2000000 INFO @ Sun, 21 Jun 2020 19:06:36: 11000000 INFO @ Sun, 21 Jun 2020 19:06:37: 6000000 INFO @ Sun, 21 Jun 2020 19:06:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:06:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:06:40: #1 total tags in treatment: 11593704 INFO @ Sun, 21 Jun 2020 19:06:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:06:40: #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 19:06:41: #1 tags after filtering in treatment: 11593680 INFO @ Sun, 21 Jun 2020 19:06:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:06:41: #1 finished! INFO @ Sun, 21 Jun 2020 19:06:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:06:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:06:42: #2 number of paired peaks: 651 WARNING @ Sun, 21 Jun 2020 19:06:42: Fewer paired peaks (651) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 651 pairs to build model! INFO @ Sun, 21 Jun 2020 19:06:42: start model_add_line... INFO @ Sun, 21 Jun 2020 19:06:42: start X-correlation... INFO @ Sun, 21 Jun 2020 19:06:42: end of X-cor INFO @ Sun, 21 Jun 2020 19:06:42: #2 finished! INFO @ Sun, 21 Jun 2020 19:06:42: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 19:06:42: #2 alternative fragment length(s) may be 4,122,596 bps INFO @ Sun, 21 Jun 2020 19:06:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.05_model.r INFO @ Sun, 21 Jun 2020 19:06:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:06:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:06:42: 3000000 INFO @ Sun, 21 Jun 2020 19:06:45: 7000000 INFO @ Sun, 21 Jun 2020 19:06:49: 4000000 INFO @ Sun, 21 Jun 2020 19:06:53: 8000000 INFO @ Sun, 21 Jun 2020 19:06:56: 5000000 INFO @ Sun, 21 Jun 2020 19:07:01: 9000000 INFO @ Sun, 21 Jun 2020 19:07:03: 6000000 INFO @ Sun, 21 Jun 2020 19:07:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:07:09: 10000000 INFO @ Sun, 21 Jun 2020 19:07:10: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:07:16: 11000000 INFO @ Sun, 21 Jun 2020 19:07:17: 8000000 INFO @ Sun, 21 Jun 2020 19:07:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:07:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:07:21: #1 total tags in treatment: 11593704 INFO @ Sun, 21 Jun 2020 19:07:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:07:21: #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 19:07:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:07:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:07:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.05_summits.bed INFO @ Sun, 21 Jun 2020 19:07:22: Done! INFO @ Sun, 21 Jun 2020 19:07:22: #1 tags after filtering in treatment: 11593680 INFO @ Sun, 21 Jun 2020 19:07:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:07:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:07:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:07:22: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (234 chroms): 1 millis pass2 - checking and writing primary data (2238 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:07:23: #2 number of paired peaks: 651 WARNING @ Sun, 21 Jun 2020 19:07:23: Fewer paired peaks (651) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 651 pairs to build model! INFO @ Sun, 21 Jun 2020 19:07:23: start model_add_line... INFO @ Sun, 21 Jun 2020 19:07:23: start X-correlation... INFO @ Sun, 21 Jun 2020 19:07:23: end of X-cor INFO @ Sun, 21 Jun 2020 19:07:23: #2 finished! INFO @ Sun, 21 Jun 2020 19:07:23: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 19:07:23: #2 alternative fragment length(s) may be 4,122,596 bps INFO @ Sun, 21 Jun 2020 19:07:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.10_model.r INFO @ Sun, 21 Jun 2020 19:07:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:07:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:07:24: 9000000 INFO @ Sun, 21 Jun 2020 19:07:31: 10000000 INFO @ Sun, 21 Jun 2020 19:07:37: 11000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:07:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:07:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:07:40: #1 total tags in treatment: 11593704 INFO @ Sun, 21 Jun 2020 19:07:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:07:40: #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 19:07:41: #1 tags after filtering in treatment: 11593680 INFO @ Sun, 21 Jun 2020 19:07:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:07:41: #1 finished! INFO @ Sun, 21 Jun 2020 19:07:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:07:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:07:41: #2 number of paired peaks: 651 WARNING @ Sun, 21 Jun 2020 19:07:41: Fewer paired peaks (651) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 651 pairs to build model! INFO @ Sun, 21 Jun 2020 19:07:41: start model_add_line... INFO @ Sun, 21 Jun 2020 19:07:42: start X-correlation... INFO @ Sun, 21 Jun 2020 19:07:42: end of X-cor INFO @ Sun, 21 Jun 2020 19:07:42: #2 finished! INFO @ Sun, 21 Jun 2020 19:07:42: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 19:07:42: #2 alternative fragment length(s) may be 4,122,596 bps INFO @ Sun, 21 Jun 2020 19:07:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.20_model.r INFO @ Sun, 21 Jun 2020 19:07:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:07:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:07:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:08:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:08:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:08:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.10_summits.bed INFO @ Sun, 21 Jun 2020 19:08:02: Done! pass1 - making usageList (127 chroms): 1 millis pass2 - checking and writing primary data (674 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:08:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:08:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:08:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:08:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287704/SRX287704.20_summits.bed INFO @ Sun, 21 Jun 2020 19:08:21: Done! pass1 - making usageList (79 chroms): 1 millis pass2 - checking and writing primary data (165 records, 4 fields): 3 millis CompletedMACS2peakCalling