Job ID = 6454810 SRX = SRX2592409 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:46:55 prefetch.2.10.7: 1) Downloading 'SRR5289686'... 2020-06-21T09:46:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:49:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:49:56 prefetch.2.10.7: 1) 'SRR5289686' was downloaded successfully Read 22616546 spots for SRR5289686/SRR5289686.sra Written 22616546 spots for SRR5289686/SRR5289686.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: 00:07:10 22616546 reads; of these: 22616546 (100.00%) were unpaired; of these: 1739235 (7.69%) aligned 0 times 16437262 (72.68%) aligned exactly 1 time 4440049 (19.63%) aligned >1 times 92.31% overall alignment rate Time searching: 00:07:10 Overall time: 00:07:10 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 12 files... [bam_rmdupse_core] 5742926 / 20877311 = 0.2751 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 19:04:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.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 19:04:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:04:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:04:12: 1000000 INFO @ Sun, 21 Jun 2020 19:04:18: 2000000 INFO @ Sun, 21 Jun 2020 19:04:24: 3000000 INFO @ Sun, 21 Jun 2020 19:04:30: 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 19:04:36: 5000000 INFO @ Sun, 21 Jun 2020 19:04:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.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 19:04:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:04:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:04:42: 6000000 INFO @ Sun, 21 Jun 2020 19:04:43: 1000000 INFO @ Sun, 21 Jun 2020 19:04:49: 7000000 INFO @ Sun, 21 Jun 2020 19:04:49: 2000000 INFO @ Sun, 21 Jun 2020 19:04:55: 8000000 INFO @ Sun, 21 Jun 2020 19:04:56: 3000000 INFO @ Sun, 21 Jun 2020 19:05:02: 9000000 INFO @ Sun, 21 Jun 2020 19:05:03: 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 19:05:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.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 19:05:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:05:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:05:09: 10000000 INFO @ Sun, 21 Jun 2020 19:05:09: 5000000 INFO @ Sun, 21 Jun 2020 19:05:15: 1000000 INFO @ Sun, 21 Jun 2020 19:05:16: 11000000 INFO @ Sun, 21 Jun 2020 19:05:17: 6000000 INFO @ Sun, 21 Jun 2020 19:05:23: 2000000 INFO @ Sun, 21 Jun 2020 19:05:24: 12000000 INFO @ Sun, 21 Jun 2020 19:05:24: 7000000 INFO @ Sun, 21 Jun 2020 19:05:31: 13000000 INFO @ Sun, 21 Jun 2020 19:05:31: 8000000 INFO @ Sun, 21 Jun 2020 19:05:31: 3000000 INFO @ Sun, 21 Jun 2020 19:05:38: 14000000 INFO @ Sun, 21 Jun 2020 19:05:38: 9000000 INFO @ Sun, 21 Jun 2020 19:05:39: 4000000 INFO @ Sun, 21 Jun 2020 19:05:45: 15000000 INFO @ Sun, 21 Jun 2020 19:05:45: 10000000 INFO @ Sun, 21 Jun 2020 19:05:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:05:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:05:46: #1 total tags in treatment: 15134385 INFO @ Sun, 21 Jun 2020 19:05:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:05:46: #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 19:05:46: #1 tags after filtering in treatment: 15134276 INFO @ Sun, 21 Jun 2020 19:05:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:05:46: #1 finished! INFO @ Sun, 21 Jun 2020 19:05:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:05:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:05:48: 5000000 INFO @ Sun, 21 Jun 2020 19:05:48: #2 number of paired peaks: 657 WARNING @ Sun, 21 Jun 2020 19:05:48: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Sun, 21 Jun 2020 19:05:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:05:48: start X-correlation... INFO @ Sun, 21 Jun 2020 19:05:48: end of X-cor INFO @ Sun, 21 Jun 2020 19:05:48: #2 finished! INFO @ Sun, 21 Jun 2020 19:05:48: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 19:05:48: #2 alternative fragment length(s) may be 3,157,184 bps INFO @ Sun, 21 Jun 2020 19:05:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.05_model.r INFO @ Sun, 21 Jun 2020 19:05:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:05:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:05:52: 11000000 INFO @ Sun, 21 Jun 2020 19:05:56: 6000000 INFO @ Sun, 21 Jun 2020 19:06:00: 12000000 INFO @ Sun, 21 Jun 2020 19:06:04: 7000000 INFO @ Sun, 21 Jun 2020 19:06:07: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:06:12: 8000000 INFO @ Sun, 21 Jun 2020 19:06:14: 14000000 INFO @ Sun, 21 Jun 2020 19:06:20: 9000000 INFO @ Sun, 21 Jun 2020 19:06:21: 15000000 INFO @ Sun, 21 Jun 2020 19:06:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:06:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:06:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:06:22: #1 total tags in treatment: 15134385 INFO @ Sun, 21 Jun 2020 19:06:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:06:22: #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 19:06:23: #1 tags after filtering in treatment: 15134276 INFO @ Sun, 21 Jun 2020 19:06:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:06:23: #1 finished! INFO @ Sun, 21 Jun 2020 19:06:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:06:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:06:24: #2 number of paired peaks: 657 WARNING @ Sun, 21 Jun 2020 19:06:24: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Sun, 21 Jun 2020 19:06:24: start model_add_line... INFO @ Sun, 21 Jun 2020 19:06:24: start X-correlation... INFO @ Sun, 21 Jun 2020 19:06:24: end of X-cor INFO @ Sun, 21 Jun 2020 19:06:24: #2 finished! INFO @ Sun, 21 Jun 2020 19:06:24: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 19:06:24: #2 alternative fragment length(s) may be 3,157,184 bps INFO @ Sun, 21 Jun 2020 19:06:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.10_model.r INFO @ Sun, 21 Jun 2020 19:06:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:06:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:06:28: 10000000 INFO @ Sun, 21 Jun 2020 19:06:35: 11000000 INFO @ Sun, 21 Jun 2020 19:06:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:06:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:06:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.05_summits.bed INFO @ Sun, 21 Jun 2020 19:06:41: Done! BigWig に変換しました。 pass1 - making usageList (276 chroms): 3 millis pass2 - checking and writing primary data (16103 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:06:43: 12000000 INFO @ Sun, 21 Jun 2020 19:06:51: 13000000 INFO @ Sun, 21 Jun 2020 19:06:58: 14000000 INFO @ Sun, 21 Jun 2020 19:07:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:07:06: 15000000 INFO @ Sun, 21 Jun 2020 19:07:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:07:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:07:07: #1 total tags in treatment: 15134385 INFO @ Sun, 21 Jun 2020 19:07:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:07:07: #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 19:07:07: #1 tags after filtering in treatment: 15134276 INFO @ Sun, 21 Jun 2020 19:07:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:07:07: #1 finished! INFO @ Sun, 21 Jun 2020 19:07:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:07:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:07:08: #2 number of paired peaks: 657 WARNING @ Sun, 21 Jun 2020 19:07:08: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Sun, 21 Jun 2020 19:07:08: start model_add_line... INFO @ Sun, 21 Jun 2020 19:07:09: start X-correlation... INFO @ Sun, 21 Jun 2020 19:07:09: end of X-cor INFO @ Sun, 21 Jun 2020 19:07:09: #2 finished! INFO @ Sun, 21 Jun 2020 19:07:09: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 19:07:09: #2 alternative fragment length(s) may be 3,157,184 bps INFO @ Sun, 21 Jun 2020 19:07:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.20_model.r INFO @ Sun, 21 Jun 2020 19:07:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:07:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:07:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:07:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:07:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.10_summits.bed INFO @ Sun, 21 Jun 2020 19:07:20: Done! pass1 - making usageList (192 chroms): 2 millis pass2 - checking and writing primary data (10010 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:07:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:08:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:08:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:08:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592409/SRX2592409.20_summits.bed INFO @ Sun, 21 Jun 2020 19:08:07: Done! pass1 - making usageList (129 chroms): 1 millis pass2 - checking and writing primary data (4777 records, 4 fields): 10 millis CompletedMACS2peakCalling