Job ID = 6454835 SRX = SRX2592431 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:29:59 prefetch.2.10.7: 1) Downloading 'SRR5289708'... 2020-06-21T09:29:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:32:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:32:34 prefetch.2.10.7: 'SRR5289708' is valid 2020-06-21T09:32:34 prefetch.2.10.7: 1) 'SRR5289708' was downloaded successfully Read 9589506 spots for SRR5289708/SRR5289708.sra Written 9589506 spots for SRR5289708/SRR5289708.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: 00:03:22 9589506 reads; of these: 9589506 (100.00%) were unpaired; of these: 944908 (9.85%) aligned 0 times 6056638 (63.16%) aligned exactly 1 time 2587960 (26.99%) aligned >1 times 90.15% overall alignment rate Time searching: 00:03:22 Overall time: 00:03:22 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_rmdupse_core] 3422258 / 8644598 = 0.3959 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 18:39:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.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 18:39:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:12: 1000000 INFO @ Sun, 21 Jun 2020 18:39:17: 2000000 INFO @ Sun, 21 Jun 2020 18:39:23: 3000000 INFO @ Sun, 21 Jun 2020 18:39:28: 4000000 INFO @ Sun, 21 Jun 2020 18:39:34: 5000000 INFO @ Sun, 21 Jun 2020 18:39:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:39:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:39:35: #1 total tags in treatment: 5222340 INFO @ Sun, 21 Jun 2020 18:39:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 18:39:35: #1 tags after filtering in treatment: 5222126 INFO @ Sun, 21 Jun 2020 18:39:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:36: #2 number of paired peaks: 398 WARNING @ Sun, 21 Jun 2020 18:39:36: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Sun, 21 Jun 2020 18:39:36: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:36: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:36: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:36: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:36: #2 predicted fragment length is 183 bps INFO @ Sun, 21 Jun 2020 18:39:36: #2 alternative fragment length(s) may be 183 bps INFO @ Sun, 21 Jun 2020 18:39:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.05_model.r INFO @ Sun, 21 Jun 2020 18:39:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:39:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.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 18:39:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:42: 1000000 INFO @ Sun, 21 Jun 2020 18:39:47: 2000000 INFO @ Sun, 21 Jun 2020 18:39:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:39:52: 3000000 INFO @ Sun, 21 Jun 2020 18:39:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:39:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:39:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.05_summits.bed INFO @ Sun, 21 Jun 2020 18:39:57: Done! INFO @ Sun, 21 Jun 2020 18:39:58: 4000000 pass1 - making usageList (579 chroms): 3 millis pass2 - checking and writing primary data (16763 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:40:03: 5000000 INFO @ Sun, 21 Jun 2020 18:40:04: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:40:04: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:40:04: #1 total tags in treatment: 5222340 INFO @ Sun, 21 Jun 2020 18:40:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:04: #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 18:40:05: #1 tags after filtering in treatment: 5222126 INFO @ Sun, 21 Jun 2020 18:40:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:05: #2 looking for paired plus/minus strand peaks... 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 18:40:05: #2 number of paired peaks: 398 WARNING @ Sun, 21 Jun 2020 18:40:05: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Sun, 21 Jun 2020 18:40:05: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:05: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:05: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:05: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:05: #2 predicted fragment length is 183 bps INFO @ Sun, 21 Jun 2020 18:40:05: #2 alternative fragment length(s) may be 183 bps INFO @ Sun, 21 Jun 2020 18:40:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.10_model.r INFO @ Sun, 21 Jun 2020 18:40:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:40:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.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 18:40:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:40:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:40:12: 1000000 INFO @ Sun, 21 Jun 2020 18:40:17: 2000000 INFO @ Sun, 21 Jun 2020 18:40:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:40:23: 3000000 INFO @ Sun, 21 Jun 2020 18:40:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.10_summits.bed INFO @ Sun, 21 Jun 2020 18:40:26: Done! pass1 - making usageList (429 chroms): 3 millis pass2 - checking and writing primary data (13913 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:40:28: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:40:33: 5000000 INFO @ Sun, 21 Jun 2020 18:40:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:40:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:40:35: #1 total tags in treatment: 5222340 INFO @ Sun, 21 Jun 2020 18:40:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:35: #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 18:40:35: #1 tags after filtering in treatment: 5222126 INFO @ Sun, 21 Jun 2020 18:40:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:40:36: #2 number of paired peaks: 398 WARNING @ Sun, 21 Jun 2020 18:40:36: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Sun, 21 Jun 2020 18:40:36: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:36: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:36: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:36: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:36: #2 predicted fragment length is 183 bps INFO @ Sun, 21 Jun 2020 18:40:36: #2 alternative fragment length(s) may be 183 bps INFO @ Sun, 21 Jun 2020 18:40:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.20_model.r INFO @ Sun, 21 Jun 2020 18:40:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:40:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:40:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592431/SRX2592431.20_summits.bed INFO @ Sun, 21 Jun 2020 18:40:57: Done! pass1 - making usageList (267 chroms): 2 millis pass2 - checking and writing primary data (10339 records, 4 fields): 18 millis CompletedMACS2peakCalling