Job ID = 6455608 SRX = SRX287924 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:06:51 prefetch.2.10.7: 1) Downloading 'SRR870113'... 2020-06-21T10:06:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:09:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:09:06 prefetch.2.10.7: 'SRR870113' is valid 2020-06-21T10:09:06 prefetch.2.10.7: 1) 'SRR870113' was downloaded successfully Read 13260182 spots for SRR870113/SRR870113.sra Written 13260182 spots for SRR870113/SRR870113.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: 00:03:06 13260182 reads; of these: 13260182 (100.00%) were unpaired; of these: 2215849 (16.71%) aligned 0 times 7837132 (59.10%) aligned exactly 1 time 3207201 (24.19%) aligned >1 times 83.29% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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] 1282831 / 11044333 = 0.1162 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 19:16:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.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 19:16:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:16:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:16:17: 1000000 INFO @ Sun, 21 Jun 2020 19:16:23: 2000000 INFO @ Sun, 21 Jun 2020 19:16:29: 3000000 INFO @ Sun, 21 Jun 2020 19:16:36: 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 19:16:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.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 19:16:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:16:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:16:42: 5000000 INFO @ Sun, 21 Jun 2020 19:16:47: 1000000 INFO @ Sun, 21 Jun 2020 19:16:49: 6000000 INFO @ Sun, 21 Jun 2020 19:16:54: 2000000 INFO @ Sun, 21 Jun 2020 19:16:56: 7000000 INFO @ Sun, 21 Jun 2020 19:17:01: 3000000 INFO @ Sun, 21 Jun 2020 19:17:03: 8000000 INFO @ Sun, 21 Jun 2020 19:17:08: 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 19:17:10: 9000000 INFO @ Sun, 21 Jun 2020 19:17:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.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 19:17:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:17:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:17:14: 5000000 INFO @ Sun, 21 Jun 2020 19:17:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:17:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:17:15: #1 total tags in treatment: 9761502 INFO @ Sun, 21 Jun 2020 19:17:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:17:15: #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 19:17:16: #1 tags after filtering in treatment: 9761497 INFO @ Sun, 21 Jun 2020 19:17:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:17:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:17:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:17:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:17:17: #2 number of paired peaks: 637 WARNING @ Sun, 21 Jun 2020 19:17:17: Fewer paired peaks (637) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 637 pairs to build model! INFO @ Sun, 21 Jun 2020 19:17:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:17:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:17:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:17:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:17:17: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 19:17:17: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 19:17:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.05_model.r INFO @ Sun, 21 Jun 2020 19:17:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:17:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:17:17: 1000000 INFO @ Sun, 21 Jun 2020 19:17:21: 6000000 INFO @ Sun, 21 Jun 2020 19:17:24: 2000000 INFO @ Sun, 21 Jun 2020 19:17:28: 7000000 INFO @ Sun, 21 Jun 2020 19:17:31: 3000000 INFO @ Sun, 21 Jun 2020 19:17:35: 8000000 INFO @ Sun, 21 Jun 2020 19:17:38: 4000000 INFO @ Sun, 21 Jun 2020 19:17:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:17:42: 9000000 INFO @ Sun, 21 Jun 2020 19:17:45: 5000000 INFO @ Sun, 21 Jun 2020 19:17:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:17:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:17:48: #1 total tags in treatment: 9761502 INFO @ Sun, 21 Jun 2020 19:17:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:17:48: #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 19:17:48: #1 tags after filtering in treatment: 9761497 INFO @ Sun, 21 Jun 2020 19:17:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:17:48: #1 finished! INFO @ Sun, 21 Jun 2020 19:17:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:17:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:17:49: #2 number of paired peaks: 637 WARNING @ Sun, 21 Jun 2020 19:17:49: Fewer paired peaks (637) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 637 pairs to build model! INFO @ Sun, 21 Jun 2020 19:17:49: start model_add_line... INFO @ Sun, 21 Jun 2020 19:17:49: start X-correlation... INFO @ Sun, 21 Jun 2020 19:17:49: end of X-cor INFO @ Sun, 21 Jun 2020 19:17:49: #2 finished! INFO @ Sun, 21 Jun 2020 19:17:49: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 19:17:49: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 19:17:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.10_model.r INFO @ Sun, 21 Jun 2020 19:17:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:17:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:17:51: 6000000 INFO @ Sun, 21 Jun 2020 19:17:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:17:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:17:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.05_summits.bed INFO @ Sun, 21 Jun 2020 19:17:51: Done! pass1 - making usageList (519 chroms): 2 millis pass2 - checking and writing primary data (2509 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:17:58: 7000000 INFO @ Sun, 21 Jun 2020 19:18:04: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:18:11: 9000000 INFO @ Sun, 21 Jun 2020 19:18:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:18:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:18:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:18:16: #1 total tags in treatment: 9761502 INFO @ Sun, 21 Jun 2020 19:18:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:18:16: #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 19:18:16: #1 tags after filtering in treatment: 9761497 INFO @ Sun, 21 Jun 2020 19:18:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:18:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:18:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:18:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:18:17: #2 number of paired peaks: 637 WARNING @ Sun, 21 Jun 2020 19:18:17: Fewer paired peaks (637) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 637 pairs to build model! INFO @ Sun, 21 Jun 2020 19:18:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:18:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:18:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:18:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:18:17: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 19:18:17: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 19:18:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.20_model.r INFO @ Sun, 21 Jun 2020 19:18:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:18:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:18:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:18:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:18:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.10_summits.bed INFO @ Sun, 21 Jun 2020 19:18:25: Done! pass1 - making usageList (286 chroms): 1 millis pass2 - checking and writing primary data (1146 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:18:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:18:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:18:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:18:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287924/SRX287924.20_summits.bed INFO @ Sun, 21 Jun 2020 19:18:52: Done! pass1 - making usageList (145 chroms): 1 millis pass2 - checking and writing primary data (540 records, 4 fields): 7 millis CompletedMACS2peakCalling