Job ID = 6455414 SRX = SRX287768 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:53:55 prefetch.2.10.7: 1) Downloading 'SRR869957'... 2020-06-21T09:53:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:57:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:57:43 prefetch.2.10.7: 1) 'SRR869957' was downloaded successfully Read 20507609 spots for SRR869957/SRR869957.sra Written 20507609 spots for SRR869957/SRR869957.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: 00:05:09 20507609 reads; of these: 20507609 (100.00%) were unpaired; of these: 1337109 (6.52%) aligned 0 times 16402017 (79.98%) aligned exactly 1 time 2768483 (13.50%) aligned >1 times 93.48% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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] 2694329 / 19170500 = 0.1405 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 19:10:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.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 19:10:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:10:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:10:27: 1000000 INFO @ Sun, 21 Jun 2020 19:10:36: 2000000 INFO @ Sun, 21 Jun 2020 19:10:44: 3000000 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 19:10:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.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 19:10:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:10:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:10:53: 4000000 INFO @ Sun, 21 Jun 2020 19:10:57: 1000000 INFO @ Sun, 21 Jun 2020 19:11:01: 5000000 INFO @ Sun, 21 Jun 2020 19:11:06: 2000000 INFO @ Sun, 21 Jun 2020 19:11:10: 6000000 INFO @ Sun, 21 Jun 2020 19:11:14: 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 19:11:19: 7000000 INFO @ Sun, 21 Jun 2020 19:11:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.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 19:11:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:11:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:11:23: 4000000 INFO @ Sun, 21 Jun 2020 19:11:27: 1000000 INFO @ Sun, 21 Jun 2020 19:11:28: 8000000 INFO @ Sun, 21 Jun 2020 19:11:32: 5000000 INFO @ Sun, 21 Jun 2020 19:11:36: 2000000 INFO @ Sun, 21 Jun 2020 19:11:37: 9000000 INFO @ Sun, 21 Jun 2020 19:11:41: 6000000 INFO @ Sun, 21 Jun 2020 19:11:44: 3000000 INFO @ Sun, 21 Jun 2020 19:11:47: 10000000 INFO @ Sun, 21 Jun 2020 19:11:49: 7000000 INFO @ Sun, 21 Jun 2020 19:11:52: 4000000 INFO @ Sun, 21 Jun 2020 19:11:56: 11000000 INFO @ Sun, 21 Jun 2020 19:11:58: 8000000 INFO @ Sun, 21 Jun 2020 19:12:01: 5000000 INFO @ Sun, 21 Jun 2020 19:12:05: 12000000 INFO @ Sun, 21 Jun 2020 19:12:07: 9000000 INFO @ Sun, 21 Jun 2020 19:12:09: 6000000 INFO @ Sun, 21 Jun 2020 19:12:15: 13000000 INFO @ Sun, 21 Jun 2020 19:12:15: 10000000 INFO @ Sun, 21 Jun 2020 19:12:18: 7000000 INFO @ Sun, 21 Jun 2020 19:12:24: 11000000 INFO @ Sun, 21 Jun 2020 19:12:25: 14000000 INFO @ Sun, 21 Jun 2020 19:12:26: 8000000 INFO @ Sun, 21 Jun 2020 19:12:32: 12000000 INFO @ Sun, 21 Jun 2020 19:12:34: 15000000 INFO @ Sun, 21 Jun 2020 19:12:34: 9000000 INFO @ Sun, 21 Jun 2020 19:12:41: 13000000 INFO @ Sun, 21 Jun 2020 19:12:43: 10000000 INFO @ Sun, 21 Jun 2020 19:12:44: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:12:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:12:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:12:49: #1 total tags in treatment: 16476171 INFO @ Sun, 21 Jun 2020 19:12:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:12:49: #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 19:12:49: #1 tags after filtering in treatment: 16476170 INFO @ Sun, 21 Jun 2020 19:12:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:12:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:12:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:12:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:12:51: 14000000 INFO @ Sun, 21 Jun 2020 19:12:51: #2 number of paired peaks: 466 WARNING @ Sun, 21 Jun 2020 19:12:51: Fewer paired peaks (466) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 466 pairs to build model! INFO @ Sun, 21 Jun 2020 19:12:51: start model_add_line... INFO @ Sun, 21 Jun 2020 19:12:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:12:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:12:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:12:51: #2 predicted fragment length is 139 bps INFO @ Sun, 21 Jun 2020 19:12:51: #2 alternative fragment length(s) may be 2,94,118,139 bps INFO @ Sun, 21 Jun 2020 19:12:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.05_model.r INFO @ Sun, 21 Jun 2020 19:12:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:12:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:12:51: 11000000 INFO @ Sun, 21 Jun 2020 19:12:59: 12000000 INFO @ Sun, 21 Jun 2020 19:12:59: 15000000 INFO @ Sun, 21 Jun 2020 19:13:07: 13000000 INFO @ Sun, 21 Jun 2020 19:13:08: 16000000 INFO @ Sun, 21 Jun 2020 19:13:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:12: #1 total tags in treatment: 16476171 INFO @ Sun, 21 Jun 2020 19:13:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:12: #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 19:13:13: #1 tags after filtering in treatment: 16476170 INFO @ Sun, 21 Jun 2020 19:13:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:13: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:14: #2 number of paired peaks: 466 WARNING @ Sun, 21 Jun 2020 19:13:14: Fewer paired peaks (466) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 466 pairs to build model! INFO @ Sun, 21 Jun 2020 19:13:14: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:14: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:14: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:14: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:14: #2 predicted fragment length is 139 bps INFO @ Sun, 21 Jun 2020 19:13:14: #2 alternative fragment length(s) may be 2,94,118,139 bps INFO @ Sun, 21 Jun 2020 19:13:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.10_model.r INFO @ Sun, 21 Jun 2020 19:13:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:13:16: 14000000 INFO @ Sun, 21 Jun 2020 19:13:23: 15000000 INFO @ Sun, 21 Jun 2020 19:13:26: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:13:32: 16000000 INFO @ Sun, 21 Jun 2020 19:13:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:36: #1 total tags in treatment: 16476171 INFO @ Sun, 21 Jun 2020 19:13:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:36: #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 19:13:37: #1 tags after filtering in treatment: 16476170 INFO @ Sun, 21 Jun 2020 19:13:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:38: #2 number of paired peaks: 466 WARNING @ Sun, 21 Jun 2020 19:13:38: Fewer paired peaks (466) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 466 pairs to build model! INFO @ Sun, 21 Jun 2020 19:13:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:38: #2 predicted fragment length is 139 bps INFO @ Sun, 21 Jun 2020 19:13:38: #2 alternative fragment length(s) may be 2,94,118,139 bps INFO @ Sun, 21 Jun 2020 19:13:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.20_model.r INFO @ Sun, 21 Jun 2020 19:13:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:13:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.05_summits.bed INFO @ Sun, 21 Jun 2020 19:13:46: Done! pass1 - making usageList (432 chroms): 2 millis pass2 - checking and writing primary data (2818 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:13:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.10_summits.bed INFO @ Sun, 21 Jun 2020 19:14:09: Done! pass1 - making usageList (363 chroms): 1 millis pass2 - checking and writing primary data (1257 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:14:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287768/SRX287768.20_summits.bed INFO @ Sun, 21 Jun 2020 19:14:32: Done! pass1 - making usageList (201 chroms): 1 millis pass2 - checking and writing primary data (397 records, 4 fields): 12 millis CompletedMACS2peakCalling