Job ID = 6455743 SRX = SRX288037 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:26:51 prefetch.2.10.7: 1) Downloading 'SRR870226'... 2020-06-21T10:26:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:31:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:31:04 prefetch.2.10.7: 1) 'SRR870226' was downloaded successfully Read 24477501 spots for SRR870226/SRR870226.sra Written 24477501 spots for SRR870226/SRR870226.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: 00:00:01 Multiseed full-index search: 00:06:24 24477501 reads; of these: 24477501 (100.00%) were unpaired; of these: 1910354 (7.80%) aligned 0 times 16743319 (68.40%) aligned exactly 1 time 5823828 (23.79%) aligned >1 times 92.20% overall alignment rate Time searching: 00:06:25 Overall time: 00:06:25 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] 4378145 / 22567147 = 0.1940 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 19:44:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.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 19:44:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:44:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:44:44: 1000000 INFO @ Sun, 21 Jun 2020 19:44:49: 2000000 INFO @ Sun, 21 Jun 2020 19:44:55: 3000000 INFO @ Sun, 21 Jun 2020 19:45:00: 4000000 INFO @ Sun, 21 Jun 2020 19:45:06: 5000000 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 19:45:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.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 19:45:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:45:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:45:12: 6000000 INFO @ Sun, 21 Jun 2020 19:45:15: 1000000 INFO @ Sun, 21 Jun 2020 19:45:18: 7000000 INFO @ Sun, 21 Jun 2020 19:45:22: 2000000 INFO @ Sun, 21 Jun 2020 19:45:24: 8000000 INFO @ Sun, 21 Jun 2020 19:45:29: 3000000 INFO @ Sun, 21 Jun 2020 19:45:31: 9000000 INFO @ Sun, 21 Jun 2020 19:45:36: 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 19:45:37: 10000000 INFO @ Sun, 21 Jun 2020 19:45:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.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 19:45:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:45:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:45:43: 5000000 INFO @ Sun, 21 Jun 2020 19:45:44: 11000000 INFO @ Sun, 21 Jun 2020 19:45:45: 1000000 INFO @ Sun, 21 Jun 2020 19:45:50: 6000000 INFO @ Sun, 21 Jun 2020 19:45:50: 12000000 INFO @ Sun, 21 Jun 2020 19:45:51: 2000000 INFO @ Sun, 21 Jun 2020 19:45:57: 13000000 INFO @ Sun, 21 Jun 2020 19:45:57: 7000000 INFO @ Sun, 21 Jun 2020 19:45:58: 3000000 INFO @ Sun, 21 Jun 2020 19:46:03: 14000000 INFO @ Sun, 21 Jun 2020 19:46:04: 8000000 INFO @ Sun, 21 Jun 2020 19:46:05: 4000000 INFO @ Sun, 21 Jun 2020 19:46:10: 15000000 INFO @ Sun, 21 Jun 2020 19:46:11: 9000000 INFO @ Sun, 21 Jun 2020 19:46:12: 5000000 INFO @ Sun, 21 Jun 2020 19:46:17: 16000000 INFO @ Sun, 21 Jun 2020 19:46:18: 6000000 INFO @ Sun, 21 Jun 2020 19:46:19: 10000000 INFO @ Sun, 21 Jun 2020 19:46:24: 17000000 INFO @ Sun, 21 Jun 2020 19:46:25: 7000000 INFO @ Sun, 21 Jun 2020 19:46:26: 11000000 INFO @ Sun, 21 Jun 2020 19:46:30: 18000000 INFO @ Sun, 21 Jun 2020 19:46:31: 8000000 INFO @ Sun, 21 Jun 2020 19:46:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:46:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:46:32: #1 total tags in treatment: 18189002 INFO @ Sun, 21 Jun 2020 19:46:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:46:32: #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 19:46:33: #1 tags after filtering in treatment: 18189002 INFO @ Sun, 21 Jun 2020 19:46:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:46:33: #1 finished! INFO @ Sun, 21 Jun 2020 19:46:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:46:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:46:33: 12000000 INFO @ Sun, 21 Jun 2020 19:46:34: #2 number of paired peaks: 643 WARNING @ Sun, 21 Jun 2020 19:46:34: Fewer paired peaks (643) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 643 pairs to build model! INFO @ Sun, 21 Jun 2020 19:46:34: start model_add_line... INFO @ Sun, 21 Jun 2020 19:46:34: start X-correlation... INFO @ Sun, 21 Jun 2020 19:46:34: end of X-cor INFO @ Sun, 21 Jun 2020 19:46:34: #2 finished! INFO @ Sun, 21 Jun 2020 19:46:34: #2 predicted fragment length is 212 bps INFO @ Sun, 21 Jun 2020 19:46:34: #2 alternative fragment length(s) may be 212 bps INFO @ Sun, 21 Jun 2020 19:46:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.05_model.r INFO @ Sun, 21 Jun 2020 19:46:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:46:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:46:38: 9000000 INFO @ Sun, 21 Jun 2020 19:46:40: 13000000 INFO @ Sun, 21 Jun 2020 19:46:45: 10000000 INFO @ Sun, 21 Jun 2020 19:46:47: 14000000 INFO @ Sun, 21 Jun 2020 19:46:51: 11000000 INFO @ Sun, 21 Jun 2020 19:46:55: 15000000 INFO @ Sun, 21 Jun 2020 19:46:58: 12000000 INFO @ Sun, 21 Jun 2020 19:47:03: 16000000 INFO @ Sun, 21 Jun 2020 19:47:04: 13000000 INFO @ Sun, 21 Jun 2020 19:47:10: 17000000 INFO @ Sun, 21 Jun 2020 19:47:11: 14000000 INFO @ Sun, 21 Jun 2020 19:47:17: 15000000 INFO @ Sun, 21 Jun 2020 19:47:18: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:47:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:47:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:47:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:47:19: #1 total tags in treatment: 18189002 INFO @ Sun, 21 Jun 2020 19:47:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:47:19: #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 19:47:20: #1 tags after filtering in treatment: 18189002 INFO @ Sun, 21 Jun 2020 19:47:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:47:20: #1 finished! INFO @ Sun, 21 Jun 2020 19:47:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:47:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:47:21: #2 number of paired peaks: 643 WARNING @ Sun, 21 Jun 2020 19:47:21: Fewer paired peaks (643) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 643 pairs to build model! INFO @ Sun, 21 Jun 2020 19:47:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:47:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:47:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:47:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:47:22: #2 predicted fragment length is 212 bps INFO @ Sun, 21 Jun 2020 19:47:22: #2 alternative fragment length(s) may be 212 bps INFO @ Sun, 21 Jun 2020 19:47:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.10_model.r INFO @ Sun, 21 Jun 2020 19:47:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:47:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:47:24: 16000000 INFO @ Sun, 21 Jun 2020 19:47:30: 17000000 INFO @ Sun, 21 Jun 2020 19:47:36: 18000000 INFO @ Sun, 21 Jun 2020 19:47:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:47:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:47:37: #1 total tags in treatment: 18189002 INFO @ Sun, 21 Jun 2020 19:47:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:47:37: #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 19:47:38: #1 tags after filtering in treatment: 18189002 INFO @ Sun, 21 Jun 2020 19:47:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:47:38: #1 finished! INFO @ Sun, 21 Jun 2020 19:47:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:47:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:47:39: #2 number of paired peaks: 643 WARNING @ Sun, 21 Jun 2020 19:47:39: Fewer paired peaks (643) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 643 pairs to build model! INFO @ Sun, 21 Jun 2020 19:47:39: start model_add_line... INFO @ Sun, 21 Jun 2020 19:47:40: start X-correlation... INFO @ Sun, 21 Jun 2020 19:47:40: end of X-cor INFO @ Sun, 21 Jun 2020 19:47:40: #2 finished! INFO @ Sun, 21 Jun 2020 19:47:40: #2 predicted fragment length is 212 bps INFO @ Sun, 21 Jun 2020 19:47:40: #2 alternative fragment length(s) may be 212 bps INFO @ Sun, 21 Jun 2020 19:47:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.20_model.r INFO @ Sun, 21 Jun 2020 19:47:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:47:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:47:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:47:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:47:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.05_summits.bed INFO @ Sun, 21 Jun 2020 19:47:42: Done! pass1 - making usageList (678 chroms): 2 millis pass2 - checking and writing primary data (7476 records, 4 fields): 26 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:48:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:48:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:48:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:48:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:48:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.10_summits.bed INFO @ Sun, 21 Jun 2020 19:48:29: Done! pass1 - making usageList (562 chroms): 2 millis pass2 - checking and writing primary data (5060 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:48:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:48:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:48:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288037/SRX288037.20_summits.bed INFO @ Sun, 21 Jun 2020 19:48:45: Done! pass1 - making usageList (454 chroms): 1 millis pass2 - checking and writing primary data (3054 records, 4 fields): 16 millis CompletedMACS2peakCalling