Job ID = 6456211 SRX = SRX331368 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:45:53 prefetch.2.10.7: 1) Downloading 'SRR947605'... 2020-06-21T10:45:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:49:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:49:01 prefetch.2.10.7: 'SRR947605' is valid 2020-06-21T10:49:01 prefetch.2.10.7: 1) 'SRR947605' was downloaded successfully Read 15553061 spots for SRR947605/SRR947605.sra Written 15553061 spots for SRR947605/SRR947605.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: 00:03:18 15553061 reads; of these: 15553061 (100.00%) were unpaired; of these: 782561 (5.03%) aligned 0 times 13336886 (85.75%) aligned exactly 1 time 1433614 (9.22%) aligned >1 times 94.97% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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] 1323180 / 14770500 = 0.0896 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 19:58:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.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 19:58:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:58:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:58:28: 1000000 INFO @ Sun, 21 Jun 2020 19:58:33: 2000000 INFO @ Sun, 21 Jun 2020 19:58:38: 3000000 INFO @ Sun, 21 Jun 2020 19:58:44: 4000000 INFO @ Sun, 21 Jun 2020 19:58:49: 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 19:58:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.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 19:58:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:58:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:58:55: 6000000 INFO @ Sun, 21 Jun 2020 19:58:58: 1000000 INFO @ Sun, 21 Jun 2020 19:59:01: 7000000 INFO @ Sun, 21 Jun 2020 19:59:04: 2000000 INFO @ Sun, 21 Jun 2020 19:59:07: 8000000 INFO @ Sun, 21 Jun 2020 19:59:10: 3000000 INFO @ Sun, 21 Jun 2020 19:59:13: 9000000 INFO @ Sun, 21 Jun 2020 19:59:16: 4000000 INFO @ Sun, 21 Jun 2020 19:59:19: 10000000 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 19:59:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.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 19:59:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:59:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:59:22: 5000000 INFO @ Sun, 21 Jun 2020 19:59:25: 11000000 INFO @ Sun, 21 Jun 2020 19:59:28: 1000000 INFO @ Sun, 21 Jun 2020 19:59:28: 6000000 INFO @ Sun, 21 Jun 2020 19:59:32: 12000000 INFO @ Sun, 21 Jun 2020 19:59:34: 2000000 INFO @ Sun, 21 Jun 2020 19:59:34: 7000000 INFO @ Sun, 21 Jun 2020 19:59:38: 13000000 INFO @ Sun, 21 Jun 2020 19:59:40: 3000000 INFO @ Sun, 21 Jun 2020 19:59:40: 8000000 INFO @ Sun, 21 Jun 2020 19:59:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:59:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:59:41: #1 total tags in treatment: 13447320 INFO @ Sun, 21 Jun 2020 19:59:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:59:41: #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 19:59:42: #1 tags after filtering in treatment: 13447285 INFO @ Sun, 21 Jun 2020 19:59:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:59:42: #1 finished! INFO @ Sun, 21 Jun 2020 19:59:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:59:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:59:43: #2 number of paired peaks: 901 WARNING @ Sun, 21 Jun 2020 19:59:43: Fewer paired peaks (901) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 901 pairs to build model! INFO @ Sun, 21 Jun 2020 19:59:43: start model_add_line... INFO @ Sun, 21 Jun 2020 19:59:43: start X-correlation... INFO @ Sun, 21 Jun 2020 19:59:43: end of X-cor INFO @ Sun, 21 Jun 2020 19:59:43: #2 finished! INFO @ Sun, 21 Jun 2020 19:59:43: #2 predicted fragment length is 247 bps INFO @ Sun, 21 Jun 2020 19:59:43: #2 alternative fragment length(s) may be 2,193,216,247 bps INFO @ Sun, 21 Jun 2020 19:59:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.05_model.r INFO @ Sun, 21 Jun 2020 19:59:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:59:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:59:46: 4000000 INFO @ Sun, 21 Jun 2020 19:59:46: 9000000 INFO @ Sun, 21 Jun 2020 19:59:52: 5000000 INFO @ Sun, 21 Jun 2020 19:59:52: 10000000 INFO @ Sun, 21 Jun 2020 19:59:57: 11000000 INFO @ Sun, 21 Jun 2020 19:59:57: 6000000 INFO @ Sun, 21 Jun 2020 20:00:03: 7000000 INFO @ Sun, 21 Jun 2020 20:00:04: 12000000 INFO @ Sun, 21 Jun 2020 20:00:09: 8000000 INFO @ Sun, 21 Jun 2020 20:00:09: 13000000 INFO @ Sun, 21 Jun 2020 20:00:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:00:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:00:12: #1 total tags in treatment: 13447320 INFO @ Sun, 21 Jun 2020 20:00:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:00:12: #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 20:00:13: #1 tags after filtering in treatment: 13447285 INFO @ Sun, 21 Jun 2020 20:00:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:00:13: #1 finished! INFO @ Sun, 21 Jun 2020 20:00:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:00:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:00:14: #2 number of paired peaks: 901 WARNING @ Sun, 21 Jun 2020 20:00:14: Fewer paired peaks (901) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 901 pairs to build model! INFO @ Sun, 21 Jun 2020 20:00:14: start model_add_line... INFO @ Sun, 21 Jun 2020 20:00:14: start X-correlation... INFO @ Sun, 21 Jun 2020 20:00:14: end of X-cor INFO @ Sun, 21 Jun 2020 20:00:14: #2 finished! INFO @ Sun, 21 Jun 2020 20:00:14: #2 predicted fragment length is 247 bps INFO @ Sun, 21 Jun 2020 20:00:14: #2 alternative fragment length(s) may be 2,193,216,247 bps INFO @ Sun, 21 Jun 2020 20:00:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.10_model.r INFO @ Sun, 21 Jun 2020 20:00:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:00:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:00:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:00:15: 9000000 INFO @ Sun, 21 Jun 2020 20:00:21: 10000000 INFO @ Sun, 21 Jun 2020 20:00:27: 11000000 INFO @ Sun, 21 Jun 2020 20:00:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:00:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:00:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.05_summits.bed INFO @ Sun, 21 Jun 2020 20:00:30: Done! pass1 - making usageList (120 chroms): 1 millis pass2 - checking and writing primary data (3713 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:00:34: 12000000 INFO @ Sun, 21 Jun 2020 20:00:40: 13000000 INFO @ Sun, 21 Jun 2020 20:00:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:00:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:00:43: #1 total tags in treatment: 13447320 INFO @ Sun, 21 Jun 2020 20:00:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:00:43: #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 20:00:43: #1 tags after filtering in treatment: 13447285 INFO @ Sun, 21 Jun 2020 20:00:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:00:43: #1 finished! INFO @ Sun, 21 Jun 2020 20:00:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:00:44: #2 number of paired peaks: 901 WARNING @ Sun, 21 Jun 2020 20:00:44: Fewer paired peaks (901) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 901 pairs to build model! INFO @ Sun, 21 Jun 2020 20:00:44: start model_add_line... INFO @ Sun, 21 Jun 2020 20:00:45: start X-correlation... INFO @ Sun, 21 Jun 2020 20:00:45: end of X-cor INFO @ Sun, 21 Jun 2020 20:00:45: #2 finished! INFO @ Sun, 21 Jun 2020 20:00:45: #2 predicted fragment length is 247 bps INFO @ Sun, 21 Jun 2020 20:00:45: #2 alternative fragment length(s) may be 2,193,216,247 bps INFO @ Sun, 21 Jun 2020 20:00:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.20_model.r INFO @ Sun, 21 Jun 2020 20:00:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:00:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:00:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:01:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:01:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:01:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.10_summits.bed INFO @ Sun, 21 Jun 2020 20:01:01: Done! pass1 - making usageList (75 chroms): 1 millis pass2 - checking and writing primary data (1556 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:01:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:01:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:01:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:01:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331368/SRX331368.20_summits.bed INFO @ Sun, 21 Jun 2020 20:01:33: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (455 records, 4 fields): 4 millis CompletedMACS2peakCalling