Job ID = 6452951 SRX = SRX062282 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:53:17 prefetch.2.10.7: 1) Downloading 'SRR203278'... 2020-06-21T07:53:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:55:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:55:22 prefetch.2.10.7: 'SRR203278' is valid 2020-06-21T07:55:22 prefetch.2.10.7: 1) 'SRR203278' was downloaded successfully Read 29871038 spots for SRR203278/SRR203278.sra Written 29871038 spots for SRR203278/SRR203278.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: 00:06:05 29871038 reads; of these: 29871038 (100.00%) were unpaired; of these: 5167021 (17.30%) aligned 0 times 17753781 (59.43%) aligned exactly 1 time 6950236 (23.27%) aligned >1 times 82.70% overall alignment rate Time searching: 00:06:05 Overall time: 00:06:05 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] 9061544 / 24704017 = 0.3668 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 17:06:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.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 17:06:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:06:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:06:53: 1000000 INFO @ Sun, 21 Jun 2020 17:06:59: 2000000 INFO @ Sun, 21 Jun 2020 17:07:06: 3000000 INFO @ Sun, 21 Jun 2020 17:07:12: 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 17:07:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.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 17:07:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:07:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:07:18: 5000000 INFO @ Sun, 21 Jun 2020 17:07:24: 1000000 INFO @ Sun, 21 Jun 2020 17:07:25: 6000000 INFO @ Sun, 21 Jun 2020 17:07:31: 2000000 INFO @ Sun, 21 Jun 2020 17:07:33: 7000000 INFO @ Sun, 21 Jun 2020 17:07:38: 3000000 INFO @ Sun, 21 Jun 2020 17:07:40: 8000000 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 17:07:45: 4000000 INFO @ Sun, 21 Jun 2020 17:07:47: 9000000 INFO @ Sun, 21 Jun 2020 17:07:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.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 17:07:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:07:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:07:53: 5000000 INFO @ Sun, 21 Jun 2020 17:07:54: 1000000 INFO @ Sun, 21 Jun 2020 17:07:54: 10000000 INFO @ Sun, 21 Jun 2020 17:08:00: 6000000 INFO @ Sun, 21 Jun 2020 17:08:01: 2000000 INFO @ Sun, 21 Jun 2020 17:08:01: 11000000 INFO @ Sun, 21 Jun 2020 17:08:07: 3000000 INFO @ Sun, 21 Jun 2020 17:08:07: 7000000 INFO @ Sun, 21 Jun 2020 17:08:08: 12000000 INFO @ Sun, 21 Jun 2020 17:08:14: 4000000 INFO @ Sun, 21 Jun 2020 17:08:15: 8000000 INFO @ Sun, 21 Jun 2020 17:08:16: 13000000 INFO @ Sun, 21 Jun 2020 17:08:21: 5000000 INFO @ Sun, 21 Jun 2020 17:08:22: 9000000 INFO @ Sun, 21 Jun 2020 17:08:23: 14000000 INFO @ Sun, 21 Jun 2020 17:08:27: 6000000 INFO @ Sun, 21 Jun 2020 17:08:29: 10000000 INFO @ Sun, 21 Jun 2020 17:08:30: 15000000 INFO @ Sun, 21 Jun 2020 17:08:34: 7000000 INFO @ Sun, 21 Jun 2020 17:08:35: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:08:35: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:08:35: #1 total tags in treatment: 15642473 INFO @ Sun, 21 Jun 2020 17:08:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:08:35: #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 17:08:36: #1 tags after filtering in treatment: 15642472 INFO @ Sun, 21 Jun 2020 17:08:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:08:36: #1 finished! INFO @ Sun, 21 Jun 2020 17:08:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:08:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:08:36: 11000000 INFO @ Sun, 21 Jun 2020 17:08:37: #2 number of paired peaks: 982 WARNING @ Sun, 21 Jun 2020 17:08:37: Fewer paired peaks (982) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 982 pairs to build model! INFO @ Sun, 21 Jun 2020 17:08:37: start model_add_line... INFO @ Sun, 21 Jun 2020 17:08:37: start X-correlation... INFO @ Sun, 21 Jun 2020 17:08:37: end of X-cor INFO @ Sun, 21 Jun 2020 17:08:37: #2 finished! INFO @ Sun, 21 Jun 2020 17:08:37: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 17:08:37: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 17:08:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.05_model.r INFO @ Sun, 21 Jun 2020 17:08:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:08:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:08:40: 8000000 INFO @ Sun, 21 Jun 2020 17:08:43: 12000000 INFO @ Sun, 21 Jun 2020 17:08:47: 9000000 INFO @ Sun, 21 Jun 2020 17:08:50: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:08:53: 10000000 INFO @ Sun, 21 Jun 2020 17:08:58: 14000000 INFO @ Sun, 21 Jun 2020 17:09:00: 11000000 INFO @ Sun, 21 Jun 2020 17:09:05: 15000000 INFO @ Sun, 21 Jun 2020 17:09:06: 12000000 INFO @ Sun, 21 Jun 2020 17:09:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:09:10: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:09:10: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:09:10: #1 total tags in treatment: 15642473 INFO @ Sun, 21 Jun 2020 17:09:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:09:10: #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 17:09:10: #1 tags after filtering in treatment: 15642472 INFO @ Sun, 21 Jun 2020 17:09:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:09:10: #1 finished! INFO @ Sun, 21 Jun 2020 17:09:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:09:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:09:11: #2 number of paired peaks: 982 WARNING @ Sun, 21 Jun 2020 17:09:11: Fewer paired peaks (982) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 982 pairs to build model! INFO @ Sun, 21 Jun 2020 17:09:11: start model_add_line... INFO @ Sun, 21 Jun 2020 17:09:11: start X-correlation... INFO @ Sun, 21 Jun 2020 17:09:11: end of X-cor INFO @ Sun, 21 Jun 2020 17:09:11: #2 finished! INFO @ Sun, 21 Jun 2020 17:09:11: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 17:09:11: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 17:09:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.10_model.r INFO @ Sun, 21 Jun 2020 17:09:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:09:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:09:13: 13000000 INFO @ Sun, 21 Jun 2020 17:09:18: 14000000 INFO @ Sun, 21 Jun 2020 17:09:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:09:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:09:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.05_summits.bed INFO @ Sun, 21 Jun 2020 17:09:22: Done! pass1 - making usageList (663 chroms): 2 millis pass2 - checking and writing primary data (6539 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:09:24: 15000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:09:28: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:09:28: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:09:28: #1 total tags in treatment: 15642473 INFO @ Sun, 21 Jun 2020 17:09:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:09:28: #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 17:09:28: #1 tags after filtering in treatment: 15642472 INFO @ Sun, 21 Jun 2020 17:09:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:09:28: #1 finished! INFO @ Sun, 21 Jun 2020 17:09:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:09:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:09:29: #2 number of paired peaks: 982 WARNING @ Sun, 21 Jun 2020 17:09:29: Fewer paired peaks (982) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 982 pairs to build model! INFO @ Sun, 21 Jun 2020 17:09:29: start model_add_line... INFO @ Sun, 21 Jun 2020 17:09:29: start X-correlation... INFO @ Sun, 21 Jun 2020 17:09:29: end of X-cor INFO @ Sun, 21 Jun 2020 17:09:29: #2 finished! INFO @ Sun, 21 Jun 2020 17:09:29: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 17:09:29: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 17:09:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.20_model.r INFO @ Sun, 21 Jun 2020 17:09:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:09:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:09:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:09:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:09:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:09:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.10_summits.bed INFO @ Sun, 21 Jun 2020 17:09:57: Done! pass1 - making usageList (564 chroms): 2 millis pass2 - checking and writing primary data (4166 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:10:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:10:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:10:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:10:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX062282/SRX062282.20_summits.bed INFO @ Sun, 21 Jun 2020 17:10:15: Done! pass1 - making usageList (448 chroms): 1 millis pass2 - checking and writing primary data (2777 records, 4 fields): 15 millis CompletedMACS2peakCalling