Job ID = 6459879 SRX = SRX969912 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:57:49 prefetch.2.10.7: 1) Downloading 'SRR1931628'... 2020-06-21T13:57:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T14:00:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T14:00:23 prefetch.2.10.7: 'SRR1931628' is valid 2020-06-21T14:00:23 prefetch.2.10.7: 1) 'SRR1931628' was downloaded successfully Read 14966969 spots for SRR1931628/SRR1931628.sra Written 14966969 spots for SRR1931628/SRR1931628.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:48 14966969 reads; of these: 14966969 (100.00%) were unpaired; of these: 466099 (3.11%) aligned 0 times 11635692 (77.74%) aligned exactly 1 time 2865178 (19.14%) aligned >1 times 96.89% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 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] 1671205 / 14500870 = 0.1152 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 23:08:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.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 23:08:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:08:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:09:04: 1000000 INFO @ Sun, 21 Jun 2020 23:09:10: 2000000 INFO @ Sun, 21 Jun 2020 23:09:15: 3000000 INFO @ Sun, 21 Jun 2020 23:09:20: 4000000 INFO @ Sun, 21 Jun 2020 23:09:26: 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 23:09:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.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 23:09:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:09:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:09:31: 6000000 INFO @ Sun, 21 Jun 2020 23:09:34: 1000000 INFO @ Sun, 21 Jun 2020 23:09:37: 7000000 INFO @ Sun, 21 Jun 2020 23:09:40: 2000000 INFO @ Sun, 21 Jun 2020 23:09:43: 8000000 INFO @ Sun, 21 Jun 2020 23:09:46: 3000000 INFO @ Sun, 21 Jun 2020 23:09:48: 9000000 INFO @ Sun, 21 Jun 2020 23:09:52: 4000000 INFO @ Sun, 21 Jun 2020 23:09:54: 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 23:09:57: 5000000 INFO @ Sun, 21 Jun 2020 23:09:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.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 23:09:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:09:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:10:00: 11000000 INFO @ Sun, 21 Jun 2020 23:10:03: 6000000 INFO @ Sun, 21 Jun 2020 23:10:05: 1000000 INFO @ Sun, 21 Jun 2020 23:10:06: 12000000 INFO @ Sun, 21 Jun 2020 23:10:09: 7000000 INFO @ Sun, 21 Jun 2020 23:10:10: 2000000 INFO @ Sun, 21 Jun 2020 23:10:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:10:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:10:11: #1 total tags in treatment: 12829665 INFO @ Sun, 21 Jun 2020 23:10:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:10:11: #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 23:10:12: #1 tags after filtering in treatment: 12829629 INFO @ Sun, 21 Jun 2020 23:10:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:10:12: #1 finished! INFO @ Sun, 21 Jun 2020 23:10:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:10:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:10:13: #2 number of paired peaks: 313 WARNING @ Sun, 21 Jun 2020 23:10:13: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Sun, 21 Jun 2020 23:10:13: start model_add_line... INFO @ Sun, 21 Jun 2020 23:10:13: start X-correlation... INFO @ Sun, 21 Jun 2020 23:10:13: end of X-cor INFO @ Sun, 21 Jun 2020 23:10:13: #2 finished! INFO @ Sun, 21 Jun 2020 23:10:13: #2 predicted fragment length is 176 bps INFO @ Sun, 21 Jun 2020 23:10:13: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 21 Jun 2020 23:10:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.05_model.r INFO @ Sun, 21 Jun 2020 23:10:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:10:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:10:15: 8000000 INFO @ Sun, 21 Jun 2020 23:10:16: 3000000 INFO @ Sun, 21 Jun 2020 23:10:20: 9000000 INFO @ Sun, 21 Jun 2020 23:10:22: 4000000 INFO @ Sun, 21 Jun 2020 23:10:26: 10000000 INFO @ Sun, 21 Jun 2020 23:10:28: 5000000 INFO @ Sun, 21 Jun 2020 23:10:32: 11000000 INFO @ Sun, 21 Jun 2020 23:10:34: 6000000 INFO @ Sun, 21 Jun 2020 23:10:38: 12000000 INFO @ Sun, 21 Jun 2020 23:10:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:10:40: 7000000 INFO @ Sun, 21 Jun 2020 23:10:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:10:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:10:43: #1 total tags in treatment: 12829665 INFO @ Sun, 21 Jun 2020 23:10:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:10:43: #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 23:10:44: #1 tags after filtering in treatment: 12829629 INFO @ Sun, 21 Jun 2020 23:10:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:10:44: #1 finished! INFO @ Sun, 21 Jun 2020 23:10:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:10:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:10:44: #2 number of paired peaks: 313 WARNING @ Sun, 21 Jun 2020 23:10:44: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Sun, 21 Jun 2020 23:10:44: start model_add_line... INFO @ Sun, 21 Jun 2020 23:10:45: start X-correlation... INFO @ Sun, 21 Jun 2020 23:10:45: end of X-cor INFO @ Sun, 21 Jun 2020 23:10:45: #2 finished! INFO @ Sun, 21 Jun 2020 23:10:45: #2 predicted fragment length is 176 bps INFO @ Sun, 21 Jun 2020 23:10:45: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 21 Jun 2020 23:10:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.10_model.r INFO @ Sun, 21 Jun 2020 23:10:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:10:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:10:45: 8000000 INFO @ Sun, 21 Jun 2020 23:10:51: 9000000 INFO @ Sun, 21 Jun 2020 23:10:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.05_peaks.xls INFO @ Sun, 21 Jun 2020 23:10:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:10:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.05_summits.bed INFO @ Sun, 21 Jun 2020 23:10:52: Done! pass1 - making usageList (354 chroms): 1 millis pass2 - checking and writing primary data (2650 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 23:10:56: 10000000 INFO @ Sun, 21 Jun 2020 23:11:02: 11000000 INFO @ Sun, 21 Jun 2020 23:11:07: 12000000 INFO @ Sun, 21 Jun 2020 23:11:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:11:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:11:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:11:12: #1 total tags in treatment: 12829665 INFO @ Sun, 21 Jun 2020 23:11:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:11:12: #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 23:11:12: #1 tags after filtering in treatment: 12829629 INFO @ Sun, 21 Jun 2020 23:11:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:11:12: #1 finished! INFO @ Sun, 21 Jun 2020 23:11:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:11:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:11:13: #2 number of paired peaks: 313 WARNING @ Sun, 21 Jun 2020 23:11:13: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Sun, 21 Jun 2020 23:11:13: start model_add_line... INFO @ Sun, 21 Jun 2020 23:11:13: start X-correlation... INFO @ Sun, 21 Jun 2020 23:11:13: end of X-cor INFO @ Sun, 21 Jun 2020 23:11:13: #2 finished! INFO @ Sun, 21 Jun 2020 23:11:13: #2 predicted fragment length is 176 bps INFO @ Sun, 21 Jun 2020 23:11:13: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 21 Jun 2020 23:11:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.20_model.r INFO @ Sun, 21 Jun 2020 23:11:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:11:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:11:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.10_peaks.xls INFO @ Sun, 21 Jun 2020 23:11:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:11:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.10_summits.bed INFO @ Sun, 21 Jun 2020 23:11:24: Done! BigWig に変換しました。 pass1 - making usageList (276 chroms): 1 millis pass2 - checking and writing primary data (1548 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:11:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:11:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.20_peaks.xls INFO @ Sun, 21 Jun 2020 23:11:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:11:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969912/SRX969912.20_summits.bed INFO @ Sun, 21 Jun 2020 23:11:52: Done! pass1 - making usageList (195 chroms): 1 millis pass2 - checking and writing primary data (745 records, 4 fields): 8 millis CompletedMACS2peakCalling