Job ID = 6453742 SRX = SRX1433379 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:39:02 prefetch.2.10.7: 1) Downloading 'SRR2919844'... 2020-06-21T08:39:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:43:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:43:39 prefetch.2.10.7: 1) 'SRR2919844' was downloaded successfully Read 35885621 spots for SRR2919844/SRR2919844.sra Written 35885621 spots for SRR2919844/SRR2919844.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: 00:06:10 35885621 reads; of these: 35885621 (100.00%) were unpaired; of these: 19742972 (55.02%) aligned 0 times 12951305 (36.09%) aligned exactly 1 time 3191344 (8.89%) aligned >1 times 44.98% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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] 5078350 / 16142649 = 0.3146 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 17:55:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.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 17:55:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:55:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:55:11: 1000000 INFO @ Sun, 21 Jun 2020 17:55:16: 2000000 INFO @ Sun, 21 Jun 2020 17:55:22: 3000000 INFO @ Sun, 21 Jun 2020 17:55:28: 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 17:55:33: 5000000 INFO @ Sun, 21 Jun 2020 17:55:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.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 17:55:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:55:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:55:39: 6000000 INFO @ Sun, 21 Jun 2020 17:55:42: 1000000 INFO @ Sun, 21 Jun 2020 17:55:46: 7000000 INFO @ Sun, 21 Jun 2020 17:55:48: 2000000 INFO @ Sun, 21 Jun 2020 17:55:52: 8000000 INFO @ Sun, 21 Jun 2020 17:55:55: 3000000 INFO @ Sun, 21 Jun 2020 17:55:59: 9000000 INFO @ Sun, 21 Jun 2020 17:56:01: 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 17:56:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.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 17:56:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:56:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:56:06: 10000000 INFO @ Sun, 21 Jun 2020 17:56:08: 5000000 INFO @ Sun, 21 Jun 2020 17:56:13: 11000000 INFO @ Sun, 21 Jun 2020 17:56:13: 1000000 INFO @ Sun, 21 Jun 2020 17:56:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:56:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:56:13: #1 total tags in treatment: 11064299 INFO @ Sun, 21 Jun 2020 17:56:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:13: #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 17:56:14: #1 tags after filtering in treatment: 11064173 INFO @ Sun, 21 Jun 2020 17:56:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:14: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:15: #2 number of paired peaks: 810 WARNING @ Sun, 21 Jun 2020 17:56:15: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Sun, 21 Jun 2020 17:56:15: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:15: 6000000 INFO @ Sun, 21 Jun 2020 17:56:15: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:15: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:15: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:15: #2 predicted fragment length is 156 bps INFO @ Sun, 21 Jun 2020 17:56:15: #2 alternative fragment length(s) may be 4,156 bps INFO @ Sun, 21 Jun 2020 17:56:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.05_model.r INFO @ Sun, 21 Jun 2020 17:56:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:56:21: 2000000 INFO @ Sun, 21 Jun 2020 17:56:22: 7000000 INFO @ Sun, 21 Jun 2020 17:56:29: 8000000 INFO @ Sun, 21 Jun 2020 17:56:29: 3000000 INFO @ Sun, 21 Jun 2020 17:56:36: 9000000 INFO @ Sun, 21 Jun 2020 17:56:37: 4000000 INFO @ Sun, 21 Jun 2020 17:56:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:56:43: 10000000 INFO @ Sun, 21 Jun 2020 17:56:45: 5000000 INFO @ Sun, 21 Jun 2020 17:56:50: 11000000 INFO @ Sun, 21 Jun 2020 17:56:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:56:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:56:51: #1 total tags in treatment: 11064299 INFO @ Sun, 21 Jun 2020 17:56:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:51: #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 17:56:51: #1 tags after filtering in treatment: 11064173 INFO @ Sun, 21 Jun 2020 17:56:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:51: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:52: #2 number of paired peaks: 810 WARNING @ Sun, 21 Jun 2020 17:56:52: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Sun, 21 Jun 2020 17:56:52: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:52: 6000000 INFO @ Sun, 21 Jun 2020 17:56:52: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:52: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:52: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:52: #2 predicted fragment length is 156 bps INFO @ Sun, 21 Jun 2020 17:56:52: #2 alternative fragment length(s) may be 4,156 bps INFO @ Sun, 21 Jun 2020 17:56:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.10_model.r INFO @ Sun, 21 Jun 2020 17:56:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:56:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:56:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:56:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.05_summits.bed INFO @ Sun, 21 Jun 2020 17:56:52: Done! pass1 - making usageList (386 chroms): 1 millis pass2 - checking and writing primary data (2415 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:56:59: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:57:06: 8000000 INFO @ Sun, 21 Jun 2020 17:57:14: 9000000 INFO @ Sun, 21 Jun 2020 17:57:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:57:20: 10000000 INFO @ Sun, 21 Jun 2020 17:57:28: 11000000 INFO @ Sun, 21 Jun 2020 17:57:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:57:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:57:28: #1 total tags in treatment: 11064299 INFO @ Sun, 21 Jun 2020 17:57:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:57:28: #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 17:57:28: #1 tags after filtering in treatment: 11064173 INFO @ Sun, 21 Jun 2020 17:57:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:57:28: #1 finished! INFO @ Sun, 21 Jun 2020 17:57:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:57:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:57:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:57:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:57:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.10_summits.bed INFO @ Sun, 21 Jun 2020 17:57:29: Done! pass1 - making usageList (200 chroms): 1 millis pass2 - checking and writing primary data (1007 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:57:29: #2 number of paired peaks: 810 WARNING @ Sun, 21 Jun 2020 17:57:29: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Sun, 21 Jun 2020 17:57:29: start model_add_line... INFO @ Sun, 21 Jun 2020 17:57:29: start X-correlation... INFO @ Sun, 21 Jun 2020 17:57:29: end of X-cor INFO @ Sun, 21 Jun 2020 17:57:29: #2 finished! INFO @ Sun, 21 Jun 2020 17:57:29: #2 predicted fragment length is 156 bps INFO @ Sun, 21 Jun 2020 17:57:29: #2 alternative fragment length(s) may be 4,156 bps INFO @ Sun, 21 Jun 2020 17:57:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.20_model.r INFO @ Sun, 21 Jun 2020 17:57:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:57:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:57:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:58:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:58:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:58:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433379/SRX1433379.20_summits.bed INFO @ Sun, 21 Jun 2020 17:58:07: Done! pass1 - making usageList (105 chroms): 1 millis pass2 - checking and writing primary data (378 records, 4 fields): 5 millis CompletedMACS2peakCalling