Job ID = 6459884 SRX = SRX969916 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:47:20 prefetch.2.10.7: 1) Downloading 'SRR1931632'... 2020-06-21T13:47:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:49:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:49:50 prefetch.2.10.7: 1) 'SRR1931632' was downloaded successfully Read 26059381 spots for SRR1931632/SRR1931632.sra Written 26059381 spots for SRR1931632/SRR1931632.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: 00:07:34 26059381 reads; of these: 26059381 (100.00%) were unpaired; of these: 1280580 (4.91%) aligned 0 times 19152145 (73.49%) aligned exactly 1 time 5626656 (21.59%) aligned >1 times 95.09% overall alignment rate Time searching: 00:07:34 Overall time: 00:07:34 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] 5148785 / 24778801 = 0.2078 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 23:03:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.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 23:03:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:03:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:03:32: 1000000 INFO @ Sun, 21 Jun 2020 23:03:37: 2000000 INFO @ Sun, 21 Jun 2020 23:03:42: 3000000 INFO @ Sun, 21 Jun 2020 23:03:47: 4000000 INFO @ Sun, 21 Jun 2020 23:03:51: 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 23:03:56: 6000000 INFO @ Sun, 21 Jun 2020 23:03:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.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 23:03:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:03:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:04:01: 7000000 INFO @ Sun, 21 Jun 2020 23:04:03: 1000000 INFO @ Sun, 21 Jun 2020 23:04:06: 8000000 INFO @ Sun, 21 Jun 2020 23:04:09: 2000000 INFO @ Sun, 21 Jun 2020 23:04:12: 9000000 INFO @ Sun, 21 Jun 2020 23:04:15: 3000000 INFO @ Sun, 21 Jun 2020 23:04:17: 10000000 INFO @ Sun, 21 Jun 2020 23:04:21: 4000000 INFO @ Sun, 21 Jun 2020 23:04:22: 11000000 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 23:04:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.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 23:04:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:04:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:04:27: 5000000 INFO @ Sun, 21 Jun 2020 23:04:28: 12000000 INFO @ Sun, 21 Jun 2020 23:04:33: 1000000 INFO @ Sun, 21 Jun 2020 23:04:33: 6000000 INFO @ Sun, 21 Jun 2020 23:04:33: 13000000 INFO @ Sun, 21 Jun 2020 23:04:39: 2000000 INFO @ Sun, 21 Jun 2020 23:04:39: 14000000 INFO @ Sun, 21 Jun 2020 23:04:39: 7000000 INFO @ Sun, 21 Jun 2020 23:04:45: 15000000 INFO @ Sun, 21 Jun 2020 23:04:45: 8000000 INFO @ Sun, 21 Jun 2020 23:04:45: 3000000 INFO @ Sun, 21 Jun 2020 23:04:51: 9000000 INFO @ Sun, 21 Jun 2020 23:04:51: 16000000 INFO @ Sun, 21 Jun 2020 23:04:52: 4000000 INFO @ Sun, 21 Jun 2020 23:04:57: 10000000 INFO @ Sun, 21 Jun 2020 23:04:57: 17000000 INFO @ Sun, 21 Jun 2020 23:04:58: 5000000 INFO @ Sun, 21 Jun 2020 23:05:02: 18000000 INFO @ Sun, 21 Jun 2020 23:05:03: 11000000 INFO @ Sun, 21 Jun 2020 23:05:04: 6000000 INFO @ Sun, 21 Jun 2020 23:05:08: 19000000 INFO @ Sun, 21 Jun 2020 23:05:09: 12000000 INFO @ Sun, 21 Jun 2020 23:05:10: 7000000 INFO @ Sun, 21 Jun 2020 23:05:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:05:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:05:11: #1 total tags in treatment: 19630016 INFO @ Sun, 21 Jun 2020 23:05:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:05:11: #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 23:05:12: #1 tags after filtering in treatment: 19630011 INFO @ Sun, 21 Jun 2020 23:05:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:05:12: #1 finished! INFO @ Sun, 21 Jun 2020 23:05:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:05:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:05:13: #2 number of paired peaks: 430 WARNING @ Sun, 21 Jun 2020 23:05:13: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Sun, 21 Jun 2020 23:05:13: start model_add_line... INFO @ Sun, 21 Jun 2020 23:05:13: start X-correlation... INFO @ Sun, 21 Jun 2020 23:05:13: end of X-cor INFO @ Sun, 21 Jun 2020 23:05:13: #2 finished! INFO @ Sun, 21 Jun 2020 23:05:13: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 23:05:13: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 23:05:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.05_model.r INFO @ Sun, 21 Jun 2020 23:05:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:05:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:05:14: 13000000 INFO @ Sun, 21 Jun 2020 23:05:16: 8000000 INFO @ Sun, 21 Jun 2020 23:05:20: 14000000 INFO @ Sun, 21 Jun 2020 23:05:22: 9000000 INFO @ Sun, 21 Jun 2020 23:05:26: 15000000 INFO @ Sun, 21 Jun 2020 23:05:28: 10000000 INFO @ Sun, 21 Jun 2020 23:05:32: 16000000 INFO @ Sun, 21 Jun 2020 23:05:34: 11000000 INFO @ Sun, 21 Jun 2020 23:05:38: 17000000 INFO @ Sun, 21 Jun 2020 23:05:40: 12000000 INFO @ Sun, 21 Jun 2020 23:05:44: 18000000 INFO @ Sun, 21 Jun 2020 23:05:45: 13000000 INFO @ Sun, 21 Jun 2020 23:05:50: 19000000 INFO @ Sun, 21 Jun 2020 23:05:51: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 23:05:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:05:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:05:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:05:54: #1 total tags in treatment: 19630016 INFO @ Sun, 21 Jun 2020 23:05:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:05:54: #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 23:05:54: #1 tags after filtering in treatment: 19630011 INFO @ Sun, 21 Jun 2020 23:05:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:05:54: #1 finished! INFO @ Sun, 21 Jun 2020 23:05:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:05:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:05:56: #2 number of paired peaks: 430 WARNING @ Sun, 21 Jun 2020 23:05:56: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Sun, 21 Jun 2020 23:05:56: start model_add_line... INFO @ Sun, 21 Jun 2020 23:05:56: start X-correlation... INFO @ Sun, 21 Jun 2020 23:05:56: end of X-cor INFO @ Sun, 21 Jun 2020 23:05:56: #2 finished! INFO @ Sun, 21 Jun 2020 23:05:56: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 23:05:56: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 23:05:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.10_model.r INFO @ Sun, 21 Jun 2020 23:05:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:05:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:05:57: 15000000 INFO @ Sun, 21 Jun 2020 23:06:03: 16000000 INFO @ Sun, 21 Jun 2020 23:06:09: 17000000 INFO @ Sun, 21 Jun 2020 23:06:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.05_peaks.xls INFO @ Sun, 21 Jun 2020 23:06:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:06:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.05_summits.bed INFO @ Sun, 21 Jun 2020 23:06:13: Done! pass1 - making usageList (699 chroms): 2 millis pass2 - checking and writing primary data (7910 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:06:14: 18000000 INFO @ Sun, 21 Jun 2020 23:06:20: 19000000 INFO @ Sun, 21 Jun 2020 23:06:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:06:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:06:24: #1 total tags in treatment: 19630016 INFO @ Sun, 21 Jun 2020 23:06:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:06:24: #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 23:06:24: #1 tags after filtering in treatment: 19630011 INFO @ Sun, 21 Jun 2020 23:06:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:06:24: #1 finished! INFO @ Sun, 21 Jun 2020 23:06:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:06:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:06:26: #2 number of paired peaks: 430 WARNING @ Sun, 21 Jun 2020 23:06:26: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Sun, 21 Jun 2020 23:06:26: start model_add_line... INFO @ Sun, 21 Jun 2020 23:06:26: start X-correlation... INFO @ Sun, 21 Jun 2020 23:06:26: end of X-cor INFO @ Sun, 21 Jun 2020 23:06:26: #2 finished! INFO @ Sun, 21 Jun 2020 23:06:26: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 23:06:26: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 23:06:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.20_model.r INFO @ Sun, 21 Jun 2020 23:06:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:06:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 23:06:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:06:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.10_peaks.xls INFO @ Sun, 21 Jun 2020 23:06:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:06:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.10_summits.bed INFO @ Sun, 21 Jun 2020 23:06:55: Done! pass1 - making usageList (589 chroms): 2 millis pass2 - checking and writing primary data (5450 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:07:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:07:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.20_peaks.xls INFO @ Sun, 21 Jun 2020 23:07:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:07:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969916/SRX969916.20_summits.bed INFO @ Sun, 21 Jun 2020 23:07:26: Done! pass1 - making usageList (436 chroms): 1 millis pass2 - checking and writing primary data (3225 records, 4 fields): 14 millis CompletedMACS2peakCalling