Job ID = 6454815 SRX = SRX2592414 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:29:44 prefetch.2.10.7: 1) Downloading 'SRR5289691'... 2020-06-21T09:29:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:32:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:32:59 prefetch.2.10.7: 1) 'SRR5289691' was downloaded successfully Read 21492442 spots for SRR5289691/SRR5289691.sra Written 21492442 spots for SRR5289691/SRR5289691.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: 00:06:24 21492442 reads; of these: 21492442 (100.00%) were unpaired; of these: 1694516 (7.88%) aligned 0 times 15775483 (73.40%) aligned exactly 1 time 4022443 (18.72%) aligned >1 times 92.12% overall alignment rate Time searching: 00:06:24 Overall time: 00:06:24 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] 7259557 / 19797926 = 0.3667 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 18:45:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.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 18:45:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:45:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:45:32: 1000000 INFO @ Sun, 21 Jun 2020 18:45:38: 2000000 INFO @ Sun, 21 Jun 2020 18:45:45: 3000000 INFO @ Sun, 21 Jun 2020 18:45:51: 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 18:45:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.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 18:45:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:45:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:45:58: 5000000 INFO @ Sun, 21 Jun 2020 18:46:02: 1000000 INFO @ Sun, 21 Jun 2020 18:46:04: 6000000 INFO @ Sun, 21 Jun 2020 18:46:09: 2000000 INFO @ Sun, 21 Jun 2020 18:46:11: 7000000 INFO @ Sun, 21 Jun 2020 18:46:16: 3000000 INFO @ Sun, 21 Jun 2020 18:46:18: 8000000 INFO @ Sun, 21 Jun 2020 18:46:23: 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 18:46:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.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 18:46:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:46:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:46:25: 9000000 INFO @ Sun, 21 Jun 2020 18:46:31: 5000000 INFO @ Sun, 21 Jun 2020 18:46:32: 1000000 INFO @ Sun, 21 Jun 2020 18:46:33: 10000000 INFO @ Sun, 21 Jun 2020 18:46:38: 6000000 INFO @ Sun, 21 Jun 2020 18:46:39: 2000000 INFO @ Sun, 21 Jun 2020 18:46:41: 11000000 INFO @ Sun, 21 Jun 2020 18:46:45: 7000000 INFO @ Sun, 21 Jun 2020 18:46:46: 3000000 INFO @ Sun, 21 Jun 2020 18:46:48: 12000000 INFO @ Sun, 21 Jun 2020 18:46:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:46:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:46:52: #1 total tags in treatment: 12538369 INFO @ Sun, 21 Jun 2020 18:46:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:46:52: #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 18:46:52: #1 tags after filtering in treatment: 12538246 INFO @ Sun, 21 Jun 2020 18:46:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:46:52: #1 finished! INFO @ Sun, 21 Jun 2020 18:46:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:46:52: 8000000 INFO @ Sun, 21 Jun 2020 18:46:53: 4000000 INFO @ Sun, 21 Jun 2020 18:46:53: #2 number of paired peaks: 659 WARNING @ Sun, 21 Jun 2020 18:46:53: Fewer paired peaks (659) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 659 pairs to build model! INFO @ Sun, 21 Jun 2020 18:46:53: start model_add_line... INFO @ Sun, 21 Jun 2020 18:46:53: start X-correlation... INFO @ Sun, 21 Jun 2020 18:46:53: end of X-cor INFO @ Sun, 21 Jun 2020 18:46:53: #2 finished! INFO @ Sun, 21 Jun 2020 18:46:53: #2 predicted fragment length is 182 bps INFO @ Sun, 21 Jun 2020 18:46:53: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 21 Jun 2020 18:46:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.05_model.r INFO @ Sun, 21 Jun 2020 18:46:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:46:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:46:59: 9000000 INFO @ Sun, 21 Jun 2020 18:47:00: 5000000 INFO @ Sun, 21 Jun 2020 18:47:06: 10000000 INFO @ Sun, 21 Jun 2020 18:47:07: 6000000 INFO @ Sun, 21 Jun 2020 18:47:13: 11000000 INFO @ Sun, 21 Jun 2020 18:47:13: 7000000 INFO @ Sun, 21 Jun 2020 18:47:20: 12000000 INFO @ Sun, 21 Jun 2020 18:47:20: 8000000 INFO @ Sun, 21 Jun 2020 18:47:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:47:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:47:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:47:24: #1 total tags in treatment: 12538369 INFO @ Sun, 21 Jun 2020 18:47:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:47:24: #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 18:47:24: #1 tags after filtering in treatment: 12538246 INFO @ Sun, 21 Jun 2020 18:47:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:47:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:47:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:47:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:47:26: #2 number of paired peaks: 659 WARNING @ Sun, 21 Jun 2020 18:47:26: Fewer paired peaks (659) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 659 pairs to build model! INFO @ Sun, 21 Jun 2020 18:47:26: start model_add_line... INFO @ Sun, 21 Jun 2020 18:47:26: start X-correlation... INFO @ Sun, 21 Jun 2020 18:47:26: end of X-cor INFO @ Sun, 21 Jun 2020 18:47:26: #2 finished! INFO @ Sun, 21 Jun 2020 18:47:26: #2 predicted fragment length is 182 bps INFO @ Sun, 21 Jun 2020 18:47:26: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 21 Jun 2020 18:47:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.10_model.r INFO @ Sun, 21 Jun 2020 18:47:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:47:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:47:27: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:47:34: 10000000 INFO @ Sun, 21 Jun 2020 18:47:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:47:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:47:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.05_summits.bed INFO @ Sun, 21 Jun 2020 18:47:39: Done! pass1 - making usageList (237 chroms): 3 millis pass2 - checking and writing primary data (16261 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:47:40: 11000000 INFO @ Sun, 21 Jun 2020 18:47:46: 12000000 INFO @ Sun, 21 Jun 2020 18:47:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:47:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:47:50: #1 total tags in treatment: 12538369 INFO @ Sun, 21 Jun 2020 18:47:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:47:50: #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 18:47:50: #1 tags after filtering in treatment: 12538246 INFO @ Sun, 21 Jun 2020 18:47:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:47:50: #1 finished! INFO @ Sun, 21 Jun 2020 18:47:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:47:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:47:52: #2 number of paired peaks: 659 WARNING @ Sun, 21 Jun 2020 18:47:52: Fewer paired peaks (659) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 659 pairs to build model! INFO @ Sun, 21 Jun 2020 18:47:52: start model_add_line... INFO @ Sun, 21 Jun 2020 18:47:52: start X-correlation... INFO @ Sun, 21 Jun 2020 18:47:52: end of X-cor INFO @ Sun, 21 Jun 2020 18:47:52: #2 finished! INFO @ Sun, 21 Jun 2020 18:47:52: #2 predicted fragment length is 182 bps INFO @ Sun, 21 Jun 2020 18:47:52: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 21 Jun 2020 18:47:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.20_model.r INFO @ Sun, 21 Jun 2020 18:47:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:47:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:47:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:48:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.10_summits.bed INFO @ Sun, 21 Jun 2020 18:48:11: Done! pass1 - making usageList (178 chroms): 2 millis pass2 - checking and writing primary data (11940 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:48:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:48:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592414/SRX2592414.20_summits.bed INFO @ Sun, 21 Jun 2020 18:48:37: Done! pass1 - making usageList (135 chroms): 2 millis pass2 - checking and writing primary data (7387 records, 4 fields): 12 millis CompletedMACS2peakCalling