Job ID = 6497697 SRX = SRX1021232 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:26:12 prefetch.2.10.7: 1) Downloading 'SRR2013429'... 2020-06-25T22:26:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:28:54 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:28:54 prefetch.2.10.7: 1) 'SRR2013429' was downloaded successfully Read 17090868 spots for SRR2013429/SRR2013429.sra Written 17090868 spots for SRR2013429/SRR2013429.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: 00:24:37 17090868 reads; of these: 17090868 (100.00%) were paired; of these: 5117453 (29.94%) aligned concordantly 0 times 8714502 (50.99%) aligned concordantly exactly 1 time 3258913 (19.07%) aligned concordantly >1 times ---- 5117453 pairs aligned concordantly 0 times; of these: 8584 (0.17%) aligned discordantly 1 time ---- 5108869 pairs aligned 0 times concordantly or discordantly; of these: 10217738 mates make up the pairs; of these: 9903188 (96.92%) aligned 0 times 211364 (2.07%) aligned exactly 1 time 103186 (1.01%) aligned >1 times 71.03% overall alignment rate Time searching: 00:24:37 Overall time: 00:24:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 535973 / 11971098 = 0.0448 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 @ Fri, 26 Jun 2020 08:03:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.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 @ Fri, 26 Jun 2020 08:03:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:03:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:03:11: 1000000 INFO @ Fri, 26 Jun 2020 08:03:17: 2000000 INFO @ Fri, 26 Jun 2020 08:03:22: 3000000 INFO @ Fri, 26 Jun 2020 08:03:28: 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 @ Fri, 26 Jun 2020 08:03:34: 5000000 INFO @ Fri, 26 Jun 2020 08:03:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.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 @ Fri, 26 Jun 2020 08:03:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:03:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:03:40: 6000000 INFO @ Fri, 26 Jun 2020 08:03:42: 1000000 INFO @ Fri, 26 Jun 2020 08:03:46: 7000000 INFO @ Fri, 26 Jun 2020 08:03:48: 2000000 INFO @ Fri, 26 Jun 2020 08:03:52: 8000000 INFO @ Fri, 26 Jun 2020 08:03:54: 3000000 INFO @ Fri, 26 Jun 2020 08:03:57: 9000000 INFO @ Fri, 26 Jun 2020 08:03:59: 4000000 INFO @ Fri, 26 Jun 2020 08:04:03: 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 @ Fri, 26 Jun 2020 08:04:05: 5000000 INFO @ Fri, 26 Jun 2020 08:04:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.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 @ Fri, 26 Jun 2020 08:04:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:04:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:04:10: 11000000 INFO @ Fri, 26 Jun 2020 08:04:10: 6000000 INFO @ Fri, 26 Jun 2020 08:04:11: 1000000 INFO @ Fri, 26 Jun 2020 08:04:15: 7000000 INFO @ Fri, 26 Jun 2020 08:04:16: 12000000 INFO @ Fri, 26 Jun 2020 08:04:16: 2000000 INFO @ Fri, 26 Jun 2020 08:04:21: 8000000 INFO @ Fri, 26 Jun 2020 08:04:22: 3000000 INFO @ Fri, 26 Jun 2020 08:04:22: 13000000 INFO @ Fri, 26 Jun 2020 08:04:26: 9000000 INFO @ Fri, 26 Jun 2020 08:04:27: 4000000 INFO @ Fri, 26 Jun 2020 08:04:28: 14000000 INFO @ Fri, 26 Jun 2020 08:04:31: 10000000 INFO @ Fri, 26 Jun 2020 08:04:33: 5000000 INFO @ Fri, 26 Jun 2020 08:04:34: 15000000 INFO @ Fri, 26 Jun 2020 08:04:37: 11000000 INFO @ Fri, 26 Jun 2020 08:04:38: 6000000 INFO @ Fri, 26 Jun 2020 08:04:39: 16000000 INFO @ Fri, 26 Jun 2020 08:04:42: 12000000 INFO @ Fri, 26 Jun 2020 08:04:44: 7000000 INFO @ Fri, 26 Jun 2020 08:04:45: 17000000 INFO @ Fri, 26 Jun 2020 08:04:47: 13000000 INFO @ Fri, 26 Jun 2020 08:04:49: 8000000 INFO @ Fri, 26 Jun 2020 08:04:51: 18000000 INFO @ Fri, 26 Jun 2020 08:04:53: 14000000 INFO @ Fri, 26 Jun 2020 08:04:54: 9000000 INFO @ Fri, 26 Jun 2020 08:04:57: 19000000 INFO @ Fri, 26 Jun 2020 08:04:58: 15000000 INFO @ Fri, 26 Jun 2020 08:05:00: 10000000 INFO @ Fri, 26 Jun 2020 08:05:02: 20000000 INFO @ Fri, 26 Jun 2020 08:05:04: 16000000 INFO @ Fri, 26 Jun 2020 08:05:05: 11000000 INFO @ Fri, 26 Jun 2020 08:05:09: 21000000 INFO @ Fri, 26 Jun 2020 08:05:09: 17000000 INFO @ Fri, 26 Jun 2020 08:05:10: 12000000 INFO @ Fri, 26 Jun 2020 08:05:14: 18000000 INFO @ Fri, 26 Jun 2020 08:05:14: 22000000 INFO @ Fri, 26 Jun 2020 08:05:15: 13000000 INFO @ Fri, 26 Jun 2020 08:05:19: 19000000 INFO @ Fri, 26 Jun 2020 08:05:20: 23000000 INFO @ Fri, 26 Jun 2020 08:05:20: 14000000 INFO @ Fri, 26 Jun 2020 08:05:21: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:05:21: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:05:21: #1 total tags in treatment: 11437605 INFO @ Fri, 26 Jun 2020 08:05:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:05:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:05:21: #1 tags after filtering in treatment: 10739210 INFO @ Fri, 26 Jun 2020 08:05:21: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 26 Jun 2020 08:05:21: #1 finished! INFO @ Fri, 26 Jun 2020 08:05:21: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:05:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:05:22: #2 number of paired peaks: 414 WARNING @ Fri, 26 Jun 2020 08:05:22: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Fri, 26 Jun 2020 08:05:22: start model_add_line... INFO @ Fri, 26 Jun 2020 08:05:22: start X-correlation... INFO @ Fri, 26 Jun 2020 08:05:22: end of X-cor INFO @ Fri, 26 Jun 2020 08:05:22: #2 finished! INFO @ Fri, 26 Jun 2020 08:05:22: #2 predicted fragment length is 137 bps INFO @ Fri, 26 Jun 2020 08:05:22: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 26 Jun 2020 08:05:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.05_model.r INFO @ Fri, 26 Jun 2020 08:05:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:05:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:05:24: 20000000 INFO @ Fri, 26 Jun 2020 08:05:25: 15000000 INFO @ Fri, 26 Jun 2020 08:05:29: 21000000 INFO @ Fri, 26 Jun 2020 08:05:30: 16000000 INFO @ Fri, 26 Jun 2020 08:05:34: 22000000 INFO @ Fri, 26 Jun 2020 08:05:35: 17000000 INFO @ Fri, 26 Jun 2020 08:05:39: 23000000 INFO @ Fri, 26 Jun 2020 08:05:40: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:05:40: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:05:40: #1 total tags in treatment: 11437605 INFO @ Fri, 26 Jun 2020 08:05:40: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:05:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:05:40: 18000000 INFO @ Fri, 26 Jun 2020 08:05:40: #1 tags after filtering in treatment: 10739210 INFO @ Fri, 26 Jun 2020 08:05:40: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 26 Jun 2020 08:05:40: #1 finished! INFO @ Fri, 26 Jun 2020 08:05:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:05:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:05:41: #2 number of paired peaks: 414 WARNING @ Fri, 26 Jun 2020 08:05:41: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Fri, 26 Jun 2020 08:05:41: start model_add_line... INFO @ Fri, 26 Jun 2020 08:05:41: start X-correlation... INFO @ Fri, 26 Jun 2020 08:05:41: end of X-cor INFO @ Fri, 26 Jun 2020 08:05:41: #2 finished! INFO @ Fri, 26 Jun 2020 08:05:41: #2 predicted fragment length is 137 bps INFO @ Fri, 26 Jun 2020 08:05:41: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 26 Jun 2020 08:05:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.10_model.r INFO @ Fri, 26 Jun 2020 08:05:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:05:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:05:45: 19000000 INFO @ Fri, 26 Jun 2020 08:05:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:05:50: 20000000 INFO @ Fri, 26 Jun 2020 08:05:55: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:06:00: 22000000 INFO @ Fri, 26 Jun 2020 08:06:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:06:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:06:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.05_summits.bed INFO @ Fri, 26 Jun 2020 08:06:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5517 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:06:05: 23000000 INFO @ Fri, 26 Jun 2020 08:06:06: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:06:06: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:06:06: #1 total tags in treatment: 11437605 INFO @ Fri, 26 Jun 2020 08:06:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:06:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:06:06: #1 tags after filtering in treatment: 10739210 INFO @ Fri, 26 Jun 2020 08:06:06: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 26 Jun 2020 08:06:06: #1 finished! INFO @ Fri, 26 Jun 2020 08:06:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:06:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:06:07: #2 number of paired peaks: 414 WARNING @ Fri, 26 Jun 2020 08:06:07: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Fri, 26 Jun 2020 08:06:07: start model_add_line... INFO @ Fri, 26 Jun 2020 08:06:07: start X-correlation... INFO @ Fri, 26 Jun 2020 08:06:07: end of X-cor INFO @ Fri, 26 Jun 2020 08:06:07: #2 finished! INFO @ Fri, 26 Jun 2020 08:06:07: #2 predicted fragment length is 137 bps INFO @ Fri, 26 Jun 2020 08:06:07: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 26 Jun 2020 08:06:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.20_model.r INFO @ Fri, 26 Jun 2020 08:06:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:06:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:06:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:06:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:06:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:06:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.10_summits.bed INFO @ Fri, 26 Jun 2020 08:06:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2978 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:06:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:06:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:06:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:06:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1021232/SRX1021232.20_summits.bed INFO @ Fri, 26 Jun 2020 08:06:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1411 records, 4 fields): 3 millis CompletedMACS2peakCalling