Job ID = 6498725 SRX = SRX749045 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T00:12:20 prefetch.2.10.7: 1) Downloading 'SRR1636773'... 2020-06-26T00:12:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:15:55 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:15:55 prefetch.2.10.7: 1) 'SRR1636773' was downloaded successfully Read 19537343 spots for SRR1636773/SRR1636773.sra Written 19537343 spots for SRR1636773/SRR1636773.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: 00:34:52 19537343 reads; of these: 19537343 (100.00%) were paired; of these: 4270863 (21.86%) aligned concordantly 0 times 11042070 (56.52%) aligned concordantly exactly 1 time 4224410 (21.62%) aligned concordantly >1 times ---- 4270863 pairs aligned concordantly 0 times; of these: 8650 (0.20%) aligned discordantly 1 time ---- 4262213 pairs aligned 0 times concordantly or discordantly; of these: 8524426 mates make up the pairs; of these: 8101396 (95.04%) aligned 0 times 306349 (3.59%) aligned exactly 1 time 116681 (1.37%) aligned >1 times 79.27% overall alignment rate Time searching: 00:34:52 Overall time: 00:34:52 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 16 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] 4003200 / 15260985 = 0.2623 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 10:02:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.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 10:02:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:02:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:02:21: 1000000 INFO @ Fri, 26 Jun 2020 10:02:27: 2000000 INFO @ Fri, 26 Jun 2020 10:02:33: 3000000 INFO @ Fri, 26 Jun 2020 10:02:39: 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 10:02:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.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 10:02:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:02:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:02:46: 5000000 INFO @ Fri, 26 Jun 2020 10:02:51: 1000000 INFO @ Fri, 26 Jun 2020 10:02:53: 6000000 INFO @ Fri, 26 Jun 2020 10:02:58: 2000000 INFO @ Fri, 26 Jun 2020 10:03:00: 7000000 INFO @ Fri, 26 Jun 2020 10:03:05: 3000000 INFO @ Fri, 26 Jun 2020 10:03:06: 8000000 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 10:03:12: 4000000 INFO @ Fri, 26 Jun 2020 10:03:13: 9000000 INFO @ Fri, 26 Jun 2020 10:03:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.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 10:03:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:03:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:03:19: 5000000 INFO @ Fri, 26 Jun 2020 10:03:20: 10000000 INFO @ Fri, 26 Jun 2020 10:03:21: 1000000 INFO @ Fri, 26 Jun 2020 10:03:27: 6000000 INFO @ Fri, 26 Jun 2020 10:03:27: 11000000 INFO @ Fri, 26 Jun 2020 10:03:28: 2000000 INFO @ Fri, 26 Jun 2020 10:03:34: 12000000 INFO @ Fri, 26 Jun 2020 10:03:34: 7000000 INFO @ Fri, 26 Jun 2020 10:03:35: 3000000 INFO @ Fri, 26 Jun 2020 10:03:40: 13000000 INFO @ Fri, 26 Jun 2020 10:03:41: 8000000 INFO @ Fri, 26 Jun 2020 10:03:42: 4000000 INFO @ Fri, 26 Jun 2020 10:03:47: 14000000 INFO @ Fri, 26 Jun 2020 10:03:48: 9000000 INFO @ Fri, 26 Jun 2020 10:03:49: 5000000 INFO @ Fri, 26 Jun 2020 10:03:54: 15000000 INFO @ Fri, 26 Jun 2020 10:03:55: 10000000 INFO @ Fri, 26 Jun 2020 10:03:56: 6000000 INFO @ Fri, 26 Jun 2020 10:04:01: 16000000 INFO @ Fri, 26 Jun 2020 10:04:02: 11000000 INFO @ Fri, 26 Jun 2020 10:04:03: 7000000 INFO @ Fri, 26 Jun 2020 10:04:08: 17000000 INFO @ Fri, 26 Jun 2020 10:04:09: 12000000 INFO @ Fri, 26 Jun 2020 10:04:10: 8000000 INFO @ Fri, 26 Jun 2020 10:04:15: 18000000 INFO @ Fri, 26 Jun 2020 10:04:16: 13000000 INFO @ Fri, 26 Jun 2020 10:04:17: 9000000 INFO @ Fri, 26 Jun 2020 10:04:22: 19000000 INFO @ Fri, 26 Jun 2020 10:04:23: 14000000 INFO @ Fri, 26 Jun 2020 10:04:24: 10000000 INFO @ Fri, 26 Jun 2020 10:04:29: 20000000 INFO @ Fri, 26 Jun 2020 10:04:30: 15000000 INFO @ Fri, 26 Jun 2020 10:04:31: 11000000 INFO @ Fri, 26 Jun 2020 10:04:36: 21000000 INFO @ Fri, 26 Jun 2020 10:04:37: 16000000 INFO @ Fri, 26 Jun 2020 10:04:38: 12000000 INFO @ Fri, 26 Jun 2020 10:04:43: 22000000 INFO @ Fri, 26 Jun 2020 10:04:44: 17000000 INFO @ Fri, 26 Jun 2020 10:04:45: 13000000 INFO @ Fri, 26 Jun 2020 10:04:50: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 10:04:50: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 10:04:50: #1 total tags in treatment: 11264707 INFO @ Fri, 26 Jun 2020 10:04:50: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:04:50: #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 10:04:50: #1 tags after filtering in treatment: 10449712 INFO @ Fri, 26 Jun 2020 10:04:50: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 10:04:50: #1 finished! INFO @ Fri, 26 Jun 2020 10:04:50: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:04:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:04:51: #2 number of paired peaks: 787 WARNING @ Fri, 26 Jun 2020 10:04:51: Fewer paired peaks (787) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 787 pairs to build model! INFO @ Fri, 26 Jun 2020 10:04:51: start model_add_line... INFO @ Fri, 26 Jun 2020 10:04:51: start X-correlation... INFO @ Fri, 26 Jun 2020 10:04:51: end of X-cor INFO @ Fri, 26 Jun 2020 10:04:51: #2 finished! INFO @ Fri, 26 Jun 2020 10:04:51: #2 predicted fragment length is 128 bps INFO @ Fri, 26 Jun 2020 10:04:51: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 26 Jun 2020 10:04:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.05_model.r INFO @ Fri, 26 Jun 2020 10:04:51: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:04:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:04:51: 18000000 INFO @ Fri, 26 Jun 2020 10:04:52: 14000000 INFO @ Fri, 26 Jun 2020 10:04:59: 19000000 INFO @ Fri, 26 Jun 2020 10:04:59: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 10:05:06: 16000000 INFO @ Fri, 26 Jun 2020 10:05:06: 20000000 INFO @ Fri, 26 Jun 2020 10:05:12: 17000000 INFO @ Fri, 26 Jun 2020 10:05:13: 21000000 INFO @ Fri, 26 Jun 2020 10:05:16: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:05:19: 18000000 INFO @ Fri, 26 Jun 2020 10:05:20: 22000000 INFO @ Fri, 26 Jun 2020 10:05:26: 19000000 INFO @ Fri, 26 Jun 2020 10:05:27: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 10:05:27: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 10:05:27: #1 total tags in treatment: 11264707 INFO @ Fri, 26 Jun 2020 10:05:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:05:27: #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 10:05:27: #1 tags after filtering in treatment: 10449712 INFO @ Fri, 26 Jun 2020 10:05:27: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 10:05:27: #1 finished! INFO @ Fri, 26 Jun 2020 10:05:27: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:05:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:05:28: #2 number of paired peaks: 787 WARNING @ Fri, 26 Jun 2020 10:05:28: Fewer paired peaks (787) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 787 pairs to build model! INFO @ Fri, 26 Jun 2020 10:05:28: start model_add_line... INFO @ Fri, 26 Jun 2020 10:05:28: start X-correlation... INFO @ Fri, 26 Jun 2020 10:05:28: end of X-cor INFO @ Fri, 26 Jun 2020 10:05:28: #2 finished! INFO @ Fri, 26 Jun 2020 10:05:28: #2 predicted fragment length is 128 bps INFO @ Fri, 26 Jun 2020 10:05:28: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 26 Jun 2020 10:05:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.10_model.r INFO @ Fri, 26 Jun 2020 10:05:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:05:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:05:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.05_peaks.xls INFO @ Fri, 26 Jun 2020 10:05:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:05:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.05_summits.bed INFO @ Fri, 26 Jun 2020 10:05:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4813 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:05:33: 20000000 INFO @ Fri, 26 Jun 2020 10:05:39: 21000000 INFO @ Fri, 26 Jun 2020 10:05:45: 22000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 10:05:51: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 10:05:51: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 10:05:51: #1 total tags in treatment: 11264707 INFO @ Fri, 26 Jun 2020 10:05:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:05:51: #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 10:05:51: #1 tags after filtering in treatment: 10449712 INFO @ Fri, 26 Jun 2020 10:05:51: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 10:05:51: #1 finished! INFO @ Fri, 26 Jun 2020 10:05:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:05:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:05:52: #2 number of paired peaks: 787 WARNING @ Fri, 26 Jun 2020 10:05:52: Fewer paired peaks (787) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 787 pairs to build model! INFO @ Fri, 26 Jun 2020 10:05:52: start model_add_line... INFO @ Fri, 26 Jun 2020 10:05:52: start X-correlation... INFO @ Fri, 26 Jun 2020 10:05:52: end of X-cor INFO @ Fri, 26 Jun 2020 10:05:52: #2 finished! INFO @ Fri, 26 Jun 2020 10:05:52: #2 predicted fragment length is 128 bps INFO @ Fri, 26 Jun 2020 10:05:52: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 26 Jun 2020 10:05:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.20_model.r INFO @ Fri, 26 Jun 2020 10:05:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:05:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:05:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:06:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.10_peaks.xls INFO @ Fri, 26 Jun 2020 10:06:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:06:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.10_summits.bed INFO @ Fri, 26 Jun 2020 10:06:05: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2502 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:06:18: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:06:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.20_peaks.xls INFO @ Fri, 26 Jun 2020 10:06:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:06:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749045/SRX749045.20_summits.bed INFO @ Fri, 26 Jun 2020 10:06:31: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1221 records, 4 fields): 15 millis CompletedMACS2peakCalling