Job ID = 6498732 SRX = SRX749057 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T23:55:44 prefetch.2.10.7: 1) Downloading 'SRR1636785'... 2020-06-25T23:55:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:58:58 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:58:58 prefetch.2.10.7: 1) 'SRR1636785' was downloaded successfully Read 14661296 spots for SRR1636785/SRR1636785.sra Written 14661296 spots for SRR1636785/SRR1636785.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: 00:34:47 14661296 reads; of these: 14661296 (100.00%) were paired; of these: 1000486 (6.82%) aligned concordantly 0 times 8749348 (59.68%) aligned concordantly exactly 1 time 4911462 (33.50%) aligned concordantly >1 times ---- 1000486 pairs aligned concordantly 0 times; of these: 21714 (2.17%) aligned discordantly 1 time ---- 978772 pairs aligned 0 times concordantly or discordantly; of these: 1957544 mates make up the pairs; of these: 1527604 (78.04%) aligned 0 times 285386 (14.58%) aligned exactly 1 time 144554 (7.38%) aligned >1 times 94.79% overall alignment rate Time searching: 00:34:47 Overall time: 00:34:47 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] 2132092 / 13663786 = 0.1560 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 09:42:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.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 09:42:37: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:42:37: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:42:42: 1000000 INFO @ Fri, 26 Jun 2020 09:42:48: 2000000 INFO @ Fri, 26 Jun 2020 09:42:53: 3000000 INFO @ Fri, 26 Jun 2020 09:42:59: 4000000 INFO @ Fri, 26 Jun 2020 09:43:05: 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 @ Fri, 26 Jun 2020 09:43:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.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 09:43:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:43:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:43:11: 6000000 INFO @ Fri, 26 Jun 2020 09:43:13: 1000000 INFO @ Fri, 26 Jun 2020 09:43:17: 7000000 INFO @ Fri, 26 Jun 2020 09:43:20: 2000000 INFO @ Fri, 26 Jun 2020 09:43:24: 8000000 INFO @ Fri, 26 Jun 2020 09:43:26: 3000000 INFO @ Fri, 26 Jun 2020 09:43:30: 9000000 INFO @ Fri, 26 Jun 2020 09:43:33: 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 @ Fri, 26 Jun 2020 09:43:37: 10000000 INFO @ Fri, 26 Jun 2020 09:43:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.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 09:43:37: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:43:37: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:43:39: 5000000 INFO @ Fri, 26 Jun 2020 09:43:43: 11000000 INFO @ Fri, 26 Jun 2020 09:43:43: 1000000 INFO @ Fri, 26 Jun 2020 09:43:46: 6000000 INFO @ Fri, 26 Jun 2020 09:43:50: 12000000 INFO @ Fri, 26 Jun 2020 09:43:50: 2000000 INFO @ Fri, 26 Jun 2020 09:43:52: 7000000 INFO @ Fri, 26 Jun 2020 09:43:56: 13000000 INFO @ Fri, 26 Jun 2020 09:43:57: 3000000 INFO @ Fri, 26 Jun 2020 09:43:59: 8000000 INFO @ Fri, 26 Jun 2020 09:44:03: 14000000 INFO @ Fri, 26 Jun 2020 09:44:03: 4000000 INFO @ Fri, 26 Jun 2020 09:44:06: 9000000 INFO @ Fri, 26 Jun 2020 09:44:09: 15000000 INFO @ Fri, 26 Jun 2020 09:44:10: 5000000 INFO @ Fri, 26 Jun 2020 09:44:12: 10000000 INFO @ Fri, 26 Jun 2020 09:44:16: 16000000 INFO @ Fri, 26 Jun 2020 09:44:17: 6000000 INFO @ Fri, 26 Jun 2020 09:44:19: 11000000 INFO @ Fri, 26 Jun 2020 09:44:23: 17000000 INFO @ Fri, 26 Jun 2020 09:44:24: 7000000 INFO @ Fri, 26 Jun 2020 09:44:26: 12000000 INFO @ Fri, 26 Jun 2020 09:44:29: 18000000 INFO @ Fri, 26 Jun 2020 09:44:30: 8000000 INFO @ Fri, 26 Jun 2020 09:44:33: 13000000 INFO @ Fri, 26 Jun 2020 09:44:36: 19000000 INFO @ Fri, 26 Jun 2020 09:44:37: 9000000 INFO @ Fri, 26 Jun 2020 09:44:39: 14000000 INFO @ Fri, 26 Jun 2020 09:44:43: 20000000 INFO @ Fri, 26 Jun 2020 09:44:44: 10000000 INFO @ Fri, 26 Jun 2020 09:44:46: 15000000 INFO @ Fri, 26 Jun 2020 09:44:49: 21000000 INFO @ Fri, 26 Jun 2020 09:44:51: 11000000 INFO @ Fri, 26 Jun 2020 09:44:53: 16000000 INFO @ Fri, 26 Jun 2020 09:44:56: 22000000 INFO @ Fri, 26 Jun 2020 09:44:57: 12000000 INFO @ Fri, 26 Jun 2020 09:44:59: 17000000 INFO @ Fri, 26 Jun 2020 09:45:03: 23000000 INFO @ Fri, 26 Jun 2020 09:45:04: 13000000 INFO @ Fri, 26 Jun 2020 09:45:06: 18000000 INFO @ Fri, 26 Jun 2020 09:45:06: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:45:06: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:45:06: #1 total tags in treatment: 11529932 INFO @ Fri, 26 Jun 2020 09:45:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:45:06: #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 09:45:06: #1 tags after filtering in treatment: 10715848 INFO @ Fri, 26 Jun 2020 09:45:06: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 09:45:06: #1 finished! INFO @ Fri, 26 Jun 2020 09:45:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:45:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:45:07: #2 number of paired peaks: 693 WARNING @ Fri, 26 Jun 2020 09:45:07: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Fri, 26 Jun 2020 09:45:07: start model_add_line... INFO @ Fri, 26 Jun 2020 09:45:07: start X-correlation... INFO @ Fri, 26 Jun 2020 09:45:07: end of X-cor INFO @ Fri, 26 Jun 2020 09:45:07: #2 finished! INFO @ Fri, 26 Jun 2020 09:45:07: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 09:45:07: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 26 Jun 2020 09:45:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.05_model.r INFO @ Fri, 26 Jun 2020 09:45:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:45:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:45:11: 14000000 INFO @ Fri, 26 Jun 2020 09:45:13: 19000000 INFO @ Fri, 26 Jun 2020 09:45:18: 15000000 INFO @ Fri, 26 Jun 2020 09:45:19: 20000000 INFO @ Fri, 26 Jun 2020 09:45:24: 16000000 INFO @ Fri, 26 Jun 2020 09:45:25: 21000000 INFO @ Fri, 26 Jun 2020 09:45:30: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:45:31: 17000000 INFO @ Fri, 26 Jun 2020 09:45:32: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:45:37: 18000000 INFO @ Fri, 26 Jun 2020 09:45:39: 23000000 INFO @ Fri, 26 Jun 2020 09:45:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:45:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:45:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.05_summits.bed INFO @ Fri, 26 Jun 2020 09:45:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2916 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:45:42: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:45:42: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:45:42: #1 total tags in treatment: 11529932 INFO @ Fri, 26 Jun 2020 09:45:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:45:42: #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 09:45:42: #1 tags after filtering in treatment: 10715848 INFO @ Fri, 26 Jun 2020 09:45:42: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 09:45:42: #1 finished! INFO @ Fri, 26 Jun 2020 09:45:42: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:45:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:45:43: #2 number of paired peaks: 693 WARNING @ Fri, 26 Jun 2020 09:45:43: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Fri, 26 Jun 2020 09:45:43: start model_add_line... INFO @ Fri, 26 Jun 2020 09:45:43: start X-correlation... INFO @ Fri, 26 Jun 2020 09:45:43: end of X-cor INFO @ Fri, 26 Jun 2020 09:45:43: #2 finished! INFO @ Fri, 26 Jun 2020 09:45:43: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 09:45:43: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 26 Jun 2020 09:45:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.10_model.r INFO @ Fri, 26 Jun 2020 09:45:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:45:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:45:44: 19000000 INFO @ Fri, 26 Jun 2020 09:45:50: 20000000 INFO @ Fri, 26 Jun 2020 09:45:56: 21000000 INFO @ Fri, 26 Jun 2020 09:46:02: 22000000 INFO @ Fri, 26 Jun 2020 09:46:06: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:46:08: 23000000 INFO @ Fri, 26 Jun 2020 09:46:11: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:46:11: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:46:11: #1 total tags in treatment: 11529932 INFO @ Fri, 26 Jun 2020 09:46:11: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:46:11: #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 09:46:11: #1 tags after filtering in treatment: 10715848 INFO @ Fri, 26 Jun 2020 09:46:11: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 09:46:11: #1 finished! INFO @ Fri, 26 Jun 2020 09:46:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:46:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:46:12: #2 number of paired peaks: 693 WARNING @ Fri, 26 Jun 2020 09:46:12: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Fri, 26 Jun 2020 09:46:12: start model_add_line... INFO @ Fri, 26 Jun 2020 09:46:12: start X-correlation... INFO @ Fri, 26 Jun 2020 09:46:12: end of X-cor INFO @ Fri, 26 Jun 2020 09:46:12: #2 finished! INFO @ Fri, 26 Jun 2020 09:46:12: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 09:46:12: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 26 Jun 2020 09:46:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.20_model.r INFO @ Fri, 26 Jun 2020 09:46:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:46:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:46:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:46:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:46:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.10_summits.bed INFO @ Fri, 26 Jun 2020 09:46:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1455 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:46:35: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:46:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:46:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:46:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749057/SRX749057.20_summits.bed INFO @ Fri, 26 Jun 2020 09:46:46: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (811 records, 4 fields): 2 millis CompletedMACS2peakCalling