Job ID = 6498731 SRX = SRX749056 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T23:54:29 prefetch.2.10.7: 1) Downloading 'SRR1636784'... 2020-06-25T23:54:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:59:18 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:59:18 prefetch.2.10.7: 1) 'SRR1636784' was downloaded successfully Read 21593296 spots for SRR1636784/SRR1636784.sra Written 21593296 spots for SRR1636784/SRR1636784.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: 00:42:26 21593296 reads; of these: 21593296 (100.00%) were paired; of these: 2022517 (9.37%) aligned concordantly 0 times 13843366 (64.11%) aligned concordantly exactly 1 time 5727413 (26.52%) aligned concordantly >1 times ---- 2022517 pairs aligned concordantly 0 times; of these: 15703 (0.78%) aligned discordantly 1 time ---- 2006814 pairs aligned 0 times concordantly or discordantly; of these: 4013628 mates make up the pairs; of these: 3503647 (87.29%) aligned 0 times 358837 (8.94%) aligned exactly 1 time 151144 (3.77%) aligned >1 times 91.89% overall alignment rate Time searching: 00:42:26 Overall time: 00:42:26 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 20 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] 10071908 / 19564936 = 0.5148 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 09:52:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.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 09:52:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:52:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:52:31: 1000000 INFO @ Fri, 26 Jun 2020 09:52:37: 2000000 INFO @ Fri, 26 Jun 2020 09:52:43: 3000000 INFO @ Fri, 26 Jun 2020 09:52:49: 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 09:52:55: 5000000 INFO @ Fri, 26 Jun 2020 09:52:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.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 09:52:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:52:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:53:02: 6000000 INFO @ Fri, 26 Jun 2020 09:53:02: 1000000 INFO @ Fri, 26 Jun 2020 09:53:08: 7000000 INFO @ Fri, 26 Jun 2020 09:53:08: 2000000 INFO @ Fri, 26 Jun 2020 09:53:14: 8000000 INFO @ Fri, 26 Jun 2020 09:53:15: 3000000 INFO @ Fri, 26 Jun 2020 09:53:21: 9000000 INFO @ Fri, 26 Jun 2020 09:53:21: 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 09:53:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.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 09:53:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:53:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:53:27: 10000000 INFO @ Fri, 26 Jun 2020 09:53:28: 5000000 INFO @ Fri, 26 Jun 2020 09:53:32: 1000000 INFO @ Fri, 26 Jun 2020 09:53:34: 11000000 INFO @ Fri, 26 Jun 2020 09:53:34: 6000000 INFO @ Fri, 26 Jun 2020 09:53:38: 2000000 INFO @ Fri, 26 Jun 2020 09:53:41: 12000000 INFO @ Fri, 26 Jun 2020 09:53:41: 7000000 INFO @ Fri, 26 Jun 2020 09:53:45: 3000000 INFO @ Fri, 26 Jun 2020 09:53:47: 13000000 INFO @ Fri, 26 Jun 2020 09:53:48: 8000000 INFO @ Fri, 26 Jun 2020 09:53:51: 4000000 INFO @ Fri, 26 Jun 2020 09:53:54: 14000000 INFO @ Fri, 26 Jun 2020 09:53:54: 9000000 INFO @ Fri, 26 Jun 2020 09:53:58: 5000000 INFO @ Fri, 26 Jun 2020 09:54:00: 15000000 INFO @ Fri, 26 Jun 2020 09:54:01: 10000000 INFO @ Fri, 26 Jun 2020 09:54:05: 6000000 INFO @ Fri, 26 Jun 2020 09:54:07: 16000000 INFO @ Fri, 26 Jun 2020 09:54:07: 11000000 INFO @ Fri, 26 Jun 2020 09:54:12: 7000000 INFO @ Fri, 26 Jun 2020 09:54:13: 17000000 INFO @ Fri, 26 Jun 2020 09:54:14: 12000000 INFO @ Fri, 26 Jun 2020 09:54:19: 8000000 INFO @ Fri, 26 Jun 2020 09:54:20: 18000000 INFO @ Fri, 26 Jun 2020 09:54:20: 13000000 INFO @ Fri, 26 Jun 2020 09:54:25: 9000000 INFO @ Fri, 26 Jun 2020 09:54:26: 19000000 INFO @ Fri, 26 Jun 2020 09:54:27: 14000000 INFO @ Fri, 26 Jun 2020 09:54:30: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:54:30: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:54:30: #1 total tags in treatment: 9503464 INFO @ Fri, 26 Jun 2020 09:54:30: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:54:30: #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 09:54:30: #1 tags after filtering in treatment: 8495944 INFO @ Fri, 26 Jun 2020 09:54:30: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 26 Jun 2020 09:54:30: #1 finished! INFO @ Fri, 26 Jun 2020 09:54:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:54:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:54:31: #2 number of paired peaks: 1544 INFO @ Fri, 26 Jun 2020 09:54:31: start model_add_line... INFO @ Fri, 26 Jun 2020 09:54:31: start X-correlation... INFO @ Fri, 26 Jun 2020 09:54:31: end of X-cor INFO @ Fri, 26 Jun 2020 09:54:31: #2 finished! INFO @ Fri, 26 Jun 2020 09:54:31: #2 predicted fragment length is 104 bps INFO @ Fri, 26 Jun 2020 09:54:31: #2 alternative fragment length(s) may be 104 bps INFO @ Fri, 26 Jun 2020 09:54:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.05_model.r INFO @ Fri, 26 Jun 2020 09:54:31: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:54:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:54:32: 10000000 INFO @ Fri, 26 Jun 2020 09:54:33: 15000000 INFO @ Fri, 26 Jun 2020 09:54:38: 11000000 INFO @ Fri, 26 Jun 2020 09:54:40: 16000000 INFO @ Fri, 26 Jun 2020 09:54:45: 12000000 INFO @ Fri, 26 Jun 2020 09:54:46: 17000000 INFO @ Fri, 26 Jun 2020 09:54:50: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:54:51: 13000000 INFO @ Fri, 26 Jun 2020 09:54:52: 18000000 INFO @ Fri, 26 Jun 2020 09:54:58: 14000000 INFO @ Fri, 26 Jun 2020 09:54:59: 19000000 INFO @ Fri, 26 Jun 2020 09:54:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.05_peaks.xls BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:54:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:54:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.05_summits.bed INFO @ Fri, 26 Jun 2020 09:54:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5821 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:55:02: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:55:02: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:55:02: #1 total tags in treatment: 9503464 INFO @ Fri, 26 Jun 2020 09:55:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:55:02: #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 09:55:02: #1 tags after filtering in treatment: 8495944 INFO @ Fri, 26 Jun 2020 09:55:02: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 26 Jun 2020 09:55:02: #1 finished! INFO @ Fri, 26 Jun 2020 09:55:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:55:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:55:03: #2 number of paired peaks: 1544 INFO @ Fri, 26 Jun 2020 09:55:03: start model_add_line... INFO @ Fri, 26 Jun 2020 09:55:03: start X-correlation... INFO @ Fri, 26 Jun 2020 09:55:03: end of X-cor INFO @ Fri, 26 Jun 2020 09:55:03: #2 finished! INFO @ Fri, 26 Jun 2020 09:55:03: #2 predicted fragment length is 104 bps INFO @ Fri, 26 Jun 2020 09:55:03: #2 alternative fragment length(s) may be 104 bps INFO @ Fri, 26 Jun 2020 09:55:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.10_model.r INFO @ Fri, 26 Jun 2020 09:55:03: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:55:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:55:04: 15000000 INFO @ Fri, 26 Jun 2020 09:55:10: 16000000 INFO @ Fri, 26 Jun 2020 09:55:16: 17000000 INFO @ Fri, 26 Jun 2020 09:55:21: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:55:23: 18000000 INFO @ Fri, 26 Jun 2020 09:55:29: 19000000 INFO @ Fri, 26 Jun 2020 09:55:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:55:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:55:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.10_summits.bed INFO @ Fri, 26 Jun 2020 09:55:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2841 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:55:32: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:55:32: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:55:32: #1 total tags in treatment: 9503464 INFO @ Fri, 26 Jun 2020 09:55:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:55:32: #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 09:55:32: #1 tags after filtering in treatment: 8495944 INFO @ Fri, 26 Jun 2020 09:55:32: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 26 Jun 2020 09:55:32: #1 finished! INFO @ Fri, 26 Jun 2020 09:55:32: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:55:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:55:33: #2 number of paired peaks: 1544 INFO @ Fri, 26 Jun 2020 09:55:33: start model_add_line... INFO @ Fri, 26 Jun 2020 09:55:33: start X-correlation... INFO @ Fri, 26 Jun 2020 09:55:33: end of X-cor INFO @ Fri, 26 Jun 2020 09:55:33: #2 finished! INFO @ Fri, 26 Jun 2020 09:55:33: #2 predicted fragment length is 104 bps INFO @ Fri, 26 Jun 2020 09:55:33: #2 alternative fragment length(s) may be 104 bps INFO @ Fri, 26 Jun 2020 09:55:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.20_model.r INFO @ Fri, 26 Jun 2020 09:55:33: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:55:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:55:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:56:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:56:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:56:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749056/SRX749056.20_summits.bed INFO @ Fri, 26 Jun 2020 09:56:00: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1194 records, 4 fields): 3 millis CompletedMACS2peakCalling