Job ID = 6498724 SRX = SRX749043 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T00:28:42 prefetch.2.10.7: 1) Downloading 'SRR1636771'... 2020-06-26T00:28:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:32:26 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:32:26 prefetch.2.10.7: 1) 'SRR1636771' was downloaded successfully Read 20896656 spots for SRR1636771/SRR1636771.sra Written 20896656 spots for SRR1636771/SRR1636771.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: 00:42:28 20896656 reads; of these: 20896656 (100.00%) were paired; of these: 1105810 (5.29%) aligned concordantly 0 times 14221847 (68.06%) aligned concordantly exactly 1 time 5568999 (26.65%) aligned concordantly >1 times ---- 1105810 pairs aligned concordantly 0 times; of these: 12666 (1.15%) aligned discordantly 1 time ---- 1093144 pairs aligned 0 times concordantly or discordantly; of these: 2186288 mates make up the pairs; of these: 1618295 (74.02%) aligned 0 times 412111 (18.85%) aligned exactly 1 time 155882 (7.13%) aligned >1 times 96.13% overall alignment rate Time searching: 00:42:28 Overall time: 00:42:28 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] 8499286 / 19787676 = 0.4295 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 10:27:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.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 10:27:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:27:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:27:30: 1000000 INFO @ Fri, 26 Jun 2020 10:27:35: 2000000 INFO @ Fri, 26 Jun 2020 10:27:40: 3000000 INFO @ Fri, 26 Jun 2020 10:27:44: 4000000 INFO @ Fri, 26 Jun 2020 10:27:49: 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 10:27:54: 6000000 INFO @ Fri, 26 Jun 2020 10:27:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.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 10:27:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:27:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:27:59: 7000000 INFO @ Fri, 26 Jun 2020 10:28:00: 1000000 INFO @ Fri, 26 Jun 2020 10:28:04: 8000000 INFO @ Fri, 26 Jun 2020 10:28:06: 2000000 INFO @ Fri, 26 Jun 2020 10:28:09: 9000000 INFO @ Fri, 26 Jun 2020 10:28:11: 3000000 INFO @ Fri, 26 Jun 2020 10:28:14: 10000000 INFO @ Fri, 26 Jun 2020 10:28:16: 4000000 INFO @ Fri, 26 Jun 2020 10:28:19: 11000000 INFO @ Fri, 26 Jun 2020 10:28:21: 5000000 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 10:28:24: 12000000 INFO @ Fri, 26 Jun 2020 10:28:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.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 10:28:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:28:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:28:26: 6000000 INFO @ Fri, 26 Jun 2020 10:28:30: 13000000 INFO @ Fri, 26 Jun 2020 10:28:31: 1000000 INFO @ Fri, 26 Jun 2020 10:28:32: 7000000 INFO @ Fri, 26 Jun 2020 10:28:35: 14000000 INFO @ Fri, 26 Jun 2020 10:28:37: 8000000 INFO @ Fri, 26 Jun 2020 10:28:37: 2000000 INFO @ Fri, 26 Jun 2020 10:28:40: 15000000 INFO @ Fri, 26 Jun 2020 10:28:43: 9000000 INFO @ Fri, 26 Jun 2020 10:28:44: 3000000 INFO @ Fri, 26 Jun 2020 10:28:46: 16000000 INFO @ Fri, 26 Jun 2020 10:28:48: 10000000 INFO @ Fri, 26 Jun 2020 10:28:50: 4000000 INFO @ Fri, 26 Jun 2020 10:28:51: 17000000 INFO @ Fri, 26 Jun 2020 10:28:53: 11000000 INFO @ Fri, 26 Jun 2020 10:28:56: 5000000 INFO @ Fri, 26 Jun 2020 10:28:57: 18000000 INFO @ Fri, 26 Jun 2020 10:28:59: 12000000 INFO @ Fri, 26 Jun 2020 10:29:02: 19000000 INFO @ Fri, 26 Jun 2020 10:29:02: 6000000 INFO @ Fri, 26 Jun 2020 10:29:04: 13000000 INFO @ Fri, 26 Jun 2020 10:29:07: 20000000 INFO @ Fri, 26 Jun 2020 10:29:08: 7000000 INFO @ Fri, 26 Jun 2020 10:29:10: 14000000 INFO @ Fri, 26 Jun 2020 10:29:13: 21000000 INFO @ Fri, 26 Jun 2020 10:29:15: 8000000 INFO @ Fri, 26 Jun 2020 10:29:15: 15000000 INFO @ Fri, 26 Jun 2020 10:29:18: 22000000 INFO @ Fri, 26 Jun 2020 10:29:21: 16000000 INFO @ Fri, 26 Jun 2020 10:29:21: 9000000 INFO @ Fri, 26 Jun 2020 10:29:23: 23000000 INFO @ Fri, 26 Jun 2020 10:29:24: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 10:29:24: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 10:29:24: #1 total tags in treatment: 11295282 INFO @ Fri, 26 Jun 2020 10:29:24: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:29:24: #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 10:29:24: #1 tags after filtering in treatment: 10450932 INFO @ Fri, 26 Jun 2020 10:29:24: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 10:29:24: #1 finished! INFO @ Fri, 26 Jun 2020 10:29:24: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:29:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:29:25: #2 number of paired peaks: 1137 INFO @ Fri, 26 Jun 2020 10:29:25: start model_add_line... INFO @ Fri, 26 Jun 2020 10:29:25: start X-correlation... INFO @ Fri, 26 Jun 2020 10:29:25: end of X-cor INFO @ Fri, 26 Jun 2020 10:29:25: #2 finished! INFO @ Fri, 26 Jun 2020 10:29:25: #2 predicted fragment length is 131 bps INFO @ Fri, 26 Jun 2020 10:29:25: #2 alternative fragment length(s) may be 131 bps INFO @ Fri, 26 Jun 2020 10:29:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.05_model.r INFO @ Fri, 26 Jun 2020 10:29:25: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:29:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:29:26: 17000000 INFO @ Fri, 26 Jun 2020 10:29:27: 10000000 INFO @ Fri, 26 Jun 2020 10:29:32: 18000000 INFO @ Fri, 26 Jun 2020 10:29:34: 11000000 INFO @ Fri, 26 Jun 2020 10:29:37: 19000000 INFO @ Fri, 26 Jun 2020 10:29:40: 12000000 INFO @ Fri, 26 Jun 2020 10:29:43: 20000000 INFO @ Fri, 26 Jun 2020 10:29:47: 13000000 INFO @ Fri, 26 Jun 2020 10:29:48: 21000000 INFO @ Fri, 26 Jun 2020 10:29:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:29:53: 14000000 INFO @ Fri, 26 Jun 2020 10:29:54: 22000000 INFO @ Fri, 26 Jun 2020 10:29:59: 23000000 INFO @ Fri, 26 Jun 2020 10:30:00: 15000000 INFO @ Fri, 26 Jun 2020 10:30:00: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 10:30:00: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 10:30:00: #1 total tags in treatment: 11295282 INFO @ Fri, 26 Jun 2020 10:30:00: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:30:00: #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 10:30:00: #1 tags after filtering in treatment: 10450932 INFO @ Fri, 26 Jun 2020 10:30:00: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 10:30:00: #1 finished! INFO @ Fri, 26 Jun 2020 10:30:00: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:30:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:30:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.05_peaks.xls INFO @ Fri, 26 Jun 2020 10:30:01: #2 number of paired peaks: 1137 INFO @ Fri, 26 Jun 2020 10:30:01: start model_add_line... INFO @ Fri, 26 Jun 2020 10:30:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:30:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.05_summits.bed INFO @ Fri, 26 Jun 2020 10:30:01: Done! INFO @ Fri, 26 Jun 2020 10:30:01: start X-correlation... INFO @ Fri, 26 Jun 2020 10:30:01: end of X-cor INFO @ Fri, 26 Jun 2020 10:30:01: #2 finished! INFO @ Fri, 26 Jun 2020 10:30:01: #2 predicted fragment length is 131 bps INFO @ Fri, 26 Jun 2020 10:30:01: #2 alternative fragment length(s) may be 131 bps INFO @ Fri, 26 Jun 2020 10:30:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.10_model.r INFO @ Fri, 26 Jun 2020 10:30:01: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:30:01: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6610 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:30:06: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 10:30:12: 17000000 INFO @ Fri, 26 Jun 2020 10:30:18: 18000000 INFO @ Fri, 26 Jun 2020 10:30:25: 19000000 INFO @ Fri, 26 Jun 2020 10:30:26: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:30:31: 20000000 INFO @ Fri, 26 Jun 2020 10:30:37: 21000000 INFO @ Fri, 26 Jun 2020 10:30:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.10_peaks.xls INFO @ Fri, 26 Jun 2020 10:30:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:30:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.10_summits.bed INFO @ Fri, 26 Jun 2020 10:30:38: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3876 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:30:43: 22000000 INFO @ Fri, 26 Jun 2020 10:30:48: 23000000 INFO @ Fri, 26 Jun 2020 10:30:50: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 10:30:50: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 10:30:50: #1 total tags in treatment: 11295282 INFO @ Fri, 26 Jun 2020 10:30:50: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:30:50: #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 10:30:50: #1 tags after filtering in treatment: 10450932 INFO @ Fri, 26 Jun 2020 10:30:50: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 10:30:50: #1 finished! INFO @ Fri, 26 Jun 2020 10:30:50: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:30:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:30:51: #2 number of paired peaks: 1137 INFO @ Fri, 26 Jun 2020 10:30:51: start model_add_line... INFO @ Fri, 26 Jun 2020 10:30:51: start X-correlation... INFO @ Fri, 26 Jun 2020 10:30:51: end of X-cor INFO @ Fri, 26 Jun 2020 10:30:51: #2 finished! INFO @ Fri, 26 Jun 2020 10:30:51: #2 predicted fragment length is 131 bps INFO @ Fri, 26 Jun 2020 10:30:51: #2 alternative fragment length(s) may be 131 bps INFO @ Fri, 26 Jun 2020 10:30:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.20_model.r INFO @ Fri, 26 Jun 2020 10:30:51: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:30:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 10:31:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:31:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.20_peaks.xls INFO @ Fri, 26 Jun 2020 10:31:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:31:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749043/SRX749043.20_summits.bed INFO @ Fri, 26 Jun 2020 10:31:27: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2047 records, 4 fields): 4 millis CompletedMACS2peakCalling