Job ID = 6498741 SRX = SRX749074 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 'SRR1636802'... 2020-06-26T00:12:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:16:03 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:16:03 prefetch.2.10.7: 1) 'SRR1636802' was downloaded successfully Read 19633255 spots for SRR1636802/SRR1636802.sra Written 19633255 spots for SRR1636802/SRR1636802.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: 00:18:13 19633255 reads; of these: 19633255 (100.00%) were paired; of these: 7741083 (39.43%) aligned concordantly 0 times 9700845 (49.41%) aligned concordantly exactly 1 time 2191327 (11.16%) aligned concordantly >1 times ---- 7741083 pairs aligned concordantly 0 times; of these: 10995 (0.14%) aligned discordantly 1 time ---- 7730088 pairs aligned 0 times concordantly or discordantly; of these: 15460176 mates make up the pairs; of these: 15205365 (98.35%) aligned 0 times 192301 (1.24%) aligned exactly 1 time 62510 (0.40%) aligned >1 times 61.28% overall alignment rate Time searching: 00:18:13 Overall time: 00:18:13 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] 3407574 / 11894552 = 0.2865 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 09:42:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.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 09:42:27: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:42:27: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:42:33: 1000000 INFO @ Fri, 26 Jun 2020 09:42:38: 2000000 INFO @ Fri, 26 Jun 2020 09:42:44: 3000000 INFO @ Fri, 26 Jun 2020 09:42:49: 4000000 INFO @ Fri, 26 Jun 2020 09:42:54: 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 09:42:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.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 09:42:57: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:42:57: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:43:00: 6000000 INFO @ Fri, 26 Jun 2020 09:43:02: 1000000 INFO @ Fri, 26 Jun 2020 09:43:06: 7000000 INFO @ Fri, 26 Jun 2020 09:43:07: 2000000 INFO @ Fri, 26 Jun 2020 09:43:11: 8000000 INFO @ Fri, 26 Jun 2020 09:43:12: 3000000 INFO @ Fri, 26 Jun 2020 09:43:16: 4000000 INFO @ Fri, 26 Jun 2020 09:43:17: 9000000 INFO @ Fri, 26 Jun 2020 09:43:21: 5000000 INFO @ Fri, 26 Jun 2020 09:43:22: 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 09:43:26: 6000000 INFO @ Fri, 26 Jun 2020 09:43:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.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 09:43:28: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:43:28: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:43:28: 11000000 INFO @ Fri, 26 Jun 2020 09:43:31: 7000000 INFO @ Fri, 26 Jun 2020 09:43:33: 1000000 INFO @ Fri, 26 Jun 2020 09:43:34: 12000000 INFO @ Fri, 26 Jun 2020 09:43:36: 8000000 INFO @ Fri, 26 Jun 2020 09:43:38: 2000000 INFO @ Fri, 26 Jun 2020 09:43:40: 13000000 INFO @ Fri, 26 Jun 2020 09:43:40: 9000000 INFO @ Fri, 26 Jun 2020 09:43:42: 3000000 INFO @ Fri, 26 Jun 2020 09:43:45: 10000000 INFO @ Fri, 26 Jun 2020 09:43:45: 14000000 INFO @ Fri, 26 Jun 2020 09:43:47: 4000000 INFO @ Fri, 26 Jun 2020 09:43:50: 11000000 INFO @ Fri, 26 Jun 2020 09:43:51: 15000000 INFO @ Fri, 26 Jun 2020 09:43:52: 5000000 INFO @ Fri, 26 Jun 2020 09:43:55: 12000000 INFO @ Fri, 26 Jun 2020 09:43:57: 16000000 INFO @ Fri, 26 Jun 2020 09:43:57: 6000000 INFO @ Fri, 26 Jun 2020 09:43:59: 13000000 INFO @ Fri, 26 Jun 2020 09:44:02: 7000000 INFO @ Fri, 26 Jun 2020 09:44:02: 17000000 INFO @ Fri, 26 Jun 2020 09:44:04: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:44:04: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:44:04: #1 total tags in treatment: 8485723 INFO @ Fri, 26 Jun 2020 09:44:04: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:44:04: #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 09:44:04: #1 tags after filtering in treatment: 7321835 INFO @ Fri, 26 Jun 2020 09:44:04: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 26 Jun 2020 09:44:04: #1 finished! INFO @ Fri, 26 Jun 2020 09:44:04: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:44:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:44:04: 14000000 INFO @ Fri, 26 Jun 2020 09:44:04: #2 number of paired peaks: 1924 INFO @ Fri, 26 Jun 2020 09:44:04: start model_add_line... INFO @ Fri, 26 Jun 2020 09:44:04: start X-correlation... INFO @ Fri, 26 Jun 2020 09:44:04: end of X-cor INFO @ Fri, 26 Jun 2020 09:44:04: #2 finished! INFO @ Fri, 26 Jun 2020 09:44:04: #2 predicted fragment length is 139 bps INFO @ Fri, 26 Jun 2020 09:44:04: #2 alternative fragment length(s) may be 139 bps INFO @ Fri, 26 Jun 2020 09:44:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.05_model.r INFO @ Fri, 26 Jun 2020 09:44:04: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:44:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:44:06: 8000000 INFO @ Fri, 26 Jun 2020 09:44:09: 15000000 INFO @ Fri, 26 Jun 2020 09:44:11: 9000000 INFO @ Fri, 26 Jun 2020 09:44:14: 16000000 INFO @ Fri, 26 Jun 2020 09:44:16: 10000000 INFO @ Fri, 26 Jun 2020 09:44:18: 17000000 INFO @ Fri, 26 Jun 2020 09:44:20: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:44:20: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:44:20: #1 total tags in treatment: 8485723 INFO @ Fri, 26 Jun 2020 09:44:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:44:20: #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 09:44:20: #1 tags after filtering in treatment: 7321835 INFO @ Fri, 26 Jun 2020 09:44:20: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 26 Jun 2020 09:44:20: #1 finished! INFO @ Fri, 26 Jun 2020 09:44:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:44:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:44:20: #2 number of paired peaks: 1924 INFO @ Fri, 26 Jun 2020 09:44:20: start model_add_line... INFO @ Fri, 26 Jun 2020 09:44:20: start X-correlation... INFO @ Fri, 26 Jun 2020 09:44:20: end of X-cor INFO @ Fri, 26 Jun 2020 09:44:20: #2 finished! INFO @ Fri, 26 Jun 2020 09:44:20: #2 predicted fragment length is 139 bps INFO @ Fri, 26 Jun 2020 09:44:20: #2 alternative fragment length(s) may be 139 bps INFO @ Fri, 26 Jun 2020 09:44:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.10_model.r INFO @ Fri, 26 Jun 2020 09:44:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:44:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:44:21: 11000000 INFO @ Fri, 26 Jun 2020 09:44:22: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:44:25: 12000000 INFO @ Fri, 26 Jun 2020 09:44:30: 13000000 INFO @ Fri, 26 Jun 2020 09:44:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:44:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:44:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.05_summits.bed INFO @ Fri, 26 Jun 2020 09:44:31: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12753 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:44:35: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:44:37: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:44:39: 15000000 INFO @ Fri, 26 Jun 2020 09:44:44: 16000000 INFO @ Fri, 26 Jun 2020 09:44:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:44:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:44:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.10_summits.bed INFO @ Fri, 26 Jun 2020 09:44:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6356 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:44:49: 17000000 INFO @ Fri, 26 Jun 2020 09:44:50: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:44:50: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:44:50: #1 total tags in treatment: 8485723 INFO @ Fri, 26 Jun 2020 09:44:50: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:44:50: #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 09:44:50: #1 tags after filtering in treatment: 7321835 INFO @ Fri, 26 Jun 2020 09:44:50: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 26 Jun 2020 09:44:50: #1 finished! INFO @ Fri, 26 Jun 2020 09:44:50: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:44:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:44:51: #2 number of paired peaks: 1924 INFO @ Fri, 26 Jun 2020 09:44:51: start model_add_line... INFO @ Fri, 26 Jun 2020 09:44:51: start X-correlation... INFO @ Fri, 26 Jun 2020 09:44:51: end of X-cor INFO @ Fri, 26 Jun 2020 09:44:51: #2 finished! INFO @ Fri, 26 Jun 2020 09:44:51: #2 predicted fragment length is 139 bps INFO @ Fri, 26 Jun 2020 09:44:51: #2 alternative fragment length(s) may be 139 bps INFO @ Fri, 26 Jun 2020 09:44:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.20_model.r INFO @ Fri, 26 Jun 2020 09:44:51: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:44:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:45:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:45:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:45:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:45:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749074/SRX749074.20_summits.bed INFO @ Fri, 26 Jun 2020 09:45:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3380 records, 4 fields): 4 millis CompletedMACS2peakCalling