Job ID = 6497712 SRX = SRX1056723 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:26:47 prefetch.2.10.7: 1) Downloading 'SRR2060657'... 2020-06-25T22:26:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:37:11 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:37:11 prefetch.2.10.7: verifying 'SRR2060657'... 2020-06-25T23:37:11 prefetch.2.10.7: 1) 'SRR2060657' was downloaded successfully Read 173176704 spots for SRR2060657/SRR2060657.sra Written 173176704 spots for SRR2060657/SRR2060657.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: 02:03:36 173176704 reads; of these: 173176704 (100.00%) were paired; of these: 146287101 (84.47%) aligned concordantly 0 times 20071263 (11.59%) aligned concordantly exactly 1 time 6818340 (3.94%) aligned concordantly >1 times ---- 146287101 pairs aligned concordantly 0 times; of these: 393441 (0.27%) aligned discordantly 1 time ---- 145893660 pairs aligned 0 times concordantly or discordantly; of these: 291787320 mates make up the pairs; of these: 289850635 (99.34%) aligned 0 times 1127850 (0.39%) aligned exactly 1 time 808835 (0.28%) aligned >1 times 16.31% overall alignment rate Time searching: 02:03:36 Overall time: 02:03:36 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 24 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] 20876588 / 27230419 = 0.7667 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 11:47:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.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 11:47:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 11:47:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 11:48:06: 1000000 INFO @ Fri, 26 Jun 2020 11:48:15: 2000000 INFO @ Fri, 26 Jun 2020 11:48:24: 3000000 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 11:48:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.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 11:48:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 11:48:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 11:48:33: 4000000 INFO @ Fri, 26 Jun 2020 11:48:35: 1000000 INFO @ Fri, 26 Jun 2020 11:48:42: 5000000 INFO @ Fri, 26 Jun 2020 11:48:44: 2000000 INFO @ Fri, 26 Jun 2020 11:48:51: 6000000 INFO @ Fri, 26 Jun 2020 11:48:52: 3000000 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 11:48:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.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 11:48:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 11:48:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 11:49:00: 7000000 INFO @ Fri, 26 Jun 2020 11:49:01: 4000000 INFO @ Fri, 26 Jun 2020 11:49:05: 1000000 INFO @ Fri, 26 Jun 2020 11:49:09: 8000000 INFO @ Fri, 26 Jun 2020 11:49:10: 5000000 INFO @ Fri, 26 Jun 2020 11:49:14: 2000000 INFO @ Fri, 26 Jun 2020 11:49:18: 6000000 INFO @ Fri, 26 Jun 2020 11:49:19: 9000000 INFO @ Fri, 26 Jun 2020 11:49:23: 3000000 INFO @ Fri, 26 Jun 2020 11:49:27: 7000000 INFO @ Fri, 26 Jun 2020 11:49:28: 10000000 INFO @ Fri, 26 Jun 2020 11:49:32: 4000000 INFO @ Fri, 26 Jun 2020 11:49:36: 8000000 INFO @ Fri, 26 Jun 2020 11:49:37: 11000000 INFO @ Fri, 26 Jun 2020 11:49:40: 5000000 INFO @ Fri, 26 Jun 2020 11:49:44: 9000000 INFO @ Fri, 26 Jun 2020 11:49:46: 12000000 INFO @ Fri, 26 Jun 2020 11:49:49: 6000000 INFO @ Fri, 26 Jun 2020 11:49:53: 10000000 INFO @ Fri, 26 Jun 2020 11:49:55: 13000000 INFO @ Fri, 26 Jun 2020 11:49:57: 7000000 INFO @ Fri, 26 Jun 2020 11:50:02: 11000000 INFO @ Fri, 26 Jun 2020 11:50:05: 14000000 INFO @ Fri, 26 Jun 2020 11:50:06: 8000000 INFO @ Fri, 26 Jun 2020 11:50:10: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 11:50:12: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 11:50:12: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 11:50:12: #1 total tags in treatment: 6247038 INFO @ Fri, 26 Jun 2020 11:50:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 11:50:12: #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 11:50:12: #1 tags after filtering in treatment: 5303683 INFO @ Fri, 26 Jun 2020 11:50:12: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 26 Jun 2020 11:50:12: #1 finished! INFO @ Fri, 26 Jun 2020 11:50:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 11:50:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 11:50:13: #2 number of paired peaks: 6111 INFO @ Fri, 26 Jun 2020 11:50:13: start model_add_line... INFO @ Fri, 26 Jun 2020 11:50:13: start X-correlation... INFO @ Fri, 26 Jun 2020 11:50:13: end of X-cor INFO @ Fri, 26 Jun 2020 11:50:13: #2 finished! INFO @ Fri, 26 Jun 2020 11:50:13: #2 predicted fragment length is 202 bps INFO @ Fri, 26 Jun 2020 11:50:13: #2 alternative fragment length(s) may be 202 bps INFO @ Fri, 26 Jun 2020 11:50:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.05_model.r INFO @ Fri, 26 Jun 2020 11:50:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 11:50:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 11:50:14: 9000000 INFO @ Fri, 26 Jun 2020 11:50:19: 13000000 INFO @ Fri, 26 Jun 2020 11:50:22: 10000000 INFO @ Fri, 26 Jun 2020 11:50:27: 14000000 INFO @ Fri, 26 Jun 2020 11:50:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 11:50:31: 11000000 INFO @ Fri, 26 Jun 2020 11:50:33: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 11:50:33: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 11:50:33: #1 total tags in treatment: 6247038 INFO @ Fri, 26 Jun 2020 11:50:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 11:50:33: #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 11:50:33: #1 tags after filtering in treatment: 5303683 INFO @ Fri, 26 Jun 2020 11:50:33: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 26 Jun 2020 11:50:33: #1 finished! INFO @ Fri, 26 Jun 2020 11:50:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 11:50:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 11:50:34: #2 number of paired peaks: 6111 INFO @ Fri, 26 Jun 2020 11:50:34: start model_add_line... INFO @ Fri, 26 Jun 2020 11:50:34: start X-correlation... INFO @ Fri, 26 Jun 2020 11:50:34: end of X-cor INFO @ Fri, 26 Jun 2020 11:50:34: #2 finished! INFO @ Fri, 26 Jun 2020 11:50:34: #2 predicted fragment length is 202 bps INFO @ Fri, 26 Jun 2020 11:50:34: #2 alternative fragment length(s) may be 202 bps INFO @ Fri, 26 Jun 2020 11:50:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.10_model.r INFO @ Fri, 26 Jun 2020 11:50:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 11:50:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 11:50:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.05_peaks.xls INFO @ Fri, 26 Jun 2020 11:50:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 11:50:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.05_summits.bed INFO @ Fri, 26 Jun 2020 11:50:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10252 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 11:50:39: 12000000 INFO @ Fri, 26 Jun 2020 11:50:47: 13000000 INFO @ Fri, 26 Jun 2020 11:50:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 11:50:54: 14000000 INFO @ Fri, 26 Jun 2020 11:50:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.10_peaks.xls INFO @ Fri, 26 Jun 2020 11:50:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 11:50:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.10_summits.bed INFO @ Fri, 26 Jun 2020 11:50:59: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7000 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 11:51:00: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 11:51:00: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 11:51:00: #1 total tags in treatment: 6247038 INFO @ Fri, 26 Jun 2020 11:51:00: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 11:51:00: #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 11:51:00: #1 tags after filtering in treatment: 5303683 INFO @ Fri, 26 Jun 2020 11:51:00: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 26 Jun 2020 11:51:00: #1 finished! INFO @ Fri, 26 Jun 2020 11:51:00: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 11:51:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 11:51:01: #2 number of paired peaks: 6111 INFO @ Fri, 26 Jun 2020 11:51:01: start model_add_line... INFO @ Fri, 26 Jun 2020 11:51:01: start X-correlation... INFO @ Fri, 26 Jun 2020 11:51:01: end of X-cor INFO @ Fri, 26 Jun 2020 11:51:01: #2 finished! INFO @ Fri, 26 Jun 2020 11:51:01: #2 predicted fragment length is 202 bps INFO @ Fri, 26 Jun 2020 11:51:01: #2 alternative fragment length(s) may be 202 bps INFO @ Fri, 26 Jun 2020 11:51:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.20_model.r INFO @ Fri, 26 Jun 2020 11:51:01: #3 Call peaks... INFO @ Fri, 26 Jun 2020 11:51:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 11:51:17: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 11:51:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.20_peaks.xls INFO @ Fri, 26 Jun 2020 11:51:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 11:51:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1056723/SRX1056723.20_summits.bed INFO @ Fri, 26 Jun 2020 11:51:26: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4222 records, 4 fields): 6 millis CompletedMACS2peakCalling