Job ID = 6497812 SRX = SRX1728715 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:48:27 prefetch.2.10.7: 1) Downloading 'SRR3452732'... 2020-06-25T22:48:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:51:43 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:51:43 prefetch.2.10.7: 1) 'SRR3452732' was downloaded successfully 2020-06-25T22:51:43 prefetch.2.10.7: 'SRR3452732' has 0 unresolved dependencies Read 14027013 spots for SRR3452732/SRR3452732.sra Written 14027013 spots for SRR3452732/SRR3452732.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: 00:23:27 14027013 reads; of these: 14027013 (100.00%) were paired; of these: 1330469 (9.49%) aligned concordantly 0 times 10111753 (72.09%) aligned concordantly exactly 1 time 2584791 (18.43%) aligned concordantly >1 times ---- 1330469 pairs aligned concordantly 0 times; of these: 439681 (33.05%) aligned discordantly 1 time ---- 890788 pairs aligned 0 times concordantly or discordantly; of these: 1781576 mates make up the pairs; of these: 977363 (54.86%) aligned 0 times 508464 (28.54%) aligned exactly 1 time 295749 (16.60%) aligned >1 times 96.52% overall alignment rate Time searching: 00:23:28 Overall time: 00:23:28 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 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] 164465 / 13126948 = 0.0125 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 08:25:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.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 08:25:51: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:25:51: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:25:57: 1000000 INFO @ Fri, 26 Jun 2020 08:26:03: 2000000 INFO @ Fri, 26 Jun 2020 08:26:08: 3000000 INFO @ Fri, 26 Jun 2020 08:26:14: 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 08:26:20: 5000000 INFO @ Fri, 26 Jun 2020 08:26:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.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 08:26:21: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:26:21: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:26:26: 6000000 INFO @ Fri, 26 Jun 2020 08:26:26: 1000000 INFO @ Fri, 26 Jun 2020 08:26:31: 7000000 INFO @ Fri, 26 Jun 2020 08:26:32: 2000000 INFO @ Fri, 26 Jun 2020 08:26:37: 3000000 INFO @ Fri, 26 Jun 2020 08:26:37: 8000000 INFO @ Fri, 26 Jun 2020 08:26:42: 4000000 INFO @ Fri, 26 Jun 2020 08:26:43: 9000000 INFO @ Fri, 26 Jun 2020 08:26:47: 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 08:26:49: 10000000 INFO @ Fri, 26 Jun 2020 08:26:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.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 08:26:51: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:26:51: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:26:53: 6000000 INFO @ Fri, 26 Jun 2020 08:26:55: 11000000 INFO @ Fri, 26 Jun 2020 08:26:57: 1000000 INFO @ Fri, 26 Jun 2020 08:26:58: 7000000 INFO @ Fri, 26 Jun 2020 08:27:01: 12000000 INFO @ Fri, 26 Jun 2020 08:27:03: 2000000 INFO @ Fri, 26 Jun 2020 08:27:04: 8000000 INFO @ Fri, 26 Jun 2020 08:27:07: 13000000 INFO @ Fri, 26 Jun 2020 08:27:09: 9000000 INFO @ Fri, 26 Jun 2020 08:27:09: 3000000 INFO @ Fri, 26 Jun 2020 08:27:14: 14000000 INFO @ Fri, 26 Jun 2020 08:27:15: 10000000 INFO @ Fri, 26 Jun 2020 08:27:15: 4000000 INFO @ Fri, 26 Jun 2020 08:27:20: 15000000 INFO @ Fri, 26 Jun 2020 08:27:20: 11000000 INFO @ Fri, 26 Jun 2020 08:27:21: 5000000 INFO @ Fri, 26 Jun 2020 08:27:25: 12000000 INFO @ Fri, 26 Jun 2020 08:27:26: 16000000 INFO @ Fri, 26 Jun 2020 08:27:28: 6000000 INFO @ Fri, 26 Jun 2020 08:27:31: 13000000 INFO @ Fri, 26 Jun 2020 08:27:32: 17000000 INFO @ Fri, 26 Jun 2020 08:27:34: 7000000 INFO @ Fri, 26 Jun 2020 08:27:36: 14000000 INFO @ Fri, 26 Jun 2020 08:27:38: 18000000 INFO @ Fri, 26 Jun 2020 08:27:40: 8000000 INFO @ Fri, 26 Jun 2020 08:27:42: 15000000 INFO @ Fri, 26 Jun 2020 08:27:45: 19000000 INFO @ Fri, 26 Jun 2020 08:27:46: 9000000 INFO @ Fri, 26 Jun 2020 08:27:47: 16000000 INFO @ Fri, 26 Jun 2020 08:27:51: 20000000 INFO @ Fri, 26 Jun 2020 08:27:52: 10000000 INFO @ Fri, 26 Jun 2020 08:27:52: 17000000 INFO @ Fri, 26 Jun 2020 08:27:57: 21000000 INFO @ Fri, 26 Jun 2020 08:27:58: 18000000 INFO @ Fri, 26 Jun 2020 08:27:59: 11000000 INFO @ Fri, 26 Jun 2020 08:28:04: 19000000 INFO @ Fri, 26 Jun 2020 08:28:04: 22000000 INFO @ Fri, 26 Jun 2020 08:28:05: 12000000 INFO @ Fri, 26 Jun 2020 08:28:09: 20000000 INFO @ Fri, 26 Jun 2020 08:28:10: 23000000 INFO @ Fri, 26 Jun 2020 08:28:11: 13000000 INFO @ Fri, 26 Jun 2020 08:28:15: 21000000 INFO @ Fri, 26 Jun 2020 08:28:17: 24000000 INFO @ Fri, 26 Jun 2020 08:28:17: 14000000 INFO @ Fri, 26 Jun 2020 08:28:21: 22000000 INFO @ Fri, 26 Jun 2020 08:28:23: 25000000 INFO @ Fri, 26 Jun 2020 08:28:23: 15000000 INFO @ Fri, 26 Jun 2020 08:28:26: 23000000 INFO @ Fri, 26 Jun 2020 08:28:29: 26000000 INFO @ Fri, 26 Jun 2020 08:28:30: 16000000 INFO @ Fri, 26 Jun 2020 08:28:32: 24000000 INFO @ Fri, 26 Jun 2020 08:28:34: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:28:34: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:28:34: #1 total tags in treatment: 12534296 INFO @ Fri, 26 Jun 2020 08:28:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:28:34: #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 08:28:34: #1 tags after filtering in treatment: 11808217 INFO @ Fri, 26 Jun 2020 08:28:34: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 26 Jun 2020 08:28:34: #1 finished! INFO @ Fri, 26 Jun 2020 08:28:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:28:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:28:35: #2 number of paired peaks: 1014 INFO @ Fri, 26 Jun 2020 08:28:35: start model_add_line... INFO @ Fri, 26 Jun 2020 08:28:35: start X-correlation... INFO @ Fri, 26 Jun 2020 08:28:35: end of X-cor INFO @ Fri, 26 Jun 2020 08:28:35: #2 finished! INFO @ Fri, 26 Jun 2020 08:28:35: #2 predicted fragment length is 192 bps INFO @ Fri, 26 Jun 2020 08:28:35: #2 alternative fragment length(s) may be 4,192 bps INFO @ Fri, 26 Jun 2020 08:28:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.05_model.r INFO @ Fri, 26 Jun 2020 08:28:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:28:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:28:36: 17000000 INFO @ Fri, 26 Jun 2020 08:28:37: 25000000 INFO @ Fri, 26 Jun 2020 08:28:42: 18000000 INFO @ Fri, 26 Jun 2020 08:28:43: 26000000 INFO @ Fri, 26 Jun 2020 08:28:47: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:28:47: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:28:47: #1 total tags in treatment: 12534296 INFO @ Fri, 26 Jun 2020 08:28:47: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:28:47: #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 08:28:47: #1 tags after filtering in treatment: 11808217 INFO @ Fri, 26 Jun 2020 08:28:47: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 26 Jun 2020 08:28:47: #1 finished! INFO @ Fri, 26 Jun 2020 08:28:47: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:28:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:28:48: 19000000 INFO @ Fri, 26 Jun 2020 08:28:48: #2 number of paired peaks: 1014 INFO @ Fri, 26 Jun 2020 08:28:48: start model_add_line... INFO @ Fri, 26 Jun 2020 08:28:49: start X-correlation... INFO @ Fri, 26 Jun 2020 08:28:49: end of X-cor INFO @ Fri, 26 Jun 2020 08:28:49: #2 finished! INFO @ Fri, 26 Jun 2020 08:28:49: #2 predicted fragment length is 192 bps INFO @ Fri, 26 Jun 2020 08:28:49: #2 alternative fragment length(s) may be 4,192 bps INFO @ Fri, 26 Jun 2020 08:28:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.10_model.r INFO @ Fri, 26 Jun 2020 08:28:49: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:28:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:28:54: 20000000 INFO @ Fri, 26 Jun 2020 08:29:00: 21000000 INFO @ Fri, 26 Jun 2020 08:29:05: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:29:06: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:29:12: 23000000 INFO @ Fri, 26 Jun 2020 08:29:18: 24000000 INFO @ Fri, 26 Jun 2020 08:29:20: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:29:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:29:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:29:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.05_summits.bed INFO @ Fri, 26 Jun 2020 08:29:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1882 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:29:24: 25000000 INFO @ Fri, 26 Jun 2020 08:29:30: 26000000 INFO @ Fri, 26 Jun 2020 08:29:34: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:29:34: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:29:34: #1 total tags in treatment: 12534296 INFO @ Fri, 26 Jun 2020 08:29:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:29:34: #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 08:29:35: #1 tags after filtering in treatment: 11808217 INFO @ Fri, 26 Jun 2020 08:29:35: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 26 Jun 2020 08:29:35: #1 finished! INFO @ Fri, 26 Jun 2020 08:29:35: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:29:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:29:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:29:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:29:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.10_summits.bed INFO @ Fri, 26 Jun 2020 08:29:35: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1042 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:29:35: #2 number of paired peaks: 1014 INFO @ Fri, 26 Jun 2020 08:29:35: start model_add_line... INFO @ Fri, 26 Jun 2020 08:29:36: start X-correlation... INFO @ Fri, 26 Jun 2020 08:29:36: end of X-cor INFO @ Fri, 26 Jun 2020 08:29:36: #2 finished! INFO @ Fri, 26 Jun 2020 08:29:36: #2 predicted fragment length is 192 bps INFO @ Fri, 26 Jun 2020 08:29:36: #2 alternative fragment length(s) may be 4,192 bps INFO @ Fri, 26 Jun 2020 08:29:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.20_model.r INFO @ Fri, 26 Jun 2020 08:29:36: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:29:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:30:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:30:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:30:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:30:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1728715/SRX1728715.20_summits.bed INFO @ Fri, 26 Jun 2020 08:30:22: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (557 records, 4 fields): 2 millis CompletedMACS2peakCalling