Job ID = 6498448 SRX = SRX511346 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T23:36:30 prefetch.2.10.7: 1) Downloading 'SRR1217608'... 2020-06-25T23:36:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:38:21 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:38:21 prefetch.2.10.7: 'SRR1217608' is valid 2020-06-25T23:38:21 prefetch.2.10.7: 1) 'SRR1217608' was downloaded successfully Read 6249841 spots for SRR1217608/SRR1217608.sra Written 6249841 spots for SRR1217608/SRR1217608.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: 00:11:11 6249841 reads; of these: 6249841 (100.00%) were paired; of these: 1029792 (16.48%) aligned concordantly 0 times 3833833 (61.34%) aligned concordantly exactly 1 time 1386216 (22.18%) aligned concordantly >1 times ---- 1029792 pairs aligned concordantly 0 times; of these: 3216 (0.31%) aligned discordantly 1 time ---- 1026576 pairs aligned 0 times concordantly or discordantly; of these: 2053152 mates make up the pairs; of these: 1909747 (93.02%) aligned 0 times 105054 (5.12%) aligned exactly 1 time 38351 (1.87%) aligned >1 times 84.72% overall alignment rate Time searching: 00:11:11 Overall time: 00:11:11 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 8 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] 513579 / 5219690 = 0.0984 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 08:53:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.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 08:53:19: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:53:19: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:53:24: 1000000 INFO @ Fri, 26 Jun 2020 08:53:30: 2000000 INFO @ Fri, 26 Jun 2020 08:53:35: 3000000 INFO @ Fri, 26 Jun 2020 08:53:40: 4000000 INFO @ Fri, 26 Jun 2020 08:53:46: 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 08:53:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.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 08:53:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:53:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:53:51: 6000000 INFO @ Fri, 26 Jun 2020 08:53:55: 1000000 INFO @ Fri, 26 Jun 2020 08:53:57: 7000000 INFO @ Fri, 26 Jun 2020 08:54:00: 2000000 INFO @ Fri, 26 Jun 2020 08:54:03: 8000000 INFO @ Fri, 26 Jun 2020 08:54:06: 3000000 INFO @ Fri, 26 Jun 2020 08:54:08: 9000000 INFO @ Fri, 26 Jun 2020 08:54:12: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:54:12: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:54:12: #1 total tags in treatment: 4706684 INFO @ Fri, 26 Jun 2020 08:54:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:54:12: #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 08:54:12: #1 tags after filtering in treatment: 4503277 INFO @ Fri, 26 Jun 2020 08:54:12: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 26 Jun 2020 08:54:12: #1 finished! INFO @ Fri, 26 Jun 2020 08:54:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:54:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:54:12: 4000000 INFO @ Fri, 26 Jun 2020 08:54:12: #2 number of paired peaks: 1152 INFO @ Fri, 26 Jun 2020 08:54:12: start model_add_line... INFO @ Fri, 26 Jun 2020 08:54:12: start X-correlation... INFO @ Fri, 26 Jun 2020 08:54:12: end of X-cor INFO @ Fri, 26 Jun 2020 08:54:12: #2 finished! INFO @ Fri, 26 Jun 2020 08:54:12: #2 predicted fragment length is 151 bps INFO @ Fri, 26 Jun 2020 08:54:12: #2 alternative fragment length(s) may be 151 bps INFO @ Fri, 26 Jun 2020 08:54:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.05_model.r INFO @ Fri, 26 Jun 2020 08:54:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:54:12: #3 Pre-compute pvalue-qvalue table... 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 08:54:17: 5000000 INFO @ Fri, 26 Jun 2020 08:54:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.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 08:54:19: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:54:19: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:54:23: 6000000 INFO @ Fri, 26 Jun 2020 08:54:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:54:25: 1000000 INFO @ Fri, 26 Jun 2020 08:54:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:54:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:54:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.05_summits.bed INFO @ Fri, 26 Jun 2020 08:54:29: Done! INFO @ Fri, 26 Jun 2020 08:54:29: 7000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3687 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:54:31: 2000000 INFO @ Fri, 26 Jun 2020 08:54:35: 8000000 INFO @ Fri, 26 Jun 2020 08:54:37: 3000000 INFO @ Fri, 26 Jun 2020 08:54:41: 9000000 INFO @ Fri, 26 Jun 2020 08:54:43: 4000000 INFO @ Fri, 26 Jun 2020 08:54:44: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:54:44: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:54:44: #1 total tags in treatment: 4706684 INFO @ Fri, 26 Jun 2020 08:54:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:54:44: #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 08:54:44: #1 tags after filtering in treatment: 4503277 INFO @ Fri, 26 Jun 2020 08:54:44: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 26 Jun 2020 08:54:44: #1 finished! INFO @ Fri, 26 Jun 2020 08:54:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:54:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:54:45: #2 number of paired peaks: 1152 INFO @ Fri, 26 Jun 2020 08:54:45: start model_add_line... INFO @ Fri, 26 Jun 2020 08:54:45: start X-correlation... INFO @ Fri, 26 Jun 2020 08:54:45: end of X-cor INFO @ Fri, 26 Jun 2020 08:54:45: #2 finished! INFO @ Fri, 26 Jun 2020 08:54:45: #2 predicted fragment length is 151 bps INFO @ Fri, 26 Jun 2020 08:54:45: #2 alternative fragment length(s) may be 151 bps INFO @ Fri, 26 Jun 2020 08:54:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.10_model.r INFO @ Fri, 26 Jun 2020 08:54:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:54:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:54:48: 5000000 INFO @ Fri, 26 Jun 2020 08:54:54: 6000000 INFO @ Fri, 26 Jun 2020 08:54:56: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:54:59: 7000000 INFO @ Fri, 26 Jun 2020 08:55:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:55:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:55:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.10_summits.bed INFO @ Fri, 26 Jun 2020 08:55:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2353 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:55:05: 8000000 INFO @ Fri, 26 Jun 2020 08:55:10: 9000000 INFO @ Fri, 26 Jun 2020 08:55:13: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:55:13: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:55:13: #1 total tags in treatment: 4706684 INFO @ Fri, 26 Jun 2020 08:55:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:55:13: #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 08:55:13: #1 tags after filtering in treatment: 4503277 INFO @ Fri, 26 Jun 2020 08:55:13: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 26 Jun 2020 08:55:13: #1 finished! INFO @ Fri, 26 Jun 2020 08:55:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:55:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:55:13: #2 number of paired peaks: 1152 INFO @ Fri, 26 Jun 2020 08:55:13: start model_add_line... INFO @ Fri, 26 Jun 2020 08:55:14: start X-correlation... INFO @ Fri, 26 Jun 2020 08:55:14: end of X-cor INFO @ Fri, 26 Jun 2020 08:55:14: #2 finished! INFO @ Fri, 26 Jun 2020 08:55:14: #2 predicted fragment length is 151 bps INFO @ Fri, 26 Jun 2020 08:55:14: #2 alternative fragment length(s) may be 151 bps INFO @ Fri, 26 Jun 2020 08:55:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.20_model.r INFO @ Fri, 26 Jun 2020 08:55:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:55:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:55:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:55:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:55:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:55:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511346/SRX511346.20_summits.bed INFO @ Fri, 26 Jun 2020 08:55:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1257 records, 4 fields): 3 millis CompletedMACS2peakCalling