Job ID = 6498720 SRX = SRX749039 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T23:49:03 prefetch.2.10.7: 1) Downloading 'SRR1636767'... 2020-06-25T23:49:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:54:02 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:54:02 prefetch.2.10.7: 1) 'SRR1636767' was downloaded successfully Read 20077304 spots for SRR1636767/SRR1636767.sra Written 20077304 spots for SRR1636767/SRR1636767.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: 00:21:49 20077304 reads; of these: 20077304 (100.00%) were paired; of these: 8821091 (43.94%) aligned concordantly 0 times 8796575 (43.81%) aligned concordantly exactly 1 time 2459638 (12.25%) aligned concordantly >1 times ---- 8821091 pairs aligned concordantly 0 times; of these: 8498 (0.10%) aligned discordantly 1 time ---- 8812593 pairs aligned 0 times concordantly or discordantly; of these: 17625186 mates make up the pairs; of these: 17394029 (98.69%) aligned 0 times 181721 (1.03%) aligned exactly 1 time 49436 (0.28%) aligned >1 times 56.68% overall alignment rate Time searching: 00:21:49 Overall time: 00:21:49 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] 3259100 / 11256115 = 0.2895 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 09:23:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.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 09:23:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:23:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:23:28: 1000000 INFO @ Fri, 26 Jun 2020 09:23:33: 2000000 INFO @ Fri, 26 Jun 2020 09:23:38: 3000000 INFO @ Fri, 26 Jun 2020 09:23:43: 4000000 INFO @ Fri, 26 Jun 2020 09:23:48: 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 09:23:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.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 09:23:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:23:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:23:53: 6000000 INFO @ Fri, 26 Jun 2020 09:23:58: 1000000 INFO @ Fri, 26 Jun 2020 09:23:59: 7000000 INFO @ Fri, 26 Jun 2020 09:24:04: 2000000 INFO @ Fri, 26 Jun 2020 09:24:04: 8000000 INFO @ Fri, 26 Jun 2020 09:24:09: 3000000 INFO @ Fri, 26 Jun 2020 09:24:09: 9000000 INFO @ Fri, 26 Jun 2020 09:24:14: 4000000 INFO @ Fri, 26 Jun 2020 09:24:15: 10000000 INFO @ Fri, 26 Jun 2020 09:24:20: 5000000 INFO @ Fri, 26 Jun 2020 09:24:20: 11000000 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 09:24:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.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 09:24:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:24:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:24:25: 6000000 INFO @ Fri, 26 Jun 2020 09:24:25: 12000000 INFO @ Fri, 26 Jun 2020 09:24:29: 1000000 INFO @ Fri, 26 Jun 2020 09:24:31: 7000000 INFO @ Fri, 26 Jun 2020 09:24:31: 13000000 INFO @ Fri, 26 Jun 2020 09:24:35: 2000000 INFO @ Fri, 26 Jun 2020 09:24:36: 8000000 INFO @ Fri, 26 Jun 2020 09:24:37: 14000000 INFO @ Fri, 26 Jun 2020 09:24:41: 3000000 INFO @ Fri, 26 Jun 2020 09:24:41: 9000000 INFO @ Fri, 26 Jun 2020 09:24:42: 15000000 INFO @ Fri, 26 Jun 2020 09:24:47: 10000000 INFO @ Fri, 26 Jun 2020 09:24:47: 4000000 INFO @ Fri, 26 Jun 2020 09:24:48: 16000000 INFO @ Fri, 26 Jun 2020 09:24:49: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:24:49: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:24:49: #1 total tags in treatment: 7998154 INFO @ Fri, 26 Jun 2020 09:24:49: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:24:49: #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 09:24:49: #1 tags after filtering in treatment: 6652047 INFO @ Fri, 26 Jun 2020 09:24:49: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 26 Jun 2020 09:24:49: #1 finished! INFO @ Fri, 26 Jun 2020 09:24:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:24:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:24:50: #2 number of paired peaks: 1633 INFO @ Fri, 26 Jun 2020 09:24:50: start model_add_line... INFO @ Fri, 26 Jun 2020 09:24:50: start X-correlation... INFO @ Fri, 26 Jun 2020 09:24:50: end of X-cor INFO @ Fri, 26 Jun 2020 09:24:50: #2 finished! INFO @ Fri, 26 Jun 2020 09:24:50: #2 predicted fragment length is 138 bps INFO @ Fri, 26 Jun 2020 09:24:50: #2 alternative fragment length(s) may be 138 bps INFO @ Fri, 26 Jun 2020 09:24:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.05_model.r INFO @ Fri, 26 Jun 2020 09:24:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:24:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:24:52: 11000000 INFO @ Fri, 26 Jun 2020 09:24:53: 5000000 INFO @ Fri, 26 Jun 2020 09:24:58: 12000000 INFO @ Fri, 26 Jun 2020 09:24:59: 6000000 INFO @ Fri, 26 Jun 2020 09:25:03: 13000000 INFO @ Fri, 26 Jun 2020 09:25:04: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:25:04: 7000000 INFO @ Fri, 26 Jun 2020 09:25:09: 14000000 INFO @ Fri, 26 Jun 2020 09:25:10: 8000000 INFO @ Fri, 26 Jun 2020 09:25:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:25:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:25:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.05_summits.bed INFO @ Fri, 26 Jun 2020 09:25:12: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6644 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:25:14: 15000000 INFO @ Fri, 26 Jun 2020 09:25:15: 9000000 INFO @ Fri, 26 Jun 2020 09:25:19: 16000000 INFO @ Fri, 26 Jun 2020 09:25:20: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:25:20: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:25:20: #1 total tags in treatment: 7998154 INFO @ Fri, 26 Jun 2020 09:25:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:25:20: #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 09:25:20: #1 tags after filtering in treatment: 6652047 INFO @ Fri, 26 Jun 2020 09:25:20: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 26 Jun 2020 09:25:20: #1 finished! INFO @ Fri, 26 Jun 2020 09:25:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:25:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:25:21: 10000000 INFO @ Fri, 26 Jun 2020 09:25:21: #2 number of paired peaks: 1633 INFO @ Fri, 26 Jun 2020 09:25:21: start model_add_line... INFO @ Fri, 26 Jun 2020 09:25:21: start X-correlation... INFO @ Fri, 26 Jun 2020 09:25:21: end of X-cor INFO @ Fri, 26 Jun 2020 09:25:21: #2 finished! INFO @ Fri, 26 Jun 2020 09:25:21: #2 predicted fragment length is 138 bps INFO @ Fri, 26 Jun 2020 09:25:21: #2 alternative fragment length(s) may be 138 bps INFO @ Fri, 26 Jun 2020 09:25:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.10_model.r INFO @ Fri, 26 Jun 2020 09:25:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:25:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:25:26: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:25:32: 12000000 INFO @ Fri, 26 Jun 2020 09:25:36: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:25:37: 13000000 INFO @ Fri, 26 Jun 2020 09:25:42: 14000000 INFO @ Fri, 26 Jun 2020 09:25:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:25:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:25:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.10_summits.bed INFO @ Fri, 26 Jun 2020 09:25:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3850 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:25:47: 15000000 INFO @ Fri, 26 Jun 2020 09:25:53: 16000000 INFO @ Fri, 26 Jun 2020 09:25:54: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:25:54: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:25:54: #1 total tags in treatment: 7998154 INFO @ Fri, 26 Jun 2020 09:25:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:25:54: #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 09:25:54: #1 tags after filtering in treatment: 6652047 INFO @ Fri, 26 Jun 2020 09:25:54: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 26 Jun 2020 09:25:54: #1 finished! INFO @ Fri, 26 Jun 2020 09:25:54: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:25:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:25:55: #2 number of paired peaks: 1633 INFO @ Fri, 26 Jun 2020 09:25:55: start model_add_line... INFO @ Fri, 26 Jun 2020 09:25:55: start X-correlation... INFO @ Fri, 26 Jun 2020 09:25:55: end of X-cor INFO @ Fri, 26 Jun 2020 09:25:55: #2 finished! INFO @ Fri, 26 Jun 2020 09:25:55: #2 predicted fragment length is 138 bps INFO @ Fri, 26 Jun 2020 09:25:55: #2 alternative fragment length(s) may be 138 bps INFO @ Fri, 26 Jun 2020 09:25:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.20_model.r INFO @ Fri, 26 Jun 2020 09:25:55: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:25:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:26:09: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:26:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:26:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:26:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749039/SRX749039.20_summits.bed INFO @ Fri, 26 Jun 2020 09:26:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2258 records, 4 fields): 4 millis CompletedMACS2peakCalling