Job ID = 6498742 SRX = SRX749078 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T23:55:15 prefetch.2.10.7: 1) Downloading 'SRR1636806'... 2020-06-25T23:55:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:58:31 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:58:31 prefetch.2.10.7: 1) 'SRR1636806' was downloaded successfully Read 13077613 spots for SRR1636806/SRR1636806.sra Written 13077613 spots for SRR1636806/SRR1636806.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:28:07 13077613 reads; of these: 13077613 (100.00%) were paired; of these: 1569463 (12.00%) aligned concordantly 0 times 8151950 (62.34%) aligned concordantly exactly 1 time 3356200 (25.66%) aligned concordantly >1 times ---- 1569463 pairs aligned concordantly 0 times; of these: 5636 (0.36%) aligned discordantly 1 time ---- 1563827 pairs aligned 0 times concordantly or discordantly; of these: 3127654 mates make up the pairs; of these: 2836205 (90.68%) aligned 0 times 212115 (6.78%) aligned exactly 1 time 79334 (2.54%) aligned >1 times 89.16% overall alignment rate Time searching: 00:28:08 Overall time: 00:28:08 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] 4020460 / 11502983 = 0.3495 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 09:34:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.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 09:34:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:34:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:34:48: 1000000 INFO @ Fri, 26 Jun 2020 09:34:54: 2000000 INFO @ Fri, 26 Jun 2020 09:35:00: 3000000 INFO @ Fri, 26 Jun 2020 09:35:05: 4000000 INFO @ Fri, 26 Jun 2020 09:35:11: 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 09:35:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.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 09:35:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:35:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:35:16: 6000000 INFO @ Fri, 26 Jun 2020 09:35:19: 1000000 INFO @ Fri, 26 Jun 2020 09:35:22: 7000000 INFO @ Fri, 26 Jun 2020 09:35:25: 2000000 INFO @ Fri, 26 Jun 2020 09:35:28: 8000000 INFO @ Fri, 26 Jun 2020 09:35:32: 3000000 INFO @ Fri, 26 Jun 2020 09:35:34: 9000000 INFO @ Fri, 26 Jun 2020 09:35:38: 4000000 INFO @ Fri, 26 Jun 2020 09:35:40: 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 09:35:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.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 09:35:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:35:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:35:44: 5000000 INFO @ Fri, 26 Jun 2020 09:35:46: 11000000 INFO @ Fri, 26 Jun 2020 09:35:49: 1000000 INFO @ Fri, 26 Jun 2020 09:35:50: 6000000 INFO @ Fri, 26 Jun 2020 09:35:52: 12000000 INFO @ Fri, 26 Jun 2020 09:35:55: 2000000 INFO @ Fri, 26 Jun 2020 09:35:56: 7000000 INFO @ Fri, 26 Jun 2020 09:35:58: 13000000 INFO @ Fri, 26 Jun 2020 09:36:01: 3000000 INFO @ Fri, 26 Jun 2020 09:36:02: 8000000 INFO @ Fri, 26 Jun 2020 09:36:04: 14000000 INFO @ Fri, 26 Jun 2020 09:36:07: 4000000 INFO @ Fri, 26 Jun 2020 09:36:08: 9000000 INFO @ Fri, 26 Jun 2020 09:36:10: 15000000 INFO @ Fri, 26 Jun 2020 09:36:12: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:36:12: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:36:12: #1 total tags in treatment: 7489008 INFO @ Fri, 26 Jun 2020 09:36:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:36:12: #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 09:36:12: #1 tags after filtering in treatment: 6984792 INFO @ Fri, 26 Jun 2020 09:36:12: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 09:36:12: #1 finished! INFO @ Fri, 26 Jun 2020 09:36:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:36:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:36:13: #2 number of paired peaks: 1134 INFO @ Fri, 26 Jun 2020 09:36:13: start model_add_line... INFO @ Fri, 26 Jun 2020 09:36:13: start X-correlation... INFO @ Fri, 26 Jun 2020 09:36:13: end of X-cor INFO @ Fri, 26 Jun 2020 09:36:13: #2 finished! INFO @ Fri, 26 Jun 2020 09:36:13: #2 predicted fragment length is 129 bps INFO @ Fri, 26 Jun 2020 09:36:13: #2 alternative fragment length(s) may be 129 bps INFO @ Fri, 26 Jun 2020 09:36:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.05_model.r INFO @ Fri, 26 Jun 2020 09:36:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:36:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:36:14: 5000000 INFO @ Fri, 26 Jun 2020 09:36:15: 10000000 INFO @ Fri, 26 Jun 2020 09:36:20: 6000000 INFO @ Fri, 26 Jun 2020 09:36:21: 11000000 INFO @ Fri, 26 Jun 2020 09:36:26: 7000000 INFO @ Fri, 26 Jun 2020 09:36:27: 12000000 INFO @ Fri, 26 Jun 2020 09:36:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:36:31: 8000000 INFO @ Fri, 26 Jun 2020 09:36:33: 13000000 INFO @ Fri, 26 Jun 2020 09:36:37: 9000000 INFO @ Fri, 26 Jun 2020 09:36:39: 14000000 INFO @ Fri, 26 Jun 2020 09:36:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:36:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:36:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.05_summits.bed INFO @ Fri, 26 Jun 2020 09:36:40: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5667 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:36:43: 10000000 INFO @ Fri, 26 Jun 2020 09:36:45: 15000000 INFO @ Fri, 26 Jun 2020 09:36:47: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:36:47: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:36:47: #1 total tags in treatment: 7489008 INFO @ Fri, 26 Jun 2020 09:36:47: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:36:47: #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 09:36:47: #1 tags after filtering in treatment: 6984792 INFO @ Fri, 26 Jun 2020 09:36:47: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 09:36:47: #1 finished! INFO @ Fri, 26 Jun 2020 09:36:47: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:36:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:36:47: #2 number of paired peaks: 1134 INFO @ Fri, 26 Jun 2020 09:36:47: start model_add_line... INFO @ Fri, 26 Jun 2020 09:36:48: start X-correlation... INFO @ Fri, 26 Jun 2020 09:36:48: end of X-cor INFO @ Fri, 26 Jun 2020 09:36:48: #2 finished! INFO @ Fri, 26 Jun 2020 09:36:48: #2 predicted fragment length is 129 bps INFO @ Fri, 26 Jun 2020 09:36:48: #2 alternative fragment length(s) may be 129 bps INFO @ Fri, 26 Jun 2020 09:36:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.10_model.r INFO @ Fri, 26 Jun 2020 09:36:48: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:36:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:36:49: 11000000 INFO @ Fri, 26 Jun 2020 09:36:55: 12000000 INFO @ Fri, 26 Jun 2020 09:37:00: 13000000 INFO @ Fri, 26 Jun 2020 09:37:05: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:37:06: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:37:11: 15000000 INFO @ Fri, 26 Jun 2020 09:37:13: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:37:13: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:37:13: #1 total tags in treatment: 7489008 INFO @ Fri, 26 Jun 2020 09:37:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:37:13: #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 09:37:13: #1 tags after filtering in treatment: 6984792 INFO @ Fri, 26 Jun 2020 09:37:13: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 09:37:13: #1 finished! INFO @ Fri, 26 Jun 2020 09:37:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:37:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:37:14: #2 number of paired peaks: 1134 INFO @ Fri, 26 Jun 2020 09:37:14: start model_add_line... INFO @ Fri, 26 Jun 2020 09:37:14: start X-correlation... INFO @ Fri, 26 Jun 2020 09:37:14: end of X-cor INFO @ Fri, 26 Jun 2020 09:37:14: #2 finished! INFO @ Fri, 26 Jun 2020 09:37:14: #2 predicted fragment length is 129 bps INFO @ Fri, 26 Jun 2020 09:37:14: #2 alternative fragment length(s) may be 129 bps INFO @ Fri, 26 Jun 2020 09:37:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.20_model.r INFO @ Fri, 26 Jun 2020 09:37:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:37:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:37:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:37:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:37:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.10_summits.bed INFO @ Fri, 26 Jun 2020 09:37:15: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2927 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:37:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:37:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:37:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:37:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749078/SRX749078.20_summits.bed INFO @ Fri, 26 Jun 2020 09:37:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1144 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。