Job ID = 6626524 SRX = SRX5736498 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15035971 spots for SRR8956909/SRR8956909.sra Written 15035971 spots for SRR8956909/SRR8956909.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626742 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:39:42 15035971 reads; of these: 15035971 (100.00%) were paired; of these: 5521456 (36.72%) aligned concordantly 0 times 6091907 (40.52%) aligned concordantly exactly 1 time 3422608 (22.76%) aligned concordantly >1 times ---- 5521456 pairs aligned concordantly 0 times; of these: 749832 (13.58%) aligned discordantly 1 time ---- 4771624 pairs aligned 0 times concordantly or discordantly; of these: 9543248 mates make up the pairs; of these: 7830511 (82.05%) aligned 0 times 500127 (5.24%) aligned exactly 1 time 1212610 (12.71%) aligned >1 times 73.96% overall alignment rate Time searching: 00:39:42 Overall time: 00:39:42 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] 2995065 / 10250330 = 0.2922 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 @ Tue, 14 Jul 2020 08:06:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.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 @ Tue, 14 Jul 2020 08:06:46: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:06:46: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:06:52: 1000000 INFO @ Tue, 14 Jul 2020 08:06:57: 2000000 INFO @ Tue, 14 Jul 2020 08:07:02: 3000000 INFO @ Tue, 14 Jul 2020 08:07:07: 4000000 INFO @ Tue, 14 Jul 2020 08:07:13: 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 @ Tue, 14 Jul 2020 08:07:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.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 @ Tue, 14 Jul 2020 08:07:16: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:07:16: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:07:18: 6000000 INFO @ Tue, 14 Jul 2020 08:07:23: 1000000 INFO @ Tue, 14 Jul 2020 08:07:24: 7000000 INFO @ Tue, 14 Jul 2020 08:07:29: 2000000 INFO @ Tue, 14 Jul 2020 08:07:29: 8000000 INFO @ Tue, 14 Jul 2020 08:07:34: 3000000 INFO @ Tue, 14 Jul 2020 08:07:35: 9000000 INFO @ Tue, 14 Jul 2020 08:07:40: 4000000 INFO @ Tue, 14 Jul 2020 08:07:40: 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 @ Tue, 14 Jul 2020 08:07:46: 11000000 INFO @ Tue, 14 Jul 2020 08:07:46: 5000000 INFO @ Tue, 14 Jul 2020 08:07:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.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 @ Tue, 14 Jul 2020 08:07:46: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:07:46: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:07:51: 12000000 INFO @ Tue, 14 Jul 2020 08:07:52: 6000000 INFO @ Tue, 14 Jul 2020 08:07:53: 1000000 INFO @ Tue, 14 Jul 2020 08:07:56: 13000000 INFO @ Tue, 14 Jul 2020 08:07:58: 7000000 INFO @ Tue, 14 Jul 2020 08:07:59: 2000000 INFO @ Tue, 14 Jul 2020 08:08:02: 14000000 INFO @ Tue, 14 Jul 2020 08:08:04: 8000000 INFO @ Tue, 14 Jul 2020 08:08:06: 3000000 INFO @ Tue, 14 Jul 2020 08:08:07: 15000000 INFO @ Tue, 14 Jul 2020 08:08:10: 9000000 INFO @ Tue, 14 Jul 2020 08:08:12: 4000000 INFO @ Tue, 14 Jul 2020 08:08:13: 16000000 INFO @ Tue, 14 Jul 2020 08:08:14: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:08:14: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:08:14: #1 total tags in treatment: 6718693 INFO @ Tue, 14 Jul 2020 08:08:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:08:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:08:14: #1 tags after filtering in treatment: 6129633 INFO @ Tue, 14 Jul 2020 08:08:14: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 14 Jul 2020 08:08:14: #1 finished! INFO @ Tue, 14 Jul 2020 08:08:14: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:08:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:08:15: #2 number of paired peaks: 1098 INFO @ Tue, 14 Jul 2020 08:08:15: start model_add_line... INFO @ Tue, 14 Jul 2020 08:08:15: start X-correlation... INFO @ Tue, 14 Jul 2020 08:08:15: end of X-cor INFO @ Tue, 14 Jul 2020 08:08:15: #2 finished! INFO @ Tue, 14 Jul 2020 08:08:15: #2 predicted fragment length is 260 bps INFO @ Tue, 14 Jul 2020 08:08:15: #2 alternative fragment length(s) may be 260 bps INFO @ Tue, 14 Jul 2020 08:08:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.05_model.r INFO @ Tue, 14 Jul 2020 08:08:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:08:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:08:15: 10000000 INFO @ Tue, 14 Jul 2020 08:08:18: 5000000 INFO @ Tue, 14 Jul 2020 08:08:21: 11000000 INFO @ Tue, 14 Jul 2020 08:08:25: 6000000 INFO @ Tue, 14 Jul 2020 08:08:27: 12000000 INFO @ Tue, 14 Jul 2020 08:08:29: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:08:31: 7000000 INFO @ Tue, 14 Jul 2020 08:08:32: 13000000 INFO @ Tue, 14 Jul 2020 08:08:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:08:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:08:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.05_summits.bed INFO @ Tue, 14 Jul 2020 08:08:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7080 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:08:37: 8000000 INFO @ Tue, 14 Jul 2020 08:08:38: 14000000 INFO @ Tue, 14 Jul 2020 08:08:43: 15000000 INFO @ Tue, 14 Jul 2020 08:08:44: 9000000 INFO @ Tue, 14 Jul 2020 08:08:49: 16000000 INFO @ Tue, 14 Jul 2020 08:08:50: 10000000 INFO @ Tue, 14 Jul 2020 08:08:50: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:08:50: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:08:50: #1 total tags in treatment: 6718693 INFO @ Tue, 14 Jul 2020 08:08:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:08:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:08:50: #1 tags after filtering in treatment: 6129633 INFO @ Tue, 14 Jul 2020 08:08:50: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 14 Jul 2020 08:08:50: #1 finished! INFO @ Tue, 14 Jul 2020 08:08:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:08:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:08:51: #2 number of paired peaks: 1098 INFO @ Tue, 14 Jul 2020 08:08:51: start model_add_line... INFO @ Tue, 14 Jul 2020 08:08:51: start X-correlation... INFO @ Tue, 14 Jul 2020 08:08:51: end of X-cor INFO @ Tue, 14 Jul 2020 08:08:51: #2 finished! INFO @ Tue, 14 Jul 2020 08:08:51: #2 predicted fragment length is 260 bps INFO @ Tue, 14 Jul 2020 08:08:51: #2 alternative fragment length(s) may be 260 bps INFO @ Tue, 14 Jul 2020 08:08:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.10_model.r INFO @ Tue, 14 Jul 2020 08:08:51: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:08:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:08:56: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:09:02: 12000000 INFO @ Tue, 14 Jul 2020 08:09:05: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:09:08: 13000000 INFO @ Tue, 14 Jul 2020 08:09:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:09:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:09:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.10_summits.bed INFO @ Tue, 14 Jul 2020 08:09:12: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3840 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:09:14: 14000000 INFO @ Tue, 14 Jul 2020 08:09:20: 15000000 INFO @ Tue, 14 Jul 2020 08:09:25: 16000000 INFO @ Tue, 14 Jul 2020 08:09:27: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:09:27: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:09:27: #1 total tags in treatment: 6718693 INFO @ Tue, 14 Jul 2020 08:09:27: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:09:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:09:27: #1 tags after filtering in treatment: 6129633 INFO @ Tue, 14 Jul 2020 08:09:27: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 14 Jul 2020 08:09:27: #1 finished! INFO @ Tue, 14 Jul 2020 08:09:27: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:09:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:09:27: #2 number of paired peaks: 1098 INFO @ Tue, 14 Jul 2020 08:09:27: start model_add_line... INFO @ Tue, 14 Jul 2020 08:09:27: start X-correlation... INFO @ Tue, 14 Jul 2020 08:09:28: end of X-cor INFO @ Tue, 14 Jul 2020 08:09:28: #2 finished! INFO @ Tue, 14 Jul 2020 08:09:28: #2 predicted fragment length is 260 bps INFO @ Tue, 14 Jul 2020 08:09:28: #2 alternative fragment length(s) may be 260 bps INFO @ Tue, 14 Jul 2020 08:09:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.20_model.r INFO @ Tue, 14 Jul 2020 08:09:28: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:09:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:09:42: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:09:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:09:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:09:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736498/SRX5736498.20_summits.bed INFO @ Tue, 14 Jul 2020 08:09:48: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1463 records, 4 fields): 3 millis CompletedMACS2peakCalling