Job ID = 6527683 SRX = SRX2065447 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T13:49:44 prefetch.2.10.7: 1) Downloading 'SRR4095606'... 2020-06-29T13:49:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:51:23 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:51:23 prefetch.2.10.7: 'SRR4095606' is valid 2020-06-29T13:51:23 prefetch.2.10.7: 1) 'SRR4095606' was downloaded successfully 2020-06-29T13:51:23 prefetch.2.10.7: 'SRR4095606' has 0 unresolved dependencies Read 4638126 spots for SRR4095606/SRR4095606.sra Written 4638126 spots for SRR4095606/SRR4095606.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: 00:06:14 4638126 reads; of these: 4638126 (100.00%) were paired; of these: 903320 (19.48%) aligned concordantly 0 times 2816179 (60.72%) aligned concordantly exactly 1 time 918627 (19.81%) aligned concordantly >1 times ---- 903320 pairs aligned concordantly 0 times; of these: 44449 (4.92%) aligned discordantly 1 time ---- 858871 pairs aligned 0 times concordantly or discordantly; of these: 1717742 mates make up the pairs; of these: 1410658 (82.12%) aligned 0 times 199021 (11.59%) aligned exactly 1 time 108063 (6.29%) aligned >1 times 84.79% overall alignment rate Time searching: 00:06:14 Overall time: 00:06:14 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_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] 3206071 / 3777648 = 0.8487 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 @ Mon, 29 Jun 2020 23:02:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.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 @ Mon, 29 Jun 2020 23:02:18: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:02:18: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:02:23: 1000000 INFO @ Mon, 29 Jun 2020 23:02:25: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:02:25: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:02:25: #1 total tags in treatment: 556259 INFO @ Mon, 29 Jun 2020 23:02:25: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:02:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:02:25: #1 tags after filtering in treatment: 441467 INFO @ Mon, 29 Jun 2020 23:02:25: #1 Redundant rate of treatment: 0.21 INFO @ Mon, 29 Jun 2020 23:02:25: #1 finished! INFO @ Mon, 29 Jun 2020 23:02:25: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:02:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:02:26: #2 number of paired peaks: 1917 INFO @ Mon, 29 Jun 2020 23:02:26: start model_add_line... INFO @ Mon, 29 Jun 2020 23:02:26: start X-correlation... INFO @ Mon, 29 Jun 2020 23:02:26: end of X-cor INFO @ Mon, 29 Jun 2020 23:02:26: #2 finished! INFO @ Mon, 29 Jun 2020 23:02:26: #2 predicted fragment length is 208 bps INFO @ Mon, 29 Jun 2020 23:02:26: #2 alternative fragment length(s) may be 4,208 bps INFO @ Mon, 29 Jun 2020 23:02:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.05_model.r INFO @ Mon, 29 Jun 2020 23:02:26: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:02:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:02:27: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:02:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:02:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:02:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.05_summits.bed INFO @ Mon, 29 Jun 2020 23:02:27: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (100 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Mon, 29 Jun 2020 23:02:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.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 @ Mon, 29 Jun 2020 23:02:48: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:02:48: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:02:53: 1000000 INFO @ Mon, 29 Jun 2020 23:02:55: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:02:55: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:02:55: #1 total tags in treatment: 556259 INFO @ Mon, 29 Jun 2020 23:02:55: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:02:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:02:55: #1 tags after filtering in treatment: 441467 INFO @ Mon, 29 Jun 2020 23:02:55: #1 Redundant rate of treatment: 0.21 INFO @ Mon, 29 Jun 2020 23:02:55: #1 finished! INFO @ Mon, 29 Jun 2020 23:02:55: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:02:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:02:56: #2 number of paired peaks: 1917 INFO @ Mon, 29 Jun 2020 23:02:56: start model_add_line... INFO @ Mon, 29 Jun 2020 23:02:56: start X-correlation... INFO @ Mon, 29 Jun 2020 23:02:56: end of X-cor INFO @ Mon, 29 Jun 2020 23:02:56: #2 finished! INFO @ Mon, 29 Jun 2020 23:02:56: #2 predicted fragment length is 208 bps INFO @ Mon, 29 Jun 2020 23:02:56: #2 alternative fragment length(s) may be 4,208 bps INFO @ Mon, 29 Jun 2020 23:02:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.10_model.r INFO @ Mon, 29 Jun 2020 23:02:56: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:02:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:02:57: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:02:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:02:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:02:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.10_summits.bed INFO @ Mon, 29 Jun 2020 23:02:57: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (10 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Mon, 29 Jun 2020 23:03:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.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 @ Mon, 29 Jun 2020 23:03:18: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:03:18: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:03:23: 1000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:03:26: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:03:26: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:03:26: #1 total tags in treatment: 556259 INFO @ Mon, 29 Jun 2020 23:03:26: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:03:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:03:26: #1 tags after filtering in treatment: 441467 INFO @ Mon, 29 Jun 2020 23:03:26: #1 Redundant rate of treatment: 0.21 INFO @ Mon, 29 Jun 2020 23:03:26: #1 finished! INFO @ Mon, 29 Jun 2020 23:03:26: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:03:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:03:26: #2 number of paired peaks: 1917 INFO @ Mon, 29 Jun 2020 23:03:26: start model_add_line... INFO @ Mon, 29 Jun 2020 23:03:26: start X-correlation... INFO @ Mon, 29 Jun 2020 23:03:26: end of X-cor INFO @ Mon, 29 Jun 2020 23:03:26: #2 finished! INFO @ Mon, 29 Jun 2020 23:03:26: #2 predicted fragment length is 208 bps INFO @ Mon, 29 Jun 2020 23:03:26: #2 alternative fragment length(s) may be 4,208 bps INFO @ Mon, 29 Jun 2020 23:03:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.20_model.r INFO @ Mon, 29 Jun 2020 23:03:26: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:03:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:03:27: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:03:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:03:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:03:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2065447/SRX2065447.20_summits.bed INFO @ Mon, 29 Jun 2020 23:03:27: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling