Job ID = 16439602 SRX = SRX11548836 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11419253 spots for SRR15243007/SRR15243007.sra Written 11419253 spots for SRR15243007/SRR15243007.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439712 ("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: 00:17:19 11419253 reads; of these: 11419253 (100.00%) were paired; of these: 4409620 (38.62%) aligned concordantly 0 times 5601280 (49.05%) aligned concordantly exactly 1 time 1408353 (12.33%) aligned concordantly >1 times ---- 4409620 pairs aligned concordantly 0 times; of these: 77078 (1.75%) aligned discordantly 1 time ---- 4332542 pairs aligned 0 times concordantly or discordantly; of these: 8665084 mates make up the pairs; of these: 8343802 (96.29%) aligned 0 times 174533 (2.01%) aligned exactly 1 time 146749 (1.69%) aligned >1 times 63.47% overall alignment rate Time searching: 00:17:19 Overall time: 00:17:19 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] 1194499 / 7043580 = 0.1696 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:02:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.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, 02 Aug 2022 16:02:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:02:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:02:22: 1000000 INFO @ Tue, 02 Aug 2022 16:02:30: 2000000 INFO @ Tue, 02 Aug 2022 16:02:38: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:02:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.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, 02 Aug 2022 16:02:42: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:02:42: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:02:46: 4000000 INFO @ Tue, 02 Aug 2022 16:02:52: 1000000 INFO @ Tue, 02 Aug 2022 16:02:54: 5000000 INFO @ Tue, 02 Aug 2022 16:03:02: 2000000 INFO @ Tue, 02 Aug 2022 16:03:03: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:03:11: 3000000 INFO @ Tue, 02 Aug 2022 16:03:12: 7000000 INFO @ Tue, 02 Aug 2022 16:03:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.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, 02 Aug 2022 16:03:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:03:13: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:03:21: 4000000 INFO @ Tue, 02 Aug 2022 16:03:21: 8000000 INFO @ Tue, 02 Aug 2022 16:03:22: 1000000 INFO @ Tue, 02 Aug 2022 16:03:30: 5000000 INFO @ Tue, 02 Aug 2022 16:03:31: 9000000 INFO @ Tue, 02 Aug 2022 16:03:32: 2000000 INFO @ Tue, 02 Aug 2022 16:03:40: 6000000 INFO @ Tue, 02 Aug 2022 16:03:40: 10000000 INFO @ Tue, 02 Aug 2022 16:03:41: 3000000 INFO @ Tue, 02 Aug 2022 16:03:49: 7000000 INFO @ Tue, 02 Aug 2022 16:03:50: 11000000 INFO @ Tue, 02 Aug 2022 16:03:51: 4000000 INFO @ Tue, 02 Aug 2022 16:03:58: 8000000 INFO @ Tue, 02 Aug 2022 16:03:59: 12000000 INFO @ Tue, 02 Aug 2022 16:04:00: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:04:00: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:04:00: #1 total tags in treatment: 5817397 INFO @ Tue, 02 Aug 2022 16:04:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:04:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:04:00: #1 tags after filtering in treatment: 5194832 INFO @ Tue, 02 Aug 2022 16:04:00: 5000000 INFO @ Tue, 02 Aug 2022 16:04:00: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 02 Aug 2022 16:04:00: #1 finished! INFO @ Tue, 02 Aug 2022 16:04:00: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:04:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:04:01: #2 number of paired peaks: 3050 INFO @ Tue, 02 Aug 2022 16:04:01: start model_add_line... INFO @ Tue, 02 Aug 2022 16:04:01: start X-correlation... INFO @ Tue, 02 Aug 2022 16:04:01: end of X-cor INFO @ Tue, 02 Aug 2022 16:04:01: #2 finished! INFO @ Tue, 02 Aug 2022 16:04:01: #2 predicted fragment length is 191 bps INFO @ Tue, 02 Aug 2022 16:04:01: #2 alternative fragment length(s) may be 191 bps INFO @ Tue, 02 Aug 2022 16:04:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.05_model.r INFO @ Tue, 02 Aug 2022 16:04:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:04:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:04:07: 9000000 INFO @ Tue, 02 Aug 2022 16:04:09: 6000000 INFO @ Tue, 02 Aug 2022 16:04:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:04:16: 10000000 INFO @ Tue, 02 Aug 2022 16:04:17: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:04:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:04:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:04:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.05_summits.bed INFO @ Tue, 02 Aug 2022 16:04:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4925 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:04:24: 11000000 INFO @ Tue, 02 Aug 2022 16:04:26: 8000000 INFO @ Tue, 02 Aug 2022 16:04:33: 12000000 INFO @ Tue, 02 Aug 2022 16:04:33: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:04:33: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:04:33: #1 total tags in treatment: 5817397 INFO @ Tue, 02 Aug 2022 16:04:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:04:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:04:34: #1 tags after filtering in treatment: 5194832 INFO @ Tue, 02 Aug 2022 16:04:34: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 02 Aug 2022 16:04:34: #1 finished! INFO @ Tue, 02 Aug 2022 16:04:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:04:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:04:34: 9000000 INFO @ Tue, 02 Aug 2022 16:04:34: #2 number of paired peaks: 3050 INFO @ Tue, 02 Aug 2022 16:04:34: start model_add_line... INFO @ Tue, 02 Aug 2022 16:04:34: start X-correlation... INFO @ Tue, 02 Aug 2022 16:04:34: end of X-cor INFO @ Tue, 02 Aug 2022 16:04:34: #2 finished! INFO @ Tue, 02 Aug 2022 16:04:34: #2 predicted fragment length is 191 bps INFO @ Tue, 02 Aug 2022 16:04:34: #2 alternative fragment length(s) may be 191 bps INFO @ Tue, 02 Aug 2022 16:04:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.10_model.r INFO @ Tue, 02 Aug 2022 16:04:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:04:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:04:41: 10000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:04:48: 11000000 INFO @ Tue, 02 Aug 2022 16:04:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:04:55: 12000000 INFO @ Tue, 02 Aug 2022 16:04:56: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:04:56: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:04:56: #1 total tags in treatment: 5817397 INFO @ Tue, 02 Aug 2022 16:04:56: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:04:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:04:56: #1 tags after filtering in treatment: 5194832 INFO @ Tue, 02 Aug 2022 16:04:56: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 02 Aug 2022 16:04:56: #1 finished! INFO @ Tue, 02 Aug 2022 16:04:56: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:04:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:04:56: #2 number of paired peaks: 3050 INFO @ Tue, 02 Aug 2022 16:04:56: start model_add_line... INFO @ Tue, 02 Aug 2022 16:04:57: start X-correlation... INFO @ Tue, 02 Aug 2022 16:04:57: end of X-cor INFO @ Tue, 02 Aug 2022 16:04:57: #2 finished! INFO @ Tue, 02 Aug 2022 16:04:57: #2 predicted fragment length is 191 bps INFO @ Tue, 02 Aug 2022 16:04:57: #2 alternative fragment length(s) may be 191 bps INFO @ Tue, 02 Aug 2022 16:04:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.20_model.r INFO @ Tue, 02 Aug 2022 16:04:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:04:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:04:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:04:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:04:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.10_summits.bed INFO @ Tue, 02 Aug 2022 16:04:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3868 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:05:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:05:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:05:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:05:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11548836/SRX11548836.20_summits.bed INFO @ Tue, 02 Aug 2022 16:05:19: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2831 records, 4 fields): 169 millis CompletedMACS2peakCalling