Job ID = 16439595 SRX = SRX11548834 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15992060 spots for SRR15243005/SRR15243005.sra Written 15992060 spots for SRR15243005/SRR15243005.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439842 ("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: 00:35:17 15992060 reads; of these: 15992060 (100.00%) were paired; of these: 3564184 (22.29%) aligned concordantly 0 times 9423498 (58.93%) aligned concordantly exactly 1 time 3004378 (18.79%) aligned concordantly >1 times ---- 3564184 pairs aligned concordantly 0 times; of these: 235681 (6.61%) aligned discordantly 1 time ---- 3328503 pairs aligned 0 times concordantly or discordantly; of these: 6657006 mates make up the pairs; of these: 6012419 (90.32%) aligned 0 times 320481 (4.81%) aligned exactly 1 time 324106 (4.87%) aligned >1 times 81.20% overall alignment rate Time searching: 00:35:17 Overall time: 00:35:17 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] 2673194 / 12653541 = 0.2113 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 16:23:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.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 16:23:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:23:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:23:21: 1000000 INFO @ Tue, 02 Aug 2022 16:23:27: 2000000 INFO @ Tue, 02 Aug 2022 16:23:33: 3000000 INFO @ Tue, 02 Aug 2022 16:23:39: 4000000 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 16:23:45: 5000000 INFO @ Tue, 02 Aug 2022 16:23:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.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 16:23:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:23:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:23:51: 6000000 INFO @ Tue, 02 Aug 2022 16:23:51: 1000000 INFO @ Tue, 02 Aug 2022 16:23:57: 2000000 INFO @ Tue, 02 Aug 2022 16:23:58: 7000000 INFO @ Tue, 02 Aug 2022 16:24:03: 3000000 INFO @ Tue, 02 Aug 2022 16:24:04: 8000000 INFO @ Tue, 02 Aug 2022 16:24:10: 4000000 INFO @ Tue, 02 Aug 2022 16:24:10: 9000000 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 16:24:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.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 16:24:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:24:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:24:16: 5000000 INFO @ Tue, 02 Aug 2022 16:24:17: 10000000 INFO @ Tue, 02 Aug 2022 16:24:22: 1000000 INFO @ Tue, 02 Aug 2022 16:24:23: 6000000 INFO @ Tue, 02 Aug 2022 16:24:23: 11000000 INFO @ Tue, 02 Aug 2022 16:24:28: 2000000 INFO @ Tue, 02 Aug 2022 16:24:29: 7000000 INFO @ Tue, 02 Aug 2022 16:24:30: 12000000 INFO @ Tue, 02 Aug 2022 16:24:34: 3000000 INFO @ Tue, 02 Aug 2022 16:24:35: 8000000 INFO @ Tue, 02 Aug 2022 16:24:37: 13000000 INFO @ Tue, 02 Aug 2022 16:24:40: 4000000 INFO @ Tue, 02 Aug 2022 16:24:42: 9000000 INFO @ Tue, 02 Aug 2022 16:24:43: 14000000 INFO @ Tue, 02 Aug 2022 16:24:46: 5000000 INFO @ Tue, 02 Aug 2022 16:24:49: 10000000 INFO @ Tue, 02 Aug 2022 16:24:50: 15000000 INFO @ Tue, 02 Aug 2022 16:24:52: 6000000 INFO @ Tue, 02 Aug 2022 16:24:55: 11000000 INFO @ Tue, 02 Aug 2022 16:24:57: 16000000 INFO @ Tue, 02 Aug 2022 16:24:59: 7000000 INFO @ Tue, 02 Aug 2022 16:25:01: 12000000 INFO @ Tue, 02 Aug 2022 16:25:04: 17000000 INFO @ Tue, 02 Aug 2022 16:25:05: 8000000 INFO @ Tue, 02 Aug 2022 16:25:08: 13000000 INFO @ Tue, 02 Aug 2022 16:25:11: 18000000 INFO @ Tue, 02 Aug 2022 16:25:11: 9000000 INFO @ Tue, 02 Aug 2022 16:25:14: 14000000 INFO @ Tue, 02 Aug 2022 16:25:17: 10000000 INFO @ Tue, 02 Aug 2022 16:25:18: 19000000 INFO @ Tue, 02 Aug 2022 16:25:20: 15000000 INFO @ Tue, 02 Aug 2022 16:25:23: 11000000 INFO @ Tue, 02 Aug 2022 16:25:24: 20000000 INFO @ Tue, 02 Aug 2022 16:25:26: 16000000 INFO @ Tue, 02 Aug 2022 16:25:28: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 16:25:28: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 16:25:28: #1 total tags in treatment: 9770102 INFO @ Tue, 02 Aug 2022 16:25:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:25:28: #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 16:25:29: #1 tags after filtering in treatment: 8713790 INFO @ Tue, 02 Aug 2022 16:25:29: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 02 Aug 2022 16:25:29: #1 finished! INFO @ Tue, 02 Aug 2022 16:25:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:25:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:25:29: 12000000 INFO @ Tue, 02 Aug 2022 16:25:29: #2 number of paired peaks: 2339 INFO @ Tue, 02 Aug 2022 16:25:29: start model_add_line... INFO @ Tue, 02 Aug 2022 16:25:30: start X-correlation... INFO @ Tue, 02 Aug 2022 16:25:30: end of X-cor INFO @ Tue, 02 Aug 2022 16:25:30: #2 finished! INFO @ Tue, 02 Aug 2022 16:25:30: #2 predicted fragment length is 206 bps INFO @ Tue, 02 Aug 2022 16:25:30: #2 alternative fragment length(s) may be 206 bps INFO @ Tue, 02 Aug 2022 16:25:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.05_model.r INFO @ Tue, 02 Aug 2022 16:25:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:25:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:25:33: 17000000 INFO @ Tue, 02 Aug 2022 16:25:36: 13000000 INFO @ Tue, 02 Aug 2022 16:25:39: 18000000 INFO @ Tue, 02 Aug 2022 16:25:42: 14000000 INFO @ Tue, 02 Aug 2022 16:25:45: 19000000 INFO @ Tue, 02 Aug 2022 16:25:48: 15000000 INFO @ Tue, 02 Aug 2022 16:25:51: 20000000 INFO @ Tue, 02 Aug 2022 16:25:54: 16000000 INFO @ Tue, 02 Aug 2022 16:25:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:25:55: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 16:25:55: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 16:25:55: #1 total tags in treatment: 9770102 INFO @ Tue, 02 Aug 2022 16:25:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:25:55: #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 16:25:55: #1 tags after filtering in treatment: 8713790 INFO @ Tue, 02 Aug 2022 16:25:55: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 02 Aug 2022 16:25:55: #1 finished! INFO @ Tue, 02 Aug 2022 16:25:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:25:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:25:56: #2 number of paired peaks: 2339 INFO @ Tue, 02 Aug 2022 16:25:56: start model_add_line... INFO @ Tue, 02 Aug 2022 16:25:56: start X-correlation... INFO @ Tue, 02 Aug 2022 16:25:56: end of X-cor INFO @ Tue, 02 Aug 2022 16:25:56: #2 finished! INFO @ Tue, 02 Aug 2022 16:25:56: #2 predicted fragment length is 206 bps INFO @ Tue, 02 Aug 2022 16:25:56: #2 alternative fragment length(s) may be 206 bps INFO @ Tue, 02 Aug 2022 16:25:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.10_model.r INFO @ Tue, 02 Aug 2022 16:25:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:25:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:26:00: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:26:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:26:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:26:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.05_summits.bed INFO @ Tue, 02 Aug 2022 16:26:06: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5356 records, 4 fields): 56 millis INFO @ Tue, 02 Aug 2022 16:26:06: 18000000 CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:26:12: 19000000 INFO @ Tue, 02 Aug 2022 16:26:18: 20000000 INFO @ Tue, 02 Aug 2022 16:26:20: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:26:22: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 16:26:22: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 16:26:22: #1 total tags in treatment: 9770102 INFO @ Tue, 02 Aug 2022 16:26:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:26:22: #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 16:26:22: #1 tags after filtering in treatment: 8713790 INFO @ Tue, 02 Aug 2022 16:26:22: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 02 Aug 2022 16:26:22: #1 finished! INFO @ Tue, 02 Aug 2022 16:26:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:26:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:26:23: #2 number of paired peaks: 2339 INFO @ Tue, 02 Aug 2022 16:26:23: start model_add_line... INFO @ Tue, 02 Aug 2022 16:26:23: start X-correlation... INFO @ Tue, 02 Aug 2022 16:26:23: end of X-cor INFO @ Tue, 02 Aug 2022 16:26:23: #2 finished! INFO @ Tue, 02 Aug 2022 16:26:23: #2 predicted fragment length is 206 bps INFO @ Tue, 02 Aug 2022 16:26:23: #2 alternative fragment length(s) may be 206 bps INFO @ Tue, 02 Aug 2022 16:26:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.20_model.r INFO @ Tue, 02 Aug 2022 16:26:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:26:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:26:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:26:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:26:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.10_summits.bed INFO @ Tue, 02 Aug 2022 16:26:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4213 records, 4 fields): 79 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:26:46: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:26:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:26:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:26:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11548834/SRX11548834.20_summits.bed INFO @ Tue, 02 Aug 2022 16:26:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3091 records, 4 fields): 15 millis CompletedMACS2peakCalling