Job ID = 16439363 SRX = SRX13453885 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8260706 spots for SRR17276253/SRR17276253.sra Written 8260706 spots for SRR17276253/SRR17276253.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439495 ("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: 00:18:54 8260706 reads; of these: 8260706 (100.00%) were paired; of these: 1285166 (15.56%) aligned concordantly 0 times 5247505 (63.52%) aligned concordantly exactly 1 time 1728035 (20.92%) aligned concordantly >1 times ---- 1285166 pairs aligned concordantly 0 times; of these: 751959 (58.51%) aligned discordantly 1 time ---- 533207 pairs aligned 0 times concordantly or discordantly; of these: 1066414 mates make up the pairs; of these: 402820 (37.77%) aligned 0 times 246759 (23.14%) aligned exactly 1 time 416835 (39.09%) aligned >1 times 97.56% overall alignment rate Time searching: 00:18:54 Overall time: 00:18:54 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] 61531 / 7673566 = 0.0080 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 15:23:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.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 15:23:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:23:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:23:56: 1000000 INFO @ Tue, 02 Aug 2022 15:24:02: 2000000 INFO @ Tue, 02 Aug 2022 15:24:09: 3000000 INFO @ Tue, 02 Aug 2022 15:24:15: 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 15:24:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.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 15:24:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:24:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:24:22: 5000000 INFO @ Tue, 02 Aug 2022 15:24:26: 1000000 INFO @ Tue, 02 Aug 2022 15:24:29: 6000000 INFO @ Tue, 02 Aug 2022 15:24:33: 2000000 INFO @ Tue, 02 Aug 2022 15:24:35: 7000000 INFO @ Tue, 02 Aug 2022 15:24:40: 3000000 INFO @ Tue, 02 Aug 2022 15:24:42: 8000000 INFO @ Tue, 02 Aug 2022 15:24:46: 4000000 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 15:24:49: 9000000 INFO @ Tue, 02 Aug 2022 15:24:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.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 15:24:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:24:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:24:53: 5000000 INFO @ Tue, 02 Aug 2022 15:24:56: 10000000 INFO @ Tue, 02 Aug 2022 15:24:56: 1000000 INFO @ Tue, 02 Aug 2022 15:25:00: 6000000 INFO @ Tue, 02 Aug 2022 15:25:03: 11000000 INFO @ Tue, 02 Aug 2022 15:25:03: 2000000 INFO @ Tue, 02 Aug 2022 15:25:07: 7000000 INFO @ Tue, 02 Aug 2022 15:25:09: 12000000 INFO @ Tue, 02 Aug 2022 15:25:10: 3000000 INFO @ Tue, 02 Aug 2022 15:25:13: 8000000 INFO @ Tue, 02 Aug 2022 15:25:16: 13000000 INFO @ Tue, 02 Aug 2022 15:25:16: 4000000 INFO @ Tue, 02 Aug 2022 15:25:20: 9000000 INFO @ Tue, 02 Aug 2022 15:25:23: 14000000 INFO @ Tue, 02 Aug 2022 15:25:23: 5000000 INFO @ Tue, 02 Aug 2022 15:25:27: 10000000 INFO @ Tue, 02 Aug 2022 15:25:30: 6000000 INFO @ Tue, 02 Aug 2022 15:25:30: 15000000 INFO @ Tue, 02 Aug 2022 15:25:33: 11000000 INFO @ Tue, 02 Aug 2022 15:25:37: 7000000 INFO @ Tue, 02 Aug 2022 15:25:37: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:25:37: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:25:37: #1 total tags in treatment: 6914501 INFO @ Tue, 02 Aug 2022 15:25:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:25:37: #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 15:25:37: #1 tags after filtering in treatment: 6725190 INFO @ Tue, 02 Aug 2022 15:25:37: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:25:37: #1 finished! INFO @ Tue, 02 Aug 2022 15:25:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:25:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:25:38: #2 number of paired peaks: 131 WARNING @ Tue, 02 Aug 2022 15:25:38: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Tue, 02 Aug 2022 15:25:38: start model_add_line... INFO @ Tue, 02 Aug 2022 15:25:38: start X-correlation... INFO @ Tue, 02 Aug 2022 15:25:38: end of X-cor INFO @ Tue, 02 Aug 2022 15:25:38: #2 finished! INFO @ Tue, 02 Aug 2022 15:25:38: #2 predicted fragment length is 152 bps INFO @ Tue, 02 Aug 2022 15:25:38: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 02 Aug 2022 15:25:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.05_model.r INFO @ Tue, 02 Aug 2022 15:25:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:25:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:25:40: 12000000 INFO @ Tue, 02 Aug 2022 15:25:43: 8000000 INFO @ Tue, 02 Aug 2022 15:25:47: 13000000 INFO @ Tue, 02 Aug 2022 15:25:50: 9000000 INFO @ Tue, 02 Aug 2022 15:25:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:25:54: 14000000 INFO @ Tue, 02 Aug 2022 15:25:56: 10000000 INFO @ Tue, 02 Aug 2022 15:26:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:26:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:26:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.05_summits.bed INFO @ Tue, 02 Aug 2022 15:26:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (724 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:26:01: 15000000 INFO @ Tue, 02 Aug 2022 15:26:03: 11000000 INFO @ Tue, 02 Aug 2022 15:26:08: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:26:08: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:26:08: #1 total tags in treatment: 6914501 INFO @ Tue, 02 Aug 2022 15:26:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:26:08: #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 15:26:08: #1 tags after filtering in treatment: 6725190 INFO @ Tue, 02 Aug 2022 15:26:08: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:26:08: #1 finished! INFO @ Tue, 02 Aug 2022 15:26:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:26:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:26:08: #2 number of paired peaks: 131 WARNING @ Tue, 02 Aug 2022 15:26:08: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Tue, 02 Aug 2022 15:26:08: start model_add_line... INFO @ Tue, 02 Aug 2022 15:26:08: start X-correlation... INFO @ Tue, 02 Aug 2022 15:26:08: end of X-cor INFO @ Tue, 02 Aug 2022 15:26:08: #2 finished! INFO @ Tue, 02 Aug 2022 15:26:08: #2 predicted fragment length is 152 bps INFO @ Tue, 02 Aug 2022 15:26:08: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 02 Aug 2022 15:26:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.10_model.r INFO @ Tue, 02 Aug 2022 15:26:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:26:08: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:26:09: 12000000 INFO @ Tue, 02 Aug 2022 15:26:15: 13000000 INFO @ Tue, 02 Aug 2022 15:26:21: 14000000 INFO @ Tue, 02 Aug 2022 15:26:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:26:27: 15000000 INFO @ Tue, 02 Aug 2022 15:26:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:26:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:26:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.10_summits.bed INFO @ Tue, 02 Aug 2022 15:26:29: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (487 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:26:33: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:26:33: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:26:33: #1 total tags in treatment: 6914501 INFO @ Tue, 02 Aug 2022 15:26:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:26:33: #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 15:26:33: #1 tags after filtering in treatment: 6725190 INFO @ Tue, 02 Aug 2022 15:26:33: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:26:33: #1 finished! INFO @ Tue, 02 Aug 2022 15:26:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:26:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:26:33: #2 number of paired peaks: 131 WARNING @ Tue, 02 Aug 2022 15:26:33: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Tue, 02 Aug 2022 15:26:33: start model_add_line... INFO @ Tue, 02 Aug 2022 15:26:33: start X-correlation... INFO @ Tue, 02 Aug 2022 15:26:33: end of X-cor INFO @ Tue, 02 Aug 2022 15:26:33: #2 finished! INFO @ Tue, 02 Aug 2022 15:26:33: #2 predicted fragment length is 152 bps INFO @ Tue, 02 Aug 2022 15:26:33: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 02 Aug 2022 15:26:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.20_model.r INFO @ Tue, 02 Aug 2022 15:26:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:26:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:26:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:26:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:26:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:26:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453885/SRX13453885.20_summits.bed INFO @ Tue, 02 Aug 2022 15:26:55: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (303 records, 4 fields): 16 millis CompletedMACS2peakCalling