Job ID = 16439344 SRX = SRX13453876 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10021606 spots for SRR17276262/SRR17276262.sra Written 10021606 spots for SRR17276262/SRR17276262.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439514 ("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: 00:25:05 10021606 reads; of these: 10021606 (100.00%) were paired; of these: 1001143 (9.99%) aligned concordantly 0 times 6477071 (64.63%) aligned concordantly exactly 1 time 2543392 (25.38%) aligned concordantly >1 times ---- 1001143 pairs aligned concordantly 0 times; of these: 476130 (47.56%) aligned discordantly 1 time ---- 525013 pairs aligned 0 times concordantly or discordantly; of these: 1050026 mates make up the pairs; of these: 403023 (38.38%) aligned 0 times 268506 (25.57%) aligned exactly 1 time 378497 (36.05%) aligned >1 times 97.99% overall alignment rate Time searching: 00:25:05 Overall time: 00:25:05 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] 84153 / 9433982 = 0.0089 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 15:29:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.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 15:29:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:29:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:29:22: 1000000 INFO @ Tue, 02 Aug 2022 15:29:29: 2000000 INFO @ Tue, 02 Aug 2022 15:29:36: 3000000 INFO @ Tue, 02 Aug 2022 15:29:43: 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 15:29:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.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 15:29:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:29:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:29:50: 5000000 INFO @ Tue, 02 Aug 2022 15:29:53: 1000000 INFO @ Tue, 02 Aug 2022 15:29:58: 6000000 INFO @ Tue, 02 Aug 2022 15:30:00: 2000000 INFO @ Tue, 02 Aug 2022 15:30:06: 7000000 INFO @ Tue, 02 Aug 2022 15:30:08: 3000000 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 15:30:14: 8000000 INFO @ Tue, 02 Aug 2022 15:30:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.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 15:30:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:30:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:30:16: 4000000 INFO @ Tue, 02 Aug 2022 15:30:22: 9000000 INFO @ Tue, 02 Aug 2022 15:30:23: 1000000 INFO @ Tue, 02 Aug 2022 15:30:24: 5000000 INFO @ Tue, 02 Aug 2022 15:30:29: 10000000 INFO @ Tue, 02 Aug 2022 15:30:31: 2000000 INFO @ Tue, 02 Aug 2022 15:30:32: 6000000 INFO @ Tue, 02 Aug 2022 15:30:38: 11000000 INFO @ Tue, 02 Aug 2022 15:30:39: 3000000 INFO @ Tue, 02 Aug 2022 15:30:40: 7000000 INFO @ Tue, 02 Aug 2022 15:30:46: 12000000 INFO @ Tue, 02 Aug 2022 15:30:47: 4000000 INFO @ Tue, 02 Aug 2022 15:30:48: 8000000 INFO @ Tue, 02 Aug 2022 15:30:54: 13000000 INFO @ Tue, 02 Aug 2022 15:30:54: 5000000 INFO @ Tue, 02 Aug 2022 15:30:56: 9000000 INFO @ Tue, 02 Aug 2022 15:31:02: 6000000 INFO @ Tue, 02 Aug 2022 15:31:02: 14000000 INFO @ Tue, 02 Aug 2022 15:31:04: 10000000 INFO @ Tue, 02 Aug 2022 15:31:09: 7000000 INFO @ Tue, 02 Aug 2022 15:31:11: 15000000 INFO @ Tue, 02 Aug 2022 15:31:12: 11000000 INFO @ Tue, 02 Aug 2022 15:31:17: 8000000 INFO @ Tue, 02 Aug 2022 15:31:19: 16000000 INFO @ Tue, 02 Aug 2022 15:31:20: 12000000 INFO @ Tue, 02 Aug 2022 15:31:25: 9000000 INFO @ Tue, 02 Aug 2022 15:31:27: 17000000 INFO @ Tue, 02 Aug 2022 15:31:28: 13000000 INFO @ Tue, 02 Aug 2022 15:31:32: 10000000 INFO @ Tue, 02 Aug 2022 15:31:35: 18000000 INFO @ Tue, 02 Aug 2022 15:31:37: 14000000 INFO @ Tue, 02 Aug 2022 15:31:39: 11000000 INFO @ Tue, 02 Aug 2022 15:31:44: 19000000 INFO @ Tue, 02 Aug 2022 15:31:45: 15000000 INFO @ Tue, 02 Aug 2022 15:31:47: 12000000 INFO @ Tue, 02 Aug 2022 15:31:48: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:31:48: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:31:48: #1 total tags in treatment: 8936544 INFO @ Tue, 02 Aug 2022 15:31:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:31:48: #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 15:31:48: #1 tags after filtering in treatment: 8648920 INFO @ Tue, 02 Aug 2022 15:31:48: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:31:48: #1 finished! INFO @ Tue, 02 Aug 2022 15:31:48: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:31:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:31:48: #2 number of paired peaks: 123 WARNING @ Tue, 02 Aug 2022 15:31:48: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 02 Aug 2022 15:31:48: start model_add_line... INFO @ Tue, 02 Aug 2022 15:31:48: start X-correlation... INFO @ Tue, 02 Aug 2022 15:31:48: end of X-cor INFO @ Tue, 02 Aug 2022 15:31:48: #2 finished! INFO @ Tue, 02 Aug 2022 15:31:48: #2 predicted fragment length is 160 bps INFO @ Tue, 02 Aug 2022 15:31:48: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 02 Aug 2022 15:31:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.05_model.r INFO @ Tue, 02 Aug 2022 15:31:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:31:48: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:31:53: 16000000 INFO @ Tue, 02 Aug 2022 15:31:54: 13000000 INFO @ Tue, 02 Aug 2022 15:32:01: 14000000 INFO @ Tue, 02 Aug 2022 15:32:02: 17000000 INFO @ Tue, 02 Aug 2022 15:32:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:32:09: 15000000 INFO @ Tue, 02 Aug 2022 15:32:10: 18000000 INFO @ Tue, 02 Aug 2022 15:32:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:32:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:32:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.05_summits.bed INFO @ Tue, 02 Aug 2022 15:32:15: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1651 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:32:16: 16000000 INFO @ Tue, 02 Aug 2022 15:32:18: 19000000 INFO @ Tue, 02 Aug 2022 15:32:22: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:32:22: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:32:22: #1 total tags in treatment: 8936544 INFO @ Tue, 02 Aug 2022 15:32:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:32:22: #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 15:32:22: #1 tags after filtering in treatment: 8648920 INFO @ Tue, 02 Aug 2022 15:32:22: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:32:22: #1 finished! INFO @ Tue, 02 Aug 2022 15:32:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:32:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:32:23: #2 number of paired peaks: 123 WARNING @ Tue, 02 Aug 2022 15:32:23: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 02 Aug 2022 15:32:23: start model_add_line... INFO @ Tue, 02 Aug 2022 15:32:23: start X-correlation... INFO @ Tue, 02 Aug 2022 15:32:23: end of X-cor INFO @ Tue, 02 Aug 2022 15:32:23: #2 finished! INFO @ Tue, 02 Aug 2022 15:32:23: #2 predicted fragment length is 160 bps INFO @ Tue, 02 Aug 2022 15:32:23: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 02 Aug 2022 15:32:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.10_model.r INFO @ Tue, 02 Aug 2022 15:32:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:32:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:32:23: 17000000 INFO @ Tue, 02 Aug 2022 15:32:30: 18000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:32:36: 19000000 INFO @ Tue, 02 Aug 2022 15:32:39: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:32:39: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:32:39: #1 total tags in treatment: 8936544 INFO @ Tue, 02 Aug 2022 15:32:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:32:39: #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 15:32:40: #1 tags after filtering in treatment: 8648920 INFO @ Tue, 02 Aug 2022 15:32:40: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:32:40: #1 finished! INFO @ Tue, 02 Aug 2022 15:32:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:32:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:32:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:32:40: #2 number of paired peaks: 123 WARNING @ Tue, 02 Aug 2022 15:32:40: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 02 Aug 2022 15:32:40: start model_add_line... INFO @ Tue, 02 Aug 2022 15:32:40: start X-correlation... INFO @ Tue, 02 Aug 2022 15:32:40: end of X-cor INFO @ Tue, 02 Aug 2022 15:32:40: #2 finished! INFO @ Tue, 02 Aug 2022 15:32:40: #2 predicted fragment length is 160 bps INFO @ Tue, 02 Aug 2022 15:32:40: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 02 Aug 2022 15:32:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.20_model.r INFO @ Tue, 02 Aug 2022 15:32:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:32:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:32:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:32:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:32:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.10_summits.bed INFO @ Tue, 02 Aug 2022 15:32:49: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (787 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:32:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:33:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:33:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:33:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453876/SRX13453876.20_summits.bed INFO @ Tue, 02 Aug 2022 15:33:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (376 records, 4 fields): 58 millis CompletedMACS2peakCalling