Job ID = 12266677 SRX = SRX8174039 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5300001 spots for SRR11607678/SRR11607678.sra Written 5300001 spots for SRR11607678/SRR11607678.sra Read 9183252 spots for SRR11607679/SRR11607679.sra Written 9183252 spots for SRR11607679/SRR11607679.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266921 ("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: 00:15:36 14483253 reads; of these: 14483253 (100.00%) were paired; of these: 1219790 (8.42%) aligned concordantly 0 times 5779115 (39.90%) aligned concordantly exactly 1 time 7484348 (51.68%) aligned concordantly >1 times ---- 1219790 pairs aligned concordantly 0 times; of these: 329732 (27.03%) aligned discordantly 1 time ---- 890058 pairs aligned 0 times concordantly or discordantly; of these: 1780116 mates make up the pairs; of these: 994952 (55.89%) aligned 0 times 233916 (13.14%) aligned exactly 1 time 551248 (30.97%) aligned >1 times 96.57% overall alignment rate Time searching: 00:15:36 Overall time: 00:15:36 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] 4731095 / 13467902 = 0.3513 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:27:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.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 @ Sat, 03 Apr 2021 09:27:07: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:27:07: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:27:13: 1000000 INFO @ Sat, 03 Apr 2021 09:27:19: 2000000 INFO @ Sat, 03 Apr 2021 09:27:25: 3000000 INFO @ Sat, 03 Apr 2021 09:27:30: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:27:36: 5000000 INFO @ Sat, 03 Apr 2021 09:27:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.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 @ Sat, 03 Apr 2021 09:27:37: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:27:37: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:27:42: 6000000 INFO @ Sat, 03 Apr 2021 09:27:43: 1000000 INFO @ Sat, 03 Apr 2021 09:27:49: 7000000 INFO @ Sat, 03 Apr 2021 09:27:49: 2000000 INFO @ Sat, 03 Apr 2021 09:27:54: 3000000 INFO @ Sat, 03 Apr 2021 09:27:55: 8000000 INFO @ Sat, 03 Apr 2021 09:28:00: 4000000 INFO @ Sat, 03 Apr 2021 09:28:01: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:28:06: 5000000 INFO @ Sat, 03 Apr 2021 09:28:07: 10000000 INFO @ Sat, 03 Apr 2021 09:28:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.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 @ Sat, 03 Apr 2021 09:28:07: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:28:07: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:28:11: 6000000 INFO @ Sat, 03 Apr 2021 09:28:13: 1000000 INFO @ Sat, 03 Apr 2021 09:28:14: 11000000 INFO @ Sat, 03 Apr 2021 09:28:17: 7000000 INFO @ Sat, 03 Apr 2021 09:28:19: 2000000 INFO @ Sat, 03 Apr 2021 09:28:20: 12000000 INFO @ Sat, 03 Apr 2021 09:28:23: 8000000 INFO @ Sat, 03 Apr 2021 09:28:25: 3000000 INFO @ Sat, 03 Apr 2021 09:28:26: 13000000 INFO @ Sat, 03 Apr 2021 09:28:29: 9000000 INFO @ Sat, 03 Apr 2021 09:28:30: 4000000 INFO @ Sat, 03 Apr 2021 09:28:32: 14000000 INFO @ Sat, 03 Apr 2021 09:28:35: 10000000 INFO @ Sat, 03 Apr 2021 09:28:36: 5000000 INFO @ Sat, 03 Apr 2021 09:28:38: 15000000 INFO @ Sat, 03 Apr 2021 09:28:41: 11000000 INFO @ Sat, 03 Apr 2021 09:28:42: 6000000 INFO @ Sat, 03 Apr 2021 09:28:44: 16000000 INFO @ Sat, 03 Apr 2021 09:28:46: 12000000 INFO @ Sat, 03 Apr 2021 09:28:48: 7000000 INFO @ Sat, 03 Apr 2021 09:28:51: 17000000 INFO @ Sat, 03 Apr 2021 09:28:52: 13000000 INFO @ Sat, 03 Apr 2021 09:28:54: 8000000 INFO @ Sat, 03 Apr 2021 09:28:57: 18000000 INFO @ Sat, 03 Apr 2021 09:28:58: 14000000 INFO @ Sat, 03 Apr 2021 09:28:59: 9000000 INFO @ Sat, 03 Apr 2021 09:29:00: #1 tag size is determined as 40 bps INFO @ Sat, 03 Apr 2021 09:29:00: #1 tag size = 40 INFO @ Sat, 03 Apr 2021 09:29:00: #1 total tags in treatment: 8545018 INFO @ Sat, 03 Apr 2021 09:29:00: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:29:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:29:00: #1 tags after filtering in treatment: 6807844 INFO @ Sat, 03 Apr 2021 09:29:00: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 03 Apr 2021 09:29:00: #1 finished! INFO @ Sat, 03 Apr 2021 09:29:00: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:29:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:29:01: #2 number of paired peaks: 594 WARNING @ Sat, 03 Apr 2021 09:29:01: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Sat, 03 Apr 2021 09:29:01: start model_add_line... INFO @ Sat, 03 Apr 2021 09:29:01: start X-correlation... INFO @ Sat, 03 Apr 2021 09:29:01: end of X-cor INFO @ Sat, 03 Apr 2021 09:29:01: #2 finished! INFO @ Sat, 03 Apr 2021 09:29:01: #2 predicted fragment length is 89 bps INFO @ Sat, 03 Apr 2021 09:29:01: #2 alternative fragment length(s) may be 4,89 bps INFO @ Sat, 03 Apr 2021 09:29:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.05_model.r INFO @ Sat, 03 Apr 2021 09:29:01: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:29:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:29:03: 15000000 INFO @ Sat, 03 Apr 2021 09:29:05: 10000000 INFO @ Sat, 03 Apr 2021 09:29:09: 16000000 INFO @ Sat, 03 Apr 2021 09:29:11: 11000000 INFO @ Sat, 03 Apr 2021 09:29:14: 17000000 INFO @ Sat, 03 Apr 2021 09:29:16: 12000000 INFO @ Sat, 03 Apr 2021 09:29:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:29:20: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:29:21: 13000000 INFO @ Sat, 03 Apr 2021 09:29:23: #1 tag size is determined as 40 bps INFO @ Sat, 03 Apr 2021 09:29:23: #1 tag size = 40 INFO @ Sat, 03 Apr 2021 09:29:23: #1 total tags in treatment: 8545018 INFO @ Sat, 03 Apr 2021 09:29:23: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:29:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:29:23: #1 tags after filtering in treatment: 6807844 INFO @ Sat, 03 Apr 2021 09:29:23: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 03 Apr 2021 09:29:23: #1 finished! INFO @ Sat, 03 Apr 2021 09:29:23: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:29:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:29:23: #2 number of paired peaks: 594 WARNING @ Sat, 03 Apr 2021 09:29:23: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Sat, 03 Apr 2021 09:29:23: start model_add_line... INFO @ Sat, 03 Apr 2021 09:29:23: start X-correlation... INFO @ Sat, 03 Apr 2021 09:29:24: end of X-cor INFO @ Sat, 03 Apr 2021 09:29:24: #2 finished! INFO @ Sat, 03 Apr 2021 09:29:24: #2 predicted fragment length is 89 bps INFO @ Sat, 03 Apr 2021 09:29:24: #2 alternative fragment length(s) may be 4,89 bps INFO @ Sat, 03 Apr 2021 09:29:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.10_model.r INFO @ Sat, 03 Apr 2021 09:29:24: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:29:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:29:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:29:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:29:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.05_summits.bed INFO @ Sat, 03 Apr 2021 09:29:24: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3002 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:29:27: 14000000 INFO @ Sat, 03 Apr 2021 09:29:32: 15000000 INFO @ Sat, 03 Apr 2021 09:29:37: 16000000 INFO @ Sat, 03 Apr 2021 09:29:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:29:42: 17000000 INFO @ Sat, 03 Apr 2021 09:29:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:29:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:29:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.10_summits.bed INFO @ Sat, 03 Apr 2021 09:29:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (968 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:29:47: 18000000 INFO @ Sat, 03 Apr 2021 09:29:50: #1 tag size is determined as 40 bps INFO @ Sat, 03 Apr 2021 09:29:50: #1 tag size = 40 INFO @ Sat, 03 Apr 2021 09:29:50: #1 total tags in treatment: 8545018 INFO @ Sat, 03 Apr 2021 09:29:50: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:29:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:29:50: #1 tags after filtering in treatment: 6807844 INFO @ Sat, 03 Apr 2021 09:29:50: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 03 Apr 2021 09:29:50: #1 finished! INFO @ Sat, 03 Apr 2021 09:29:50: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:29:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:29:50: #2 number of paired peaks: 594 WARNING @ Sat, 03 Apr 2021 09:29:50: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Sat, 03 Apr 2021 09:29:50: start model_add_line... INFO @ Sat, 03 Apr 2021 09:29:50: start X-correlation... INFO @ Sat, 03 Apr 2021 09:29:50: end of X-cor INFO @ Sat, 03 Apr 2021 09:29:50: #2 finished! INFO @ Sat, 03 Apr 2021 09:29:50: #2 predicted fragment length is 89 bps INFO @ Sat, 03 Apr 2021 09:29:50: #2 alternative fragment length(s) may be 4,89 bps INFO @ Sat, 03 Apr 2021 09:29:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.20_model.r INFO @ Sat, 03 Apr 2021 09:29:50: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:29:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:30:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:30:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:30:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:30:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8174039/SRX8174039.20_summits.bed INFO @ Sat, 03 Apr 2021 09:30:13: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (281 records, 4 fields): 1 millis CompletedMACS2peakCalling