Job ID = 14172205 SRX = SRX9281732 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8469336 spots for SRR12813217/SRR12813217.sra Written 8469336 spots for SRR12813217/SRR12813217.sra Read 8313380 spots for SRR12813218/SRR12813218.sra Written 8313380 spots for SRR12813218/SRR12813218.sra Read 8642993 spots for SRR12813219/SRR12813219.sra Written 8642993 spots for SRR12813219/SRR12813219.sra Read 8462261 spots for SRR12813220/SRR12813220.sra Written 8462261 spots for SRR12813220/SRR12813220.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172802 ("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: 00:22:03 33887970 reads; of these: 33887970 (100.00%) were paired; of these: 24355757 (71.87%) aligned concordantly 0 times 7855358 (23.18%) aligned concordantly exactly 1 time 1676855 (4.95%) aligned concordantly >1 times ---- 24355757 pairs aligned concordantly 0 times; of these: 90944 (0.37%) aligned discordantly 1 time ---- 24264813 pairs aligned 0 times concordantly or discordantly; of these: 48529626 mates make up the pairs; of these: 47014611 (96.88%) aligned 0 times 943150 (1.94%) aligned exactly 1 time 571865 (1.18%) aligned >1 times 30.63% overall alignment rate Time searching: 00:22:03 Overall time: 00:22:03 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] 604041 / 9557940 = 0.0632 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:20:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.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, 11 Dec 2021 15:20:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:20:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:20:14: 1000000 INFO @ Sat, 11 Dec 2021 15:20:20: 2000000 INFO @ Sat, 11 Dec 2021 15:20:26: 3000000 INFO @ Sat, 11 Dec 2021 15:20:32: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:20:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.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, 11 Dec 2021 15:20:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:20:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:20:38: 5000000 INFO @ Sat, 11 Dec 2021 15:20:44: 6000000 INFO @ Sat, 11 Dec 2021 15:20:45: 1000000 INFO @ Sat, 11 Dec 2021 15:20:51: 7000000 INFO @ Sat, 11 Dec 2021 15:20:52: 2000000 INFO @ Sat, 11 Dec 2021 15:20:57: 8000000 INFO @ Sat, 11 Dec 2021 15:20:58: 3000000 INFO @ Sat, 11 Dec 2021 15:21:03: 9000000 BedGraph に変換中... INFO @ Sat, 11 Dec 2021 15:21:04: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:21:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.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, 11 Dec 2021 15:21:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:21:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:21:10: 10000000 INFO @ Sat, 11 Dec 2021 15:21:11: 5000000 INFO @ Sat, 11 Dec 2021 15:21:14: 1000000 INFO @ Sat, 11 Dec 2021 15:21:17: 11000000 INFO @ Sat, 11 Dec 2021 15:21:18: 6000000 INFO @ Sat, 11 Dec 2021 15:21:22: 2000000 INFO @ Sat, 11 Dec 2021 15:21:24: 7000000 INFO @ Sat, 11 Dec 2021 15:21:24: 12000000 INFO @ Sat, 11 Dec 2021 15:21:30: 3000000 INFO @ Sat, 11 Dec 2021 15:21:31: 8000000 INFO @ Sat, 11 Dec 2021 15:21:32: 13000000 INFO @ Sat, 11 Dec 2021 15:21:37: 9000000 INFO @ Sat, 11 Dec 2021 15:21:38: 4000000 INFO @ Sat, 11 Dec 2021 15:21:40: 14000000 INFO @ Sat, 11 Dec 2021 15:21:44: 10000000 INFO @ Sat, 11 Dec 2021 15:21:45: 5000000 INFO @ Sat, 11 Dec 2021 15:21:48: 15000000 INFO @ Sat, 11 Dec 2021 15:21:50: 11000000 INFO @ Sat, 11 Dec 2021 15:21:53: 6000000 INFO @ Sat, 11 Dec 2021 15:21:55: 16000000 INFO @ Sat, 11 Dec 2021 15:21:57: 12000000 INFO @ Sat, 11 Dec 2021 15:22:00: 7000000 INFO @ Sat, 11 Dec 2021 15:22:03: 17000000 INFO @ Sat, 11 Dec 2021 15:22:03: 13000000 INFO @ Sat, 11 Dec 2021 15:22:07: 8000000 INFO @ Sat, 11 Dec 2021 15:22:10: 18000000 INFO @ Sat, 11 Dec 2021 15:22:10: 14000000 INFO @ Sat, 11 Dec 2021 15:22:15: 9000000 INFO @ Sat, 11 Dec 2021 15:22:17: 15000000 INFO @ Sat, 11 Dec 2021 15:22:18: 19000000 INFO @ Sat, 11 Dec 2021 15:22:21: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:22:21: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:22:21: #1 total tags in treatment: 8928856 INFO @ Sat, 11 Dec 2021 15:22:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:22:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:22:22: 10000000 INFO @ Sat, 11 Dec 2021 15:22:22: #1 tags after filtering in treatment: 7884071 INFO @ Sat, 11 Dec 2021 15:22:22: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 15:22:22: #1 finished! INFO @ Sat, 11 Dec 2021 15:22:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:22:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:22:22: #2 number of paired peaks: 792 WARNING @ Sat, 11 Dec 2021 15:22:22: Fewer paired peaks (792) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 792 pairs to build model! INFO @ Sat, 11 Dec 2021 15:22:22: start model_add_line... INFO @ Sat, 11 Dec 2021 15:22:22: start X-correlation... INFO @ Sat, 11 Dec 2021 15:22:22: end of X-cor INFO @ Sat, 11 Dec 2021 15:22:22: #2 finished! INFO @ Sat, 11 Dec 2021 15:22:22: #2 predicted fragment length is 148 bps INFO @ Sat, 11 Dec 2021 15:22:22: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sat, 11 Dec 2021 15:22:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.05_model.r INFO @ Sat, 11 Dec 2021 15:22:22: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:22:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:22:24: 16000000 INFO @ Sat, 11 Dec 2021 15:22:28: 11000000 INFO @ Sat, 11 Dec 2021 15:22:31: 17000000 INFO @ Sat, 11 Dec 2021 15:22:34: 12000000 INFO @ Sat, 11 Dec 2021 15:22:37: 18000000 INFO @ Sat, 11 Dec 2021 15:22:41: 13000000 INFO @ Sat, 11 Dec 2021 15:22:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:22:44: 19000000 INFO @ Sat, 11 Dec 2021 15:22:47: 14000000 INFO @ Sat, 11 Dec 2021 15:22:47: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:22:47: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:22:47: #1 total tags in treatment: 8928856 INFO @ Sat, 11 Dec 2021 15:22:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:22:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:22:47: #1 tags after filtering in treatment: 7884071 INFO @ Sat, 11 Dec 2021 15:22:47: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 15:22:47: #1 finished! INFO @ Sat, 11 Dec 2021 15:22:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:22:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:22:48: #2 number of paired peaks: 792 WARNING @ Sat, 11 Dec 2021 15:22:48: Fewer paired peaks (792) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 792 pairs to build model! INFO @ Sat, 11 Dec 2021 15:22:48: start model_add_line... INFO @ Sat, 11 Dec 2021 15:22:48: start X-correlation... INFO @ Sat, 11 Dec 2021 15:22:48: end of X-cor INFO @ Sat, 11 Dec 2021 15:22:48: #2 finished! INFO @ Sat, 11 Dec 2021 15:22:48: #2 predicted fragment length is 148 bps INFO @ Sat, 11 Dec 2021 15:22:48: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sat, 11 Dec 2021 15:22:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.10_model.r INFO @ Sat, 11 Dec 2021 15:22:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:22:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:22:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:22:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:22:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.05_summits.bed INFO @ Sat, 11 Dec 2021 15:22:52: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1162 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:22:54: 15000000 INFO @ Sat, 11 Dec 2021 15:23:00: 16000000 INFO @ Sat, 11 Dec 2021 15:23:06: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:23:06: 17000000 INFO @ Sat, 11 Dec 2021 15:23:12: 18000000 INFO @ Sat, 11 Dec 2021 15:23:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:23:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:23:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.10_summits.bed INFO @ Sat, 11 Dec 2021 15:23:16: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (674 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:23:19: 19000000 INFO @ Sat, 11 Dec 2021 15:23:22: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:23:22: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:23:22: #1 total tags in treatment: 8928856 INFO @ Sat, 11 Dec 2021 15:23:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:23:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:23:23: #1 tags after filtering in treatment: 7884071 INFO @ Sat, 11 Dec 2021 15:23:23: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 15:23:23: #1 finished! INFO @ Sat, 11 Dec 2021 15:23:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:23:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:23:23: #2 number of paired peaks: 792 WARNING @ Sat, 11 Dec 2021 15:23:23: Fewer paired peaks (792) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 792 pairs to build model! INFO @ Sat, 11 Dec 2021 15:23:23: start model_add_line... INFO @ Sat, 11 Dec 2021 15:23:23: start X-correlation... INFO @ Sat, 11 Dec 2021 15:23:23: end of X-cor INFO @ Sat, 11 Dec 2021 15:23:23: #2 finished! INFO @ Sat, 11 Dec 2021 15:23:23: #2 predicted fragment length is 148 bps INFO @ Sat, 11 Dec 2021 15:23:23: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sat, 11 Dec 2021 15:23:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.20_model.r INFO @ Sat, 11 Dec 2021 15:23:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:23:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:23:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:23:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:23:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:23:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281732/SRX9281732.20_summits.bed INFO @ Sat, 11 Dec 2021 15:23:50: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (290 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。