Job ID = 16439194 SRX = SRX15206471 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:46:47 prefetch.2.10.7: 1) Downloading 'SRR19139335'... 2022-08-02T05:46:47 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:47:02 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:47:03 prefetch.2.10.7: 'SRR19139335' is valid 2022-08-02T05:47:03 prefetch.2.10.7: 1) 'SRR19139335' was downloaded successfully 2022-08-02T05:47:03 prefetch.2.10.7: 'SRR19139335' has 0 unresolved dependencies Read 8878688 spots for SRR19139335/SRR19139335.sra Written 8878688 spots for SRR19139335/SRR19139335.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439309 ("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: 00:03:07 8878688 reads; of these: 8878688 (100.00%) were unpaired; of these: 697652 (7.86%) aligned 0 times 6988363 (78.71%) aligned exactly 1 time 1192673 (13.43%) aligned >1 times 92.14% overall alignment rate Time searching: 00:03:08 Overall time: 00:03:08 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_rmdupse_core] 2571968 / 8181036 = 0.3144 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 14:53:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.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 14:53:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:53:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:53:52: 1000000 INFO @ Tue, 02 Aug 2022 14:54:00: 2000000 INFO @ Tue, 02 Aug 2022 14:54:08: 3000000 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 14:54:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.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 14:54:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:54:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:54:16: 4000000 INFO @ Tue, 02 Aug 2022 14:54:22: 1000000 INFO @ Tue, 02 Aug 2022 14:54:25: 5000000 INFO @ Tue, 02 Aug 2022 14:54:30: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:54:30: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:54:30: #1 total tags in treatment: 5609068 INFO @ Tue, 02 Aug 2022 14:54:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:54:30: #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 14:54:30: #1 tags after filtering in treatment: 5609068 INFO @ Tue, 02 Aug 2022 14:54:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:54:30: #1 finished! INFO @ Tue, 02 Aug 2022 14:54:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:54:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:54:30: 2000000 INFO @ Tue, 02 Aug 2022 14:54:31: #2 number of paired peaks: 262 WARNING @ Tue, 02 Aug 2022 14:54:31: Fewer paired peaks (262) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 262 pairs to build model! INFO @ Tue, 02 Aug 2022 14:54:31: start model_add_line... INFO @ Tue, 02 Aug 2022 14:54:31: start X-correlation... INFO @ Tue, 02 Aug 2022 14:54:31: end of X-cor INFO @ Tue, 02 Aug 2022 14:54:31: #2 finished! INFO @ Tue, 02 Aug 2022 14:54:31: #2 predicted fragment length is 172 bps INFO @ Tue, 02 Aug 2022 14:54:31: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 02 Aug 2022 14:54:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.05_model.r INFO @ Tue, 02 Aug 2022 14:54:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:54:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:54:38: 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 14:54:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:54:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.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 14:54:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:54:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:54:46: 4000000 INFO @ Tue, 02 Aug 2022 14:54:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:54:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:54:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.05_summits.bed INFO @ Tue, 02 Aug 2022 14:54:49: Done! pass1 - making usageList (12 chroms): 7 millis pass2 - checking and writing primary data (825 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:54:53: 1000000 INFO @ Tue, 02 Aug 2022 14:54:54: 5000000 INFO @ Tue, 02 Aug 2022 14:54:59: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:54:59: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:54:59: #1 total tags in treatment: 5609068 INFO @ Tue, 02 Aug 2022 14:54:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:54:59: #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 14:54:59: #1 tags after filtering in treatment: 5609068 INFO @ Tue, 02 Aug 2022 14:54:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:54:59: #1 finished! INFO @ Tue, 02 Aug 2022 14:54:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:54:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:54:59: #2 number of paired peaks: 262 WARNING @ Tue, 02 Aug 2022 14:54:59: Fewer paired peaks (262) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 262 pairs to build model! INFO @ Tue, 02 Aug 2022 14:54:59: start model_add_line... INFO @ Tue, 02 Aug 2022 14:54:59: start X-correlation... INFO @ Tue, 02 Aug 2022 14:54:59: end of X-cor INFO @ Tue, 02 Aug 2022 14:54:59: #2 finished! INFO @ Tue, 02 Aug 2022 14:54:59: #2 predicted fragment length is 172 bps INFO @ Tue, 02 Aug 2022 14:54:59: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 02 Aug 2022 14:54:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.10_model.r INFO @ Tue, 02 Aug 2022 14:54:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:54:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:55:01: 2000000 INFO @ Tue, 02 Aug 2022 14:55:09: 3000000 INFO @ Tue, 02 Aug 2022 14:55:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:55:17: 4000000 INFO @ Tue, 02 Aug 2022 14:55:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:55:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:55:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.10_summits.bed INFO @ Tue, 02 Aug 2022 14:55:18: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (380 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:55:24: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:55:29: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:55:29: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:55:29: #1 total tags in treatment: 5609068 INFO @ Tue, 02 Aug 2022 14:55:29: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:55:29: #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 14:55:29: #1 tags after filtering in treatment: 5609068 INFO @ Tue, 02 Aug 2022 14:55:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:55:29: #1 finished! INFO @ Tue, 02 Aug 2022 14:55:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:55:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:55:30: #2 number of paired peaks: 262 WARNING @ Tue, 02 Aug 2022 14:55:30: Fewer paired peaks (262) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 262 pairs to build model! INFO @ Tue, 02 Aug 2022 14:55:30: start model_add_line... INFO @ Tue, 02 Aug 2022 14:55:30: start X-correlation... INFO @ Tue, 02 Aug 2022 14:55:30: end of X-cor INFO @ Tue, 02 Aug 2022 14:55:30: #2 finished! INFO @ Tue, 02 Aug 2022 14:55:30: #2 predicted fragment length is 172 bps INFO @ Tue, 02 Aug 2022 14:55:30: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 02 Aug 2022 14:55:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.20_model.r INFO @ Tue, 02 Aug 2022 14:55:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:55:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:55:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:55:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:55:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:55:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206471/SRX15206471.20_summits.bed INFO @ Tue, 02 Aug 2022 14:55:48: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (188 records, 4 fields): 14 millis CompletedMACS2peakCalling