Job ID = 16438697 SRX = SRX15206508 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:05:26 prefetch.2.10.7: 1) Downloading 'SRR19139284'... 2022-08-02T05:05:26 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:05:38 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:05:38 prefetch.2.10.7: 'SRR19139284' is valid 2022-08-02T05:05:38 prefetch.2.10.7: 1) 'SRR19139284' was downloaded successfully 2022-08-02T05:05:38 prefetch.2.10.7: 'SRR19139284' has 0 unresolved dependencies Read 8557043 spots for SRR19139284/SRR19139284.sra Written 8557043 spots for SRR19139284/SRR19139284.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438928 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:02:01 8557043 reads; of these: 8557043 (100.00%) were unpaired; of these: 1172322 (13.70%) aligned 0 times 6540006 (76.43%) aligned exactly 1 time 844715 (9.87%) aligned >1 times 86.30% overall alignment rate Time searching: 00:02:02 Overall time: 00:02:02 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] 2803669 / 7384721 = 0.3797 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 14:10:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.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 14:10:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:10:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:10:28: 1000000 INFO @ Tue, 02 Aug 2022 14:10:38: 2000000 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 14:10:47: 3000000 INFO @ Tue, 02 Aug 2022 14:10:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.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 14:10:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:10:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:10:57: 4000000 INFO @ Tue, 02 Aug 2022 14:10:58: 1000000 INFO @ Tue, 02 Aug 2022 14:11:03: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:11:03: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:11:03: #1 total tags in treatment: 4581052 INFO @ Tue, 02 Aug 2022 14:11:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:11:03: #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 14:11:03: #1 tags after filtering in treatment: 4581052 INFO @ Tue, 02 Aug 2022 14:11:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:11:03: #1 finished! INFO @ Tue, 02 Aug 2022 14:11:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:11:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:11:03: #2 number of paired peaks: 193 WARNING @ Tue, 02 Aug 2022 14:11:03: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Tue, 02 Aug 2022 14:11:03: start model_add_line... INFO @ Tue, 02 Aug 2022 14:11:03: start X-correlation... INFO @ Tue, 02 Aug 2022 14:11:03: end of X-cor INFO @ Tue, 02 Aug 2022 14:11:03: #2 finished! INFO @ Tue, 02 Aug 2022 14:11:03: #2 predicted fragment length is 193 bps INFO @ Tue, 02 Aug 2022 14:11:03: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 02 Aug 2022 14:11:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.05_model.r INFO @ Tue, 02 Aug 2022 14:11:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:11:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:11:07: 2000000 INFO @ Tue, 02 Aug 2022 14:11:13: #3 Call peaks for each chromosome... 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 14:11:16: 3000000 INFO @ Tue, 02 Aug 2022 14:11:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.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 14:11:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:11:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:11:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:11:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:11:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.05_summits.bed INFO @ Tue, 02 Aug 2022 14:11:18: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (499 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:11:25: 4000000 INFO @ Tue, 02 Aug 2022 14:11:28: 1000000 INFO @ Tue, 02 Aug 2022 14:11:30: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:11:30: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:11:30: #1 total tags in treatment: 4581052 INFO @ Tue, 02 Aug 2022 14:11:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:11:30: #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 14:11:30: #1 tags after filtering in treatment: 4581052 INFO @ Tue, 02 Aug 2022 14:11:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:11:30: #1 finished! INFO @ Tue, 02 Aug 2022 14:11:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:11:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:11:31: #2 number of paired peaks: 193 WARNING @ Tue, 02 Aug 2022 14:11:31: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Tue, 02 Aug 2022 14:11:31: start model_add_line... INFO @ Tue, 02 Aug 2022 14:11:31: start X-correlation... INFO @ Tue, 02 Aug 2022 14:11:31: end of X-cor INFO @ Tue, 02 Aug 2022 14:11:31: #2 finished! INFO @ Tue, 02 Aug 2022 14:11:31: #2 predicted fragment length is 193 bps INFO @ Tue, 02 Aug 2022 14:11:31: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 02 Aug 2022 14:11:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.10_model.r INFO @ Tue, 02 Aug 2022 14:11:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:11:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:11:39: 2000000 INFO @ Tue, 02 Aug 2022 14:11:41: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:11:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:11:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:11:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.10_summits.bed INFO @ Tue, 02 Aug 2022 14:11:46: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (209 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:11:49: 3000000 INFO @ Tue, 02 Aug 2022 14:11:59: 4000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:12:05: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:12:05: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:12:05: #1 total tags in treatment: 4581052 INFO @ Tue, 02 Aug 2022 14:12:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:12:05: #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 14:12:05: #1 tags after filtering in treatment: 4581052 INFO @ Tue, 02 Aug 2022 14:12:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:12:05: #1 finished! INFO @ Tue, 02 Aug 2022 14:12:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:12:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:12:05: #2 number of paired peaks: 193 WARNING @ Tue, 02 Aug 2022 14:12:05: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Tue, 02 Aug 2022 14:12:05: start model_add_line... INFO @ Tue, 02 Aug 2022 14:12:05: start X-correlation... INFO @ Tue, 02 Aug 2022 14:12:05: end of X-cor INFO @ Tue, 02 Aug 2022 14:12:05: #2 finished! INFO @ Tue, 02 Aug 2022 14:12:05: #2 predicted fragment length is 193 bps INFO @ Tue, 02 Aug 2022 14:12:05: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 02 Aug 2022 14:12:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.20_model.r INFO @ Tue, 02 Aug 2022 14:12:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:12:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:12:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:12:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:12:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:12:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206508/SRX15206508.20_summits.bed INFO @ Tue, 02 Aug 2022 14:12:21: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (90 records, 4 fields): 40 millis CompletedMACS2peakCalling