Job ID = 16438698 SRX = SRX15206509 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:06:11 prefetch.2.10.7: 1) Downloading 'SRR19139283'... 2022-08-02T05:06:11 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:06:20 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:06:20 prefetch.2.10.7: 'SRR19139283' is valid 2022-08-02T05:06:20 prefetch.2.10.7: 1) 'SRR19139283' was downloaded successfully 2022-08-02T05:06:20 prefetch.2.10.7: 'SRR19139283' has 0 unresolved dependencies Read 7344202 spots for SRR19139283/SRR19139283.sra Written 7344202 spots for SRR19139283/SRR19139283.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438930 ("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: 00:01:48 7344202 reads; of these: 7344202 (100.00%) were unpaired; of these: 513280 (6.99%) aligned 0 times 5667061 (77.16%) aligned exactly 1 time 1163861 (15.85%) aligned >1 times 93.01% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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] 1365596 / 6830922 = 0.1999 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 14:10:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.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 14:10:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:10:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:10:15: 1000000 INFO @ Tue, 02 Aug 2022 14:10:21: 2000000 INFO @ Tue, 02 Aug 2022 14:10:28: 3000000 INFO @ Tue, 02 Aug 2022 14:10:34: 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 14:10:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.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 14:10:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:10:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:10:41: 5000000 INFO @ Tue, 02 Aug 2022 14:10:44: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:10:44: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:10:44: #1 total tags in treatment: 5465326 INFO @ Tue, 02 Aug 2022 14:10:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:10:44: #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 14:10:44: #1 tags after filtering in treatment: 5465326 INFO @ Tue, 02 Aug 2022 14:10:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:10:44: #1 finished! INFO @ Tue, 02 Aug 2022 14:10:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:10:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:10:44: #2 number of paired peaks: 1085 INFO @ Tue, 02 Aug 2022 14:10:44: start model_add_line... INFO @ Tue, 02 Aug 2022 14:10:44: start X-correlation... INFO @ Tue, 02 Aug 2022 14:10:44: end of X-cor INFO @ Tue, 02 Aug 2022 14:10:44: #2 finished! INFO @ Tue, 02 Aug 2022 14:10:44: #2 predicted fragment length is 198 bps INFO @ Tue, 02 Aug 2022 14:10:44: #2 alternative fragment length(s) may be 198 bps INFO @ Tue, 02 Aug 2022 14:10:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.05_model.r INFO @ Tue, 02 Aug 2022 14:10:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:10:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:10:45: 1000000 INFO @ Tue, 02 Aug 2022 14:10:51: 2000000 INFO @ Tue, 02 Aug 2022 14:10:57: 3000000 INFO @ Tue, 02 Aug 2022 14:10:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:11:03: 4000000 INFO @ Tue, 02 Aug 2022 14:11:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:11:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:11:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.05_summits.bed INFO @ Tue, 02 Aug 2022 14:11:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4237 records, 4 fields): 33 millis CompletedMACS2peakCalling 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 14:11:09: 5000000 INFO @ Tue, 02 Aug 2022 14:11:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.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 14:11:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:11:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:11:11: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:11:11: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:11:11: #1 total tags in treatment: 5465326 INFO @ Tue, 02 Aug 2022 14:11:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:11:11: #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 14:11:12: #1 tags after filtering in treatment: 5465326 INFO @ Tue, 02 Aug 2022 14:11:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:11:12: #1 finished! INFO @ Tue, 02 Aug 2022 14:11:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:11:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:11:12: #2 number of paired peaks: 1085 INFO @ Tue, 02 Aug 2022 14:11:12: start model_add_line... INFO @ Tue, 02 Aug 2022 14:11:12: start X-correlation... INFO @ Tue, 02 Aug 2022 14:11:12: end of X-cor INFO @ Tue, 02 Aug 2022 14:11:12: #2 finished! INFO @ Tue, 02 Aug 2022 14:11:12: #2 predicted fragment length is 198 bps INFO @ Tue, 02 Aug 2022 14:11:12: #2 alternative fragment length(s) may be 198 bps INFO @ Tue, 02 Aug 2022 14:11:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.10_model.r INFO @ Tue, 02 Aug 2022 14:11:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:11:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:11:16: 1000000 INFO @ Tue, 02 Aug 2022 14:11:23: 2000000 INFO @ Tue, 02 Aug 2022 14:11:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:11:30: 3000000 INFO @ Tue, 02 Aug 2022 14:11:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:11:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:11:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.10_summits.bed INFO @ Tue, 02 Aug 2022 14:11:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2035 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:11:36: 4000000 INFO @ Tue, 02 Aug 2022 14:11:42: 5000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:11:45: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:11:45: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:11:45: #1 total tags in treatment: 5465326 INFO @ Tue, 02 Aug 2022 14:11:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:11:45: #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 14:11:45: #1 tags after filtering in treatment: 5465326 INFO @ Tue, 02 Aug 2022 14:11:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:11:45: #1 finished! INFO @ Tue, 02 Aug 2022 14:11:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:11:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:11:46: #2 number of paired peaks: 1085 INFO @ Tue, 02 Aug 2022 14:11:46: start model_add_line... INFO @ Tue, 02 Aug 2022 14:11:46: start X-correlation... INFO @ Tue, 02 Aug 2022 14:11:46: end of X-cor INFO @ Tue, 02 Aug 2022 14:11:46: #2 finished! INFO @ Tue, 02 Aug 2022 14:11:46: #2 predicted fragment length is 198 bps INFO @ Tue, 02 Aug 2022 14:11:46: #2 alternative fragment length(s) may be 198 bps INFO @ Tue, 02 Aug 2022 14:11:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.20_model.r INFO @ Tue, 02 Aug 2022 14:11:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:11:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:11:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:12:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:12:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:12:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206509/SRX15206509.20_summits.bed INFO @ Tue, 02 Aug 2022 14:12:05: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (783 records, 4 fields): 13 millis CompletedMACS2peakCalling