Job ID = 16439196 SRX = SRX15206473 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:47:02 prefetch.2.10.7: 1) Downloading 'SRR19139333'... 2022-08-02T05:47:02 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:47:24 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:47:24 prefetch.2.10.7: 'SRR19139333' is valid 2022-08-02T05:47:24 prefetch.2.10.7: 1) 'SRR19139333' was downloaded successfully 2022-08-02T05:47:24 prefetch.2.10.7: 'SRR19139333' has 0 unresolved dependencies Read 7656541 spots for SRR19139333/SRR19139333.sra Written 7656541 spots for SRR19139333/SRR19139333.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439307 ("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: 00:02:53 7656541 reads; of these: 7656541 (100.00%) were unpaired; of these: 471573 (6.16%) aligned 0 times 5075455 (66.29%) aligned exactly 1 time 2109513 (27.55%) aligned >1 times 93.84% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 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] 1467499 / 7184968 = 0.2042 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 14:52:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.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 14:52:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:52:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:53:01: 1000000 INFO @ Tue, 02 Aug 2022 14:53:09: 2000000 INFO @ Tue, 02 Aug 2022 14:53:16: 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 14:53:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.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 14:53:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:53:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:53:24: 4000000 INFO @ Tue, 02 Aug 2022 14:53:32: 1000000 INFO @ Tue, 02 Aug 2022 14:53:33: 5000000 INFO @ Tue, 02 Aug 2022 14:53:39: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:53:39: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:53:39: #1 total tags in treatment: 5717469 INFO @ Tue, 02 Aug 2022 14:53:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:53:39: #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 14:53:39: #1 tags after filtering in treatment: 5717469 INFO @ Tue, 02 Aug 2022 14:53:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:53:39: #1 finished! INFO @ Tue, 02 Aug 2022 14:53:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:53:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:53:40: #2 number of paired peaks: 3045 INFO @ Tue, 02 Aug 2022 14:53:40: start model_add_line... INFO @ Tue, 02 Aug 2022 14:53:40: start X-correlation... INFO @ Tue, 02 Aug 2022 14:53:40: end of X-cor INFO @ Tue, 02 Aug 2022 14:53:40: #2 finished! INFO @ Tue, 02 Aug 2022 14:53:40: #2 predicted fragment length is 195 bps INFO @ Tue, 02 Aug 2022 14:53:40: #2 alternative fragment length(s) may be 195 bps INFO @ Tue, 02 Aug 2022 14:53:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.05_model.r INFO @ Tue, 02 Aug 2022 14:53:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:53:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:53:41: 2000000 INFO @ Tue, 02 Aug 2022 14:53:48: 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 14:53:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.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 14:53:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:53:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:53:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:53:56: 4000000 INFO @ Tue, 02 Aug 2022 14:54:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:54:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:54:01: 1000000 INFO @ Tue, 02 Aug 2022 14:54:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.05_summits.bed INFO @ Tue, 02 Aug 2022 14:54:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4971 records, 4 fields): 76 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:54:05: 5000000 INFO @ Tue, 02 Aug 2022 14:54:09: 2000000 INFO @ Tue, 02 Aug 2022 14:54:11: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:54:11: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:54:11: #1 total tags in treatment: 5717469 INFO @ Tue, 02 Aug 2022 14:54:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:54:11: #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 14:54:11: #1 tags after filtering in treatment: 5717469 INFO @ Tue, 02 Aug 2022 14:54:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:54:11: #1 finished! INFO @ Tue, 02 Aug 2022 14:54:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:54:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:54:11: #2 number of paired peaks: 3045 INFO @ Tue, 02 Aug 2022 14:54:11: start model_add_line... INFO @ Tue, 02 Aug 2022 14:54:11: start X-correlation... INFO @ Tue, 02 Aug 2022 14:54:11: end of X-cor INFO @ Tue, 02 Aug 2022 14:54:11: #2 finished! INFO @ Tue, 02 Aug 2022 14:54:11: #2 predicted fragment length is 195 bps INFO @ Tue, 02 Aug 2022 14:54:11: #2 alternative fragment length(s) may be 195 bps INFO @ Tue, 02 Aug 2022 14:54:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.10_model.r INFO @ Tue, 02 Aug 2022 14:54:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:54:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:54:16: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:54:22: 4000000 INFO @ Tue, 02 Aug 2022 14:54:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:54:28: 5000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:54:32: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:54:32: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:54:32: #1 total tags in treatment: 5717469 INFO @ Tue, 02 Aug 2022 14:54:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:54:32: #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 14:54:32: #1 tags after filtering in treatment: 5717469 INFO @ Tue, 02 Aug 2022 14:54:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:54:32: #1 finished! INFO @ Tue, 02 Aug 2022 14:54:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:54:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:54:33: #2 number of paired peaks: 3045 INFO @ Tue, 02 Aug 2022 14:54:33: start model_add_line... INFO @ Tue, 02 Aug 2022 14:54:33: start X-correlation... INFO @ Tue, 02 Aug 2022 14:54:33: end of X-cor INFO @ Tue, 02 Aug 2022 14:54:33: #2 finished! INFO @ Tue, 02 Aug 2022 14:54:33: #2 predicted fragment length is 195 bps INFO @ Tue, 02 Aug 2022 14:54:33: #2 alternative fragment length(s) may be 195 bps INFO @ Tue, 02 Aug 2022 14:54:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.20_model.r INFO @ Tue, 02 Aug 2022 14:54:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:54:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:54:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:54:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:54:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.10_summits.bed INFO @ Tue, 02 Aug 2022 14:54:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2866 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:54:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:54:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:54:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:54:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206473/SRX15206473.20_summits.bed INFO @ Tue, 02 Aug 2022 14:54:56: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1388 records, 4 fields): 15 millis CompletedMACS2peakCalling