Job ID = 16439190 SRX = SRX15206467 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:44:34 prefetch.2.10.7: 1) Downloading 'SRR19139339'... 2022-08-02T05:44:34 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:44:48 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:44:48 prefetch.2.10.7: 'SRR19139339' is valid 2022-08-02T05:44:48 prefetch.2.10.7: 1) 'SRR19139339' was downloaded successfully 2022-08-02T05:44:48 prefetch.2.10.7: 'SRR19139339' has 0 unresolved dependencies Read 1804972 spots for SRR19139339/SRR19139339.sra Written 1804972 spots for SRR19139339/SRR19139339.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439277 ("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: 00:01:02 1804972 reads; of these: 1804972 (100.00%) were unpaired; of these: 46017 (2.55%) aligned 0 times 939550 (52.05%) aligned exactly 1 time 819405 (45.40%) aligned >1 times 97.45% overall alignment rate Time searching: 00:01:03 Overall time: 00:01:03 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_rmdupse_core] 42371 / 1758955 = 0.0241 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 14:47:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.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 14:47:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:47:12: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:47:25: 1000000 INFO @ Tue, 02 Aug 2022 14:47:34: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:47:34: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:47:34: #1 total tags in treatment: 1716584 INFO @ Tue, 02 Aug 2022 14:47:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:47:34: #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 14:47:34: #1 tags after filtering in treatment: 1716584 INFO @ Tue, 02 Aug 2022 14:47:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:47:34: #1 finished! INFO @ Tue, 02 Aug 2022 14:47:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:47:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:47:34: #2 number of paired peaks: 3714 INFO @ Tue, 02 Aug 2022 14:47:34: start model_add_line... INFO @ Tue, 02 Aug 2022 14:47:34: start X-correlation... INFO @ Tue, 02 Aug 2022 14:47:34: end of X-cor INFO @ Tue, 02 Aug 2022 14:47:34: #2 finished! INFO @ Tue, 02 Aug 2022 14:47:34: #2 predicted fragment length is 282 bps INFO @ Tue, 02 Aug 2022 14:47:34: #2 alternative fragment length(s) may be 282 bps INFO @ Tue, 02 Aug 2022 14:47:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.05_model.r INFO @ Tue, 02 Aug 2022 14:47:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:47:34: #3 Pre-compute pvalue-qvalue table... 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 14:47:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:47:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.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 14:47:42: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:47:42: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:47:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:47:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:47:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.05_summits.bed INFO @ Tue, 02 Aug 2022 14:47:44: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1651 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:47:53: 1000000 INFO @ Tue, 02 Aug 2022 14:48:00: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:48:00: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:48:00: #1 total tags in treatment: 1716584 INFO @ Tue, 02 Aug 2022 14:48:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:48:00: #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 14:48:00: #1 tags after filtering in treatment: 1716584 INFO @ Tue, 02 Aug 2022 14:48:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:48:00: #1 finished! INFO @ Tue, 02 Aug 2022 14:48:00: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:48:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:48:01: #2 number of paired peaks: 3714 INFO @ Tue, 02 Aug 2022 14:48:01: start model_add_line... INFO @ Tue, 02 Aug 2022 14:48:01: start X-correlation... INFO @ Tue, 02 Aug 2022 14:48:01: end of X-cor INFO @ Tue, 02 Aug 2022 14:48:01: #2 finished! INFO @ Tue, 02 Aug 2022 14:48:01: #2 predicted fragment length is 282 bps INFO @ Tue, 02 Aug 2022 14:48:01: #2 alternative fragment length(s) may be 282 bps INFO @ Tue, 02 Aug 2022 14:48:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.10_model.r INFO @ Tue, 02 Aug 2022 14:48:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:48:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:48:07: #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 14:48:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:48:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:48:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.10_summits.bed INFO @ Tue, 02 Aug 2022 14:48:10: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (450 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:48:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.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 14:48:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:48:12: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:48:24: 1000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:48:32: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:48:32: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:48:32: #1 total tags in treatment: 1716584 INFO @ Tue, 02 Aug 2022 14:48:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:48:32: #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 14:48:32: #1 tags after filtering in treatment: 1716584 INFO @ Tue, 02 Aug 2022 14:48:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:48:32: #1 finished! INFO @ Tue, 02 Aug 2022 14:48:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:48:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:48:33: #2 number of paired peaks: 3714 INFO @ Tue, 02 Aug 2022 14:48:33: start model_add_line... INFO @ Tue, 02 Aug 2022 14:48:33: start X-correlation... INFO @ Tue, 02 Aug 2022 14:48:33: end of X-cor INFO @ Tue, 02 Aug 2022 14:48:33: #2 finished! INFO @ Tue, 02 Aug 2022 14:48:33: #2 predicted fragment length is 282 bps INFO @ Tue, 02 Aug 2022 14:48:33: #2 alternative fragment length(s) may be 282 bps INFO @ Tue, 02 Aug 2022 14:48:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.20_model.r INFO @ Tue, 02 Aug 2022 14:48:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:48:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:48:39: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:48:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:48:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:48:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206467/SRX15206467.20_summits.bed INFO @ Tue, 02 Aug 2022 14:48:42: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (60 records, 4 fields): 13 millis CompletedMACS2peakCalling