Job ID = 16439186 SRX = SRX15206463 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:44:01 prefetch.2.10.7: 1) Downloading 'SRR19139343'... 2022-08-02T05:44:01 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:44:12 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:44:12 prefetch.2.10.7: 'SRR19139343' is valid 2022-08-02T05:44:12 prefetch.2.10.7: 1) 'SRR19139343' was downloaded successfully 2022-08-02T05:44:12 prefetch.2.10.7: 'SRR19139343' has 0 unresolved dependencies Read 9254970 spots for SRR19139343/SRR19139343.sra Written 9254970 spots for SRR19139343/SRR19139343.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439287 ("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: 00:03:34 9254970 reads; of these: 9254970 (100.00%) were unpaired; of these: 215479 (2.33%) aligned 0 times 3144899 (33.98%) aligned exactly 1 time 5894592 (63.69%) aligned >1 times 97.67% overall alignment rate Time searching: 00:03:34 Overall time: 00:03:34 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] 1426093 / 9039491 = 0.1578 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 14:50:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.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 14:50:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:50:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:50:22: 1000000 INFO @ Tue, 02 Aug 2022 14:50:27: 2000000 INFO @ Tue, 02 Aug 2022 14:50:32: 3000000 INFO @ Tue, 02 Aug 2022 14:50:36: 4000000 INFO @ Tue, 02 Aug 2022 14:50:41: 5000000 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 14:50:46: 6000000 INFO @ Tue, 02 Aug 2022 14:50:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.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 14:50:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:50:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:50:51: 7000000 INFO @ Tue, 02 Aug 2022 14:50:52: 1000000 INFO @ Tue, 02 Aug 2022 14:50:54: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:50:54: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:50:54: #1 total tags in treatment: 7613398 INFO @ Tue, 02 Aug 2022 14:50:54: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:50:54: #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 14:50:54: #1 tags after filtering in treatment: 7613398 INFO @ Tue, 02 Aug 2022 14:50:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:50:54: #1 finished! INFO @ Tue, 02 Aug 2022 14:50:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:50:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:50:55: #2 number of paired peaks: 5073 INFO @ Tue, 02 Aug 2022 14:50:55: start model_add_line... INFO @ Tue, 02 Aug 2022 14:50:55: start X-correlation... INFO @ Tue, 02 Aug 2022 14:50:55: end of X-cor INFO @ Tue, 02 Aug 2022 14:50:55: #2 finished! INFO @ Tue, 02 Aug 2022 14:50:55: #2 predicted fragment length is 191 bps INFO @ Tue, 02 Aug 2022 14:50:55: #2 alternative fragment length(s) may be 3,191,204 bps INFO @ Tue, 02 Aug 2022 14:50:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.05_model.r INFO @ Tue, 02 Aug 2022 14:50:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:50:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:50:57: 2000000 INFO @ Tue, 02 Aug 2022 14:51:02: 3000000 INFO @ Tue, 02 Aug 2022 14:51:07: 4000000 INFO @ Tue, 02 Aug 2022 14:51:12: 5000000 INFO @ Tue, 02 Aug 2022 14:51:14: #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 14:51:17: 6000000 INFO @ Tue, 02 Aug 2022 14:51:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.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 14:51:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:51:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:51:22: 7000000 INFO @ Tue, 02 Aug 2022 14:51:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:51:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:51:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.05_summits.bed INFO @ Tue, 02 Aug 2022 14:51:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4904 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:51:25: 1000000 INFO @ Tue, 02 Aug 2022 14:51:25: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:51:25: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:51:25: #1 total tags in treatment: 7613398 INFO @ Tue, 02 Aug 2022 14:51:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:51:25: #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 14:51:25: #1 tags after filtering in treatment: 7613398 INFO @ Tue, 02 Aug 2022 14:51:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:51:25: #1 finished! INFO @ Tue, 02 Aug 2022 14:51:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:51:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:51:26: #2 number of paired peaks: 5073 INFO @ Tue, 02 Aug 2022 14:51:26: start model_add_line... INFO @ Tue, 02 Aug 2022 14:51:26: start X-correlation... INFO @ Tue, 02 Aug 2022 14:51:26: end of X-cor INFO @ Tue, 02 Aug 2022 14:51:26: #2 finished! INFO @ Tue, 02 Aug 2022 14:51:26: #2 predicted fragment length is 191 bps INFO @ Tue, 02 Aug 2022 14:51:26: #2 alternative fragment length(s) may be 3,191,204 bps INFO @ Tue, 02 Aug 2022 14:51:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.10_model.r INFO @ Tue, 02 Aug 2022 14:51:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:51:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:51:30: 2000000 INFO @ Tue, 02 Aug 2022 14:51:36: 3000000 INFO @ Tue, 02 Aug 2022 14:51:42: 4000000 INFO @ Tue, 02 Aug 2022 14:51:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:51:47: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:51:53: 6000000 INFO @ Tue, 02 Aug 2022 14:51:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:51:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:51:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.10_summits.bed INFO @ Tue, 02 Aug 2022 14:51:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2134 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:51:58: 7000000 INFO @ Tue, 02 Aug 2022 14:52:02: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:52:02: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:52:02: #1 total tags in treatment: 7613398 INFO @ Tue, 02 Aug 2022 14:52:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:52:02: #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 14:52:02: #1 tags after filtering in treatment: 7613398 INFO @ Tue, 02 Aug 2022 14:52:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:52:02: #1 finished! INFO @ Tue, 02 Aug 2022 14:52:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:52:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:52:03: #2 number of paired peaks: 5073 INFO @ Tue, 02 Aug 2022 14:52:03: start model_add_line... INFO @ Tue, 02 Aug 2022 14:52:03: start X-correlation... INFO @ Tue, 02 Aug 2022 14:52:03: end of X-cor INFO @ Tue, 02 Aug 2022 14:52:03: #2 finished! INFO @ Tue, 02 Aug 2022 14:52:03: #2 predicted fragment length is 191 bps INFO @ Tue, 02 Aug 2022 14:52:03: #2 alternative fragment length(s) may be 3,191,204 bps INFO @ Tue, 02 Aug 2022 14:52:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.20_model.r INFO @ Tue, 02 Aug 2022 14:52:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:52:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:52:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:52:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:52:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:52:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206463/SRX15206463.20_summits.bed INFO @ Tue, 02 Aug 2022 14:52:30: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (756 records, 4 fields): 80 millis CompletedMACS2peakCalling