Job ID = 16438988 SRX = SRX15206431 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:19:39 prefetch.2.10.7: 1) Downloading 'SRR19139380'... 2022-08-02T05:19:39 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:19:51 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:19:51 prefetch.2.10.7: 'SRR19139380' is valid 2022-08-02T05:19:51 prefetch.2.10.7: 1) 'SRR19139380' was downloaded successfully 2022-08-02T05:19:51 prefetch.2.10.7: 'SRR19139380' has 0 unresolved dependencies Read 6406150 spots for SRR19139380/SRR19139380.sra Written 6406150 spots for SRR19139380/SRR19139380.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439021 ("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: 00:02:44 6406150 reads; of these: 6406150 (100.00%) were unpaired; of these: 263546 (4.11%) aligned 0 times 3622706 (56.55%) aligned exactly 1 time 2519898 (39.34%) aligned >1 times 95.89% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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] 766749 / 6142604 = 0.1248 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 14:25:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.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 14:25:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:25:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:25:09: 1000000 INFO @ Tue, 02 Aug 2022 14:25:15: 2000000 INFO @ Tue, 02 Aug 2022 14:25:21: 3000000 INFO @ Tue, 02 Aug 2022 14:25:26: 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 14:25:32: 5000000 INFO @ Tue, 02 Aug 2022 14:25:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.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 14:25:33: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:25:33: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:25:34: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:25:34: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:25:34: #1 total tags in treatment: 5375855 INFO @ Tue, 02 Aug 2022 14:25:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:25:34: #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 14:25:34: #1 tags after filtering in treatment: 5375855 INFO @ Tue, 02 Aug 2022 14:25:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:25:34: #1 finished! INFO @ Tue, 02 Aug 2022 14:25:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:25:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:25:34: #2 number of paired peaks: 3848 INFO @ Tue, 02 Aug 2022 14:25:34: start model_add_line... INFO @ Tue, 02 Aug 2022 14:25:34: start X-correlation... INFO @ Tue, 02 Aug 2022 14:25:34: end of X-cor INFO @ Tue, 02 Aug 2022 14:25:34: #2 finished! INFO @ Tue, 02 Aug 2022 14:25:34: #2 predicted fragment length is 176 bps INFO @ Tue, 02 Aug 2022 14:25:34: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 02 Aug 2022 14:25:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.05_model.r INFO @ Tue, 02 Aug 2022 14:25:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:25:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:25:39: 1000000 INFO @ Tue, 02 Aug 2022 14:25:45: 2000000 INFO @ Tue, 02 Aug 2022 14:25:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:25:51: 3000000 INFO @ Tue, 02 Aug 2022 14:25:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:25:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:25:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.05_summits.bed INFO @ Tue, 02 Aug 2022 14:25:57: 4000000 INFO @ Tue, 02 Aug 2022 14:25:57: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5326 records, 4 fields): 221 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 14:26:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.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 14:26:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:26:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:26:03: 5000000 INFO @ Tue, 02 Aug 2022 14:26:06: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:26:06: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:26:06: #1 total tags in treatment: 5375855 INFO @ Tue, 02 Aug 2022 14:26:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:26:06: #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 14:26:06: #1 tags after filtering in treatment: 5375855 INFO @ Tue, 02 Aug 2022 14:26:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:26:06: #1 finished! INFO @ Tue, 02 Aug 2022 14:26:06: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:26:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:26:06: #2 number of paired peaks: 3848 INFO @ Tue, 02 Aug 2022 14:26:06: start model_add_line... INFO @ Tue, 02 Aug 2022 14:26:06: start X-correlation... INFO @ Tue, 02 Aug 2022 14:26:06: end of X-cor INFO @ Tue, 02 Aug 2022 14:26:06: #2 finished! INFO @ Tue, 02 Aug 2022 14:26:06: #2 predicted fragment length is 176 bps INFO @ Tue, 02 Aug 2022 14:26:06: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 02 Aug 2022 14:26:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.10_model.r INFO @ Tue, 02 Aug 2022 14:26:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:26:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:26:09: 1000000 INFO @ Tue, 02 Aug 2022 14:26:15: 2000000 INFO @ Tue, 02 Aug 2022 14:26:21: 3000000 INFO @ Tue, 02 Aug 2022 14:26:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:26:26: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:26:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:26:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:26:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.10_summits.bed INFO @ Tue, 02 Aug 2022 14:26:28: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (3031 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:26:31: 5000000 INFO @ Tue, 02 Aug 2022 14:26:33: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:26:33: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:26:33: #1 total tags in treatment: 5375855 INFO @ Tue, 02 Aug 2022 14:26:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:26:33: #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 14:26:33: #1 tags after filtering in treatment: 5375855 INFO @ Tue, 02 Aug 2022 14:26:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:26:33: #1 finished! INFO @ Tue, 02 Aug 2022 14:26:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:26:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:26:34: #2 number of paired peaks: 3848 INFO @ Tue, 02 Aug 2022 14:26:34: start model_add_line... INFO @ Tue, 02 Aug 2022 14:26:34: start X-correlation... INFO @ Tue, 02 Aug 2022 14:26:34: end of X-cor INFO @ Tue, 02 Aug 2022 14:26:34: #2 finished! INFO @ Tue, 02 Aug 2022 14:26:34: #2 predicted fragment length is 176 bps INFO @ Tue, 02 Aug 2022 14:26:34: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 02 Aug 2022 14:26:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.20_model.r INFO @ Tue, 02 Aug 2022 14:26:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:26:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:26:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:26:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:26:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:26:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206431/SRX15206431.20_summits.bed INFO @ Tue, 02 Aug 2022 14:26:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1515 records, 4 fields): 38 millis CompletedMACS2peakCalling