Job ID = 16438986 SRX = SRX15206429 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:19:24 prefetch.2.10.7: 1) Downloading 'SRR19139382'... 2022-08-02T05:19:24 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:19:36 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:19:36 prefetch.2.10.7: 'SRR19139382' is valid 2022-08-02T05:19:36 prefetch.2.10.7: 1) 'SRR19139382' was downloaded successfully 2022-08-02T05:19:36 prefetch.2.10.7: 'SRR19139382' has 0 unresolved dependencies Read 8827577 spots for SRR19139382/SRR19139382.sra Written 8827577 spots for SRR19139382/SRR19139382.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439020 ("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: 00:02:15 8827577 reads; of these: 8827577 (100.00%) were unpaired; of these: 493545 (5.59%) aligned 0 times 5522897 (62.56%) aligned exactly 1 time 2811135 (31.84%) aligned >1 times 94.41% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 1634817 / 8334032 = 0.1962 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 14:24:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.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 14:24:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:24:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:24:22: 1000000 INFO @ Tue, 02 Aug 2022 14:24:28: 2000000 INFO @ Tue, 02 Aug 2022 14:24:33: 3000000 INFO @ Tue, 02 Aug 2022 14:24:39: 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 14:24:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.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 14:24:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:24:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:24:45: 5000000 INFO @ Tue, 02 Aug 2022 14:24:52: 6000000 INFO @ Tue, 02 Aug 2022 14:24:53: 1000000 INFO @ Tue, 02 Aug 2022 14:24:57: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:24:57: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:24:57: #1 total tags in treatment: 6699215 INFO @ Tue, 02 Aug 2022 14:24:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:24:57: #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 14:24:57: #1 tags after filtering in treatment: 6699215 INFO @ Tue, 02 Aug 2022 14:24:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:24:57: #1 finished! INFO @ Tue, 02 Aug 2022 14:24:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:24:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:24:58: #2 number of paired peaks: 3393 INFO @ Tue, 02 Aug 2022 14:24:58: start model_add_line... INFO @ Tue, 02 Aug 2022 14:24:58: start X-correlation... INFO @ Tue, 02 Aug 2022 14:24:58: end of X-cor INFO @ Tue, 02 Aug 2022 14:24:58: #2 finished! INFO @ Tue, 02 Aug 2022 14:24:58: #2 predicted fragment length is 205 bps INFO @ Tue, 02 Aug 2022 14:24:58: #2 alternative fragment length(s) may be 205 bps INFO @ Tue, 02 Aug 2022 14:24:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.05_model.r INFO @ Tue, 02 Aug 2022 14:24:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:24:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:25:01: 2000000 INFO @ Tue, 02 Aug 2022 14:25:08: 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 14:25:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.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 14:25:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:25:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:25:16: 4000000 INFO @ Tue, 02 Aug 2022 14:25:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:25:23: 1000000 INFO @ Tue, 02 Aug 2022 14:25:24: 5000000 INFO @ Tue, 02 Aug 2022 14:25:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:25:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:25:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.05_summits.bed INFO @ Tue, 02 Aug 2022 14:25:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7635 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:25:31: 2000000 INFO @ Tue, 02 Aug 2022 14:25:32: 6000000 INFO @ Tue, 02 Aug 2022 14:25:38: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:25:38: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:25:38: #1 total tags in treatment: 6699215 INFO @ Tue, 02 Aug 2022 14:25:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:25:38: #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 14:25:38: #1 tags after filtering in treatment: 6699215 INFO @ Tue, 02 Aug 2022 14:25:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:25:38: #1 finished! INFO @ Tue, 02 Aug 2022 14:25:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:25:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:25:38: #2 number of paired peaks: 3393 INFO @ Tue, 02 Aug 2022 14:25:38: start model_add_line... INFO @ Tue, 02 Aug 2022 14:25:38: start X-correlation... INFO @ Tue, 02 Aug 2022 14:25:38: end of X-cor INFO @ Tue, 02 Aug 2022 14:25:38: #2 finished! INFO @ Tue, 02 Aug 2022 14:25:38: #2 predicted fragment length is 205 bps INFO @ Tue, 02 Aug 2022 14:25:38: #2 alternative fragment length(s) may be 205 bps INFO @ Tue, 02 Aug 2022 14:25:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.10_model.r INFO @ Tue, 02 Aug 2022 14:25:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:25:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:25:39: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:25:47: 4000000 INFO @ Tue, 02 Aug 2022 14:25:54: 5000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:25:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:26:01: 6000000 INFO @ Tue, 02 Aug 2022 14:26:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:26:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:26:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.10_summits.bed INFO @ Tue, 02 Aug 2022 14:26:06: Done! pass1 - making usageList (14 chroms): 1 millis INFO @ Tue, 02 Aug 2022 14:26:06: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:26:06: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:26:06: #1 total tags in treatment: 6699215 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) pass2 - checking and writing primary data (4295 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:26:06: #1 tags after filtering in treatment: 6699215 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 14:26:07: #2 number of paired peaks: 3393 INFO @ Tue, 02 Aug 2022 14:26:07: start model_add_line... INFO @ Tue, 02 Aug 2022 14:26:07: start X-correlation... INFO @ Tue, 02 Aug 2022 14:26:07: end of X-cor INFO @ Tue, 02 Aug 2022 14:26:07: #2 finished! INFO @ Tue, 02 Aug 2022 14:26:07: #2 predicted fragment length is 205 bps INFO @ Tue, 02 Aug 2022 14:26:07: #2 alternative fragment length(s) may be 205 bps INFO @ Tue, 02 Aug 2022 14:26:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.20_model.r INFO @ Tue, 02 Aug 2022 14:26:07: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:26:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:26:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:26:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:26:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:26:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206429/SRX15206429.20_summits.bed INFO @ Tue, 02 Aug 2022 14:26:33: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1801 records, 4 fields): 31 millis CompletedMACS2peakCalling