Job ID = 16436543 SRX = SRX11638455 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T02:37:43 prefetch.2.10.7: 1) Downloading 'SRR15334164'... 2022-08-02T02:37:43 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:38:35 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:38:35 prefetch.2.10.7: 1) 'SRR15334164' was downloaded successfully 2022-08-02T02:38:35 prefetch.2.10.7: 'SRR15334164' has 0 unresolved dependencies Read 24191751 spots for SRR15334164/SRR15334164.sra Written 24191751 spots for SRR15334164/SRR15334164.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436806 ("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: 00:04:59 24191751 reads; of these: 24191751 (100.00%) were unpaired; of these: 4209174 (17.40%) aligned 0 times 18588197 (76.84%) aligned exactly 1 time 1394380 (5.76%) aligned >1 times 82.60% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 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_sort_core] merging from 12 files... [bam_rmdupse_core] 9622907 / 19982577 = 0.4816 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 11:48:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.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 11:48:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:48:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:48:58: 1000000 INFO @ Tue, 02 Aug 2022 11:49:03: 2000000 INFO @ Tue, 02 Aug 2022 11:49:08: 3000000 INFO @ Tue, 02 Aug 2022 11:49:14: 4000000 INFO @ Tue, 02 Aug 2022 11:49:19: 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 11:49:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.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 11:49:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:49:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:49:25: 6000000 INFO @ Tue, 02 Aug 2022 11:49:28: 1000000 INFO @ Tue, 02 Aug 2022 11:49:31: 7000000 INFO @ Tue, 02 Aug 2022 11:49:35: 2000000 INFO @ Tue, 02 Aug 2022 11:49:37: 8000000 INFO @ Tue, 02 Aug 2022 11:49:41: 3000000 INFO @ Tue, 02 Aug 2022 11:49:43: 9000000 INFO @ Tue, 02 Aug 2022 11:49:48: 4000000 INFO @ Tue, 02 Aug 2022 11:49:49: 10000000 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 11:49:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.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 11:49:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:49:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:49:52: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 11:49:52: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 11:49:52: #1 total tags in treatment: 10359670 INFO @ Tue, 02 Aug 2022 11:49:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:49:52: #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 11:49:52: #1 tags after filtering in treatment: 10359670 INFO @ Tue, 02 Aug 2022 11:49:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:49:52: #1 finished! INFO @ Tue, 02 Aug 2022 11:49:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:49:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:49:53: #2 number of paired peaks: 5384 INFO @ Tue, 02 Aug 2022 11:49:53: start model_add_line... INFO @ Tue, 02 Aug 2022 11:49:53: start X-correlation... INFO @ Tue, 02 Aug 2022 11:49:53: end of X-cor INFO @ Tue, 02 Aug 2022 11:49:53: #2 finished! INFO @ Tue, 02 Aug 2022 11:49:53: #2 predicted fragment length is 281 bps INFO @ Tue, 02 Aug 2022 11:49:53: #2 alternative fragment length(s) may be 281 bps INFO @ Tue, 02 Aug 2022 11:49:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.05_model.r INFO @ Tue, 02 Aug 2022 11:49:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:49:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:49:55: 5000000 INFO @ Tue, 02 Aug 2022 11:49:58: 1000000 INFO @ Tue, 02 Aug 2022 11:50:01: 6000000 INFO @ Tue, 02 Aug 2022 11:50:04: 2000000 INFO @ Tue, 02 Aug 2022 11:50:08: 7000000 INFO @ Tue, 02 Aug 2022 11:50:10: 3000000 INFO @ Tue, 02 Aug 2022 11:50:14: 8000000 INFO @ Tue, 02 Aug 2022 11:50:16: 4000000 INFO @ Tue, 02 Aug 2022 11:50:21: 9000000 INFO @ Tue, 02 Aug 2022 11:50:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:50:22: 5000000 INFO @ Tue, 02 Aug 2022 11:50:28: 10000000 INFO @ Tue, 02 Aug 2022 11:50:28: 6000000 INFO @ Tue, 02 Aug 2022 11:50:30: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 11:50:30: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 11:50:30: #1 total tags in treatment: 10359670 INFO @ Tue, 02 Aug 2022 11:50:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:50:30: #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 11:50:30: #1 tags after filtering in treatment: 10359670 INFO @ Tue, 02 Aug 2022 11:50:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:50:30: #1 finished! INFO @ Tue, 02 Aug 2022 11:50:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:50:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:50:31: #2 number of paired peaks: 5384 INFO @ Tue, 02 Aug 2022 11:50:31: start model_add_line... INFO @ Tue, 02 Aug 2022 11:50:31: start X-correlation... INFO @ Tue, 02 Aug 2022 11:50:31: end of X-cor INFO @ Tue, 02 Aug 2022 11:50:31: #2 finished! INFO @ Tue, 02 Aug 2022 11:50:31: #2 predicted fragment length is 281 bps INFO @ Tue, 02 Aug 2022 11:50:31: #2 alternative fragment length(s) may be 281 bps INFO @ Tue, 02 Aug 2022 11:50:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.10_model.r INFO @ Tue, 02 Aug 2022 11:50:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:50:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:50:34: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:50:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:50:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:50:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.05_summits.bed INFO @ Tue, 02 Aug 2022 11:50:37: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10261 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:50:40: 8000000 INFO @ Tue, 02 Aug 2022 11:50:45: 9000000 INFO @ Tue, 02 Aug 2022 11:50:51: 10000000 INFO @ Tue, 02 Aug 2022 11:50:53: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 11:50:53: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 11:50:53: #1 total tags in treatment: 10359670 INFO @ Tue, 02 Aug 2022 11:50:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:50:53: #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 11:50:53: #1 tags after filtering in treatment: 10359670 INFO @ Tue, 02 Aug 2022 11:50:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:50:53: #1 finished! INFO @ Tue, 02 Aug 2022 11:50:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:50:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:50:54: #2 number of paired peaks: 5384 INFO @ Tue, 02 Aug 2022 11:50:54: start model_add_line... INFO @ Tue, 02 Aug 2022 11:50:54: start X-correlation... INFO @ Tue, 02 Aug 2022 11:50:54: end of X-cor INFO @ Tue, 02 Aug 2022 11:50:54: #2 finished! INFO @ Tue, 02 Aug 2022 11:50:54: #2 predicted fragment length is 281 bps INFO @ Tue, 02 Aug 2022 11:50:54: #2 alternative fragment length(s) may be 281 bps INFO @ Tue, 02 Aug 2022 11:50:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.20_model.r INFO @ Tue, 02 Aug 2022 11:50:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:50:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:50:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:51:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:51:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:51:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.10_summits.bed INFO @ Tue, 02 Aug 2022 11:51:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7757 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:51:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:51:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:51:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:51:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11638455/SRX11638455.20_summits.bed INFO @ Tue, 02 Aug 2022 11:51:36: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5059 records, 4 fields): 29 millis CompletedMACS2peakCalling