Job ID = 16437576 SRX = ERX5847874 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T03:45:52 prefetch.2.10.7: 1) Downloading 'ERR6212884'... 2022-08-02T03:45:52 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T03:46:01 prefetch.2.10.7: HTTPS download succeed 2022-08-02T03:46:01 prefetch.2.10.7: 'ERR6212884' is valid 2022-08-02T03:46:01 prefetch.2.10.7: 1) 'ERR6212884' was downloaded successfully 2022-08-02T03:46:01 prefetch.2.10.7: 'ERR6212884' has 0 unresolved dependencies Read 2260296 spots for ERR6212884/ERR6212884.sra Written 2260296 spots for ERR6212884/ERR6212884.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437598 ("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: 00:01:52 2260296 reads; of these: 2260296 (100.00%) were paired; of these: 581640 (25.73%) aligned concordantly 0 times 1555717 (68.83%) aligned concordantly exactly 1 time 122939 (5.44%) aligned concordantly >1 times ---- 581640 pairs aligned concordantly 0 times; of these: 2367 (0.41%) aligned discordantly 1 time ---- 579273 pairs aligned 0 times concordantly or discordantly; of these: 1158546 mates make up the pairs; of these: 983131 (84.86%) aligned 0 times 159029 (13.73%) aligned exactly 1 time 16386 (1.41%) aligned >1 times 78.25% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 6666 / 1680520 = 0.0040 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 12:50:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.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 12:50:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:50:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:50:28: 1000000 INFO @ Tue, 02 Aug 2022 12:50:35: 2000000 INFO @ Tue, 02 Aug 2022 12:50:42: 3000000 INFO @ Tue, 02 Aug 2022 12:50:45: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:50:45: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:50:45: #1 total tags in treatment: 1671994 INFO @ Tue, 02 Aug 2022 12:50:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:50:45: #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 12:50:45: #1 tags after filtering in treatment: 1564131 INFO @ Tue, 02 Aug 2022 12:50:45: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 12:50:45: #1 finished! INFO @ Tue, 02 Aug 2022 12:50:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:50:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:50:46: #2 number of paired peaks: 8599 INFO @ Tue, 02 Aug 2022 12:50:46: start model_add_line... INFO @ Tue, 02 Aug 2022 12:50:46: start X-correlation... INFO @ Tue, 02 Aug 2022 12:50:46: end of X-cor INFO @ Tue, 02 Aug 2022 12:50:46: #2 finished! INFO @ Tue, 02 Aug 2022 12:50:46: #2 predicted fragment length is 159 bps INFO @ Tue, 02 Aug 2022 12:50:46: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 02 Aug 2022 12:50:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.05_model.r INFO @ Tue, 02 Aug 2022 12:50:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:50:46: #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 12:50:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:50:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.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 12:50:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:50:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:50:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:50:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:50:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.05_summits.bed INFO @ Tue, 02 Aug 2022 12:50:52: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6320 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:50:58: 1000000 INFO @ Tue, 02 Aug 2022 12:51:05: 2000000 INFO @ Tue, 02 Aug 2022 12:51:11: 3000000 INFO @ Tue, 02 Aug 2022 12:51:14: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:51:14: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:51:14: #1 total tags in treatment: 1671994 INFO @ Tue, 02 Aug 2022 12:51:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:51:14: #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 12:51:14: #1 tags after filtering in treatment: 1564131 INFO @ Tue, 02 Aug 2022 12:51:14: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 12:51:14: #1 finished! INFO @ Tue, 02 Aug 2022 12:51:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:51:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:51:15: #2 number of paired peaks: 8599 INFO @ Tue, 02 Aug 2022 12:51:15: start model_add_line... INFO @ Tue, 02 Aug 2022 12:51:15: start X-correlation... INFO @ Tue, 02 Aug 2022 12:51:15: end of X-cor INFO @ Tue, 02 Aug 2022 12:51:15: #2 finished! INFO @ Tue, 02 Aug 2022 12:51:15: #2 predicted fragment length is 159 bps INFO @ Tue, 02 Aug 2022 12:51:15: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 02 Aug 2022 12:51:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.10_model.r INFO @ Tue, 02 Aug 2022 12:51:15: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:51:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:51:19: #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 12:51:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:51:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:51:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.10_summits.bed INFO @ Tue, 02 Aug 2022 12:51:21: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5235 records, 4 fields): 82 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:51:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.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 12:51:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:51:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:51:27: 1000000 INFO @ Tue, 02 Aug 2022 12:51:32: 2000000 INFO @ Tue, 02 Aug 2022 12:51:38: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:51:40: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:51:40: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:51:40: #1 total tags in treatment: 1671994 INFO @ Tue, 02 Aug 2022 12:51:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:51:40: #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 12:51:40: #1 tags after filtering in treatment: 1564131 INFO @ Tue, 02 Aug 2022 12:51:40: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 12:51:40: #1 finished! INFO @ Tue, 02 Aug 2022 12:51:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:51:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:51:41: #2 number of paired peaks: 8599 INFO @ Tue, 02 Aug 2022 12:51:41: start model_add_line... INFO @ Tue, 02 Aug 2022 12:51:41: start X-correlation... INFO @ Tue, 02 Aug 2022 12:51:41: end of X-cor INFO @ Tue, 02 Aug 2022 12:51:41: #2 finished! INFO @ Tue, 02 Aug 2022 12:51:41: #2 predicted fragment length is 159 bps INFO @ Tue, 02 Aug 2022 12:51:41: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 02 Aug 2022 12:51:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.20_model.r INFO @ Tue, 02 Aug 2022 12:51:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:51:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:51:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:51:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:51:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:51:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX5847874/ERX5847874.20_summits.bed INFO @ Tue, 02 Aug 2022 12:51:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3035 records, 4 fields): 33 millis CompletedMACS2peakCalling BigWig に変換しました。