Job ID = 16438675 SRX = SRX14748154 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4612411 spots for SRR18645009/SRR18645009.sra Written 4612411 spots for SRR18645009/SRR18645009.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438964 ("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: 00:11:54 4612411 reads; of these: 4612411 (100.00%) were paired; of these: 391637 (8.49%) aligned concordantly 0 times 3058232 (66.30%) aligned concordantly exactly 1 time 1162542 (25.20%) aligned concordantly >1 times ---- 391637 pairs aligned concordantly 0 times; of these: 9678 (2.47%) aligned discordantly 1 time ---- 381959 pairs aligned 0 times concordantly or discordantly; of these: 763918 mates make up the pairs; of these: 551348 (72.17%) aligned 0 times 129312 (16.93%) aligned exactly 1 time 83258 (10.90%) aligned >1 times 94.02% overall alignment rate Time searching: 00:11:54 Overall time: 00:11:54 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] 105874 / 4226580 = 0.0250 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 14:18:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.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 14:18:42: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:18:42: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:18:49: 1000000 INFO @ Tue, 02 Aug 2022 14:18:56: 2000000 INFO @ Tue, 02 Aug 2022 14:19:03: 3000000 INFO @ Tue, 02 Aug 2022 14:19:10: 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 14:19:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.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 14:19:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:19:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:19:17: 5000000 INFO @ Tue, 02 Aug 2022 14:19:22: 1000000 INFO @ Tue, 02 Aug 2022 14:19:24: 6000000 INFO @ Tue, 02 Aug 2022 14:19:30: 2000000 INFO @ Tue, 02 Aug 2022 14:19:31: 7000000 INFO @ Tue, 02 Aug 2022 14:19:38: 8000000 INFO @ Tue, 02 Aug 2022 14:19:38: 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 14:19:41: #1 tag size is determined as 65 bps INFO @ Tue, 02 Aug 2022 14:19:41: #1 tag size = 65 INFO @ Tue, 02 Aug 2022 14:19:41: #1 total tags in treatment: 4115105 INFO @ Tue, 02 Aug 2022 14:19:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:19:41: #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 14:19:41: #1 tags after filtering in treatment: 3968829 INFO @ Tue, 02 Aug 2022 14:19:41: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 14:19:41: #1 finished! INFO @ Tue, 02 Aug 2022 14:19:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:19:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:19:41: #2 number of paired peaks: 1353 INFO @ Tue, 02 Aug 2022 14:19:41: start model_add_line... INFO @ Tue, 02 Aug 2022 14:19:41: start X-correlation... INFO @ Tue, 02 Aug 2022 14:19:41: end of X-cor INFO @ Tue, 02 Aug 2022 14:19:41: #2 finished! INFO @ Tue, 02 Aug 2022 14:19:41: #2 predicted fragment length is 198 bps INFO @ Tue, 02 Aug 2022 14:19:41: #2 alternative fragment length(s) may be 198 bps INFO @ Tue, 02 Aug 2022 14:19:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.05_model.r INFO @ Tue, 02 Aug 2022 14:19:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:19:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:19:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.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 14:19:42: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:19:42: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:19:46: 4000000 INFO @ Tue, 02 Aug 2022 14:19:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:19:50: 1000000 INFO @ Tue, 02 Aug 2022 14:19:54: 5000000 INFO @ Tue, 02 Aug 2022 14:19:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:19:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:19:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.05_summits.bed INFO @ Tue, 02 Aug 2022 14:19:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1351 records, 4 fields): 104 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:19:59: 2000000 INFO @ Tue, 02 Aug 2022 14:20:02: 6000000 INFO @ Tue, 02 Aug 2022 14:20:06: 3000000 INFO @ Tue, 02 Aug 2022 14:20:10: 7000000 INFO @ Tue, 02 Aug 2022 14:20:14: 4000000 INFO @ Tue, 02 Aug 2022 14:20:18: 8000000 INFO @ Tue, 02 Aug 2022 14:20:22: #1 tag size is determined as 65 bps INFO @ Tue, 02 Aug 2022 14:20:22: #1 tag size = 65 INFO @ Tue, 02 Aug 2022 14:20:22: #1 total tags in treatment: 4115105 INFO @ Tue, 02 Aug 2022 14:20:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:20:22: #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 14:20:22: #1 tags after filtering in treatment: 3968829 INFO @ Tue, 02 Aug 2022 14:20:22: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 14:20:22: #1 finished! INFO @ Tue, 02 Aug 2022 14:20:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:20:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:20:22: #2 number of paired peaks: 1353 INFO @ Tue, 02 Aug 2022 14:20:22: start model_add_line... INFO @ Tue, 02 Aug 2022 14:20:22: 5000000 INFO @ Tue, 02 Aug 2022 14:20:22: start X-correlation... INFO @ Tue, 02 Aug 2022 14:20:22: end of X-cor INFO @ Tue, 02 Aug 2022 14:20:22: #2 finished! INFO @ Tue, 02 Aug 2022 14:20:22: #2 predicted fragment length is 198 bps INFO @ Tue, 02 Aug 2022 14:20:22: #2 alternative fragment length(s) may be 198 bps INFO @ Tue, 02 Aug 2022 14:20:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.10_model.r INFO @ Tue, 02 Aug 2022 14:20:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:20:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:20:30: 6000000 INFO @ Tue, 02 Aug 2022 14:20:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:20:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:20:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:20:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.10_summits.bed INFO @ Tue, 02 Aug 2022 14:20:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (781 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:20:37: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:20:44: 8000000 INFO @ Tue, 02 Aug 2022 14:20:47: #1 tag size is determined as 65 bps INFO @ Tue, 02 Aug 2022 14:20:47: #1 tag size = 65 INFO @ Tue, 02 Aug 2022 14:20:47: #1 total tags in treatment: 4115105 INFO @ Tue, 02 Aug 2022 14:20:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:20:47: #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 14:20:47: #1 tags after filtering in treatment: 3968829 INFO @ Tue, 02 Aug 2022 14:20:47: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 14:20:47: #1 finished! INFO @ Tue, 02 Aug 2022 14:20:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:20:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:20:48: #2 number of paired peaks: 1353 INFO @ Tue, 02 Aug 2022 14:20:48: start model_add_line... INFO @ Tue, 02 Aug 2022 14:20:48: start X-correlation... INFO @ Tue, 02 Aug 2022 14:20:48: end of X-cor INFO @ Tue, 02 Aug 2022 14:20:48: #2 finished! INFO @ Tue, 02 Aug 2022 14:20:48: #2 predicted fragment length is 198 bps INFO @ Tue, 02 Aug 2022 14:20:48: #2 alternative fragment length(s) may be 198 bps INFO @ Tue, 02 Aug 2022 14:20:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.20_model.r INFO @ Tue, 02 Aug 2022 14:20:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:20:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:20:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:21:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:21:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:21:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14748154/SRX14748154.20_summits.bed INFO @ Tue, 02 Aug 2022 14:21:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (407 records, 4 fields): 48 millis CompletedMACS2peakCalling BigWig に変換しました。