Job ID = 16439367 SRX = SRX13453889 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8593253 spots for SRR17276249/SRR17276249.sra Written 8593253 spots for SRR17276249/SRR17276249.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439574 ("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: 00:29:19 8593253 reads; of these: 8593253 (100.00%) were paired; of these: 678046 (7.89%) aligned concordantly 0 times 5643540 (65.67%) aligned concordantly exactly 1 time 2271667 (26.44%) aligned concordantly >1 times ---- 678046 pairs aligned concordantly 0 times; of these: 200774 (29.61%) aligned discordantly 1 time ---- 477272 pairs aligned 0 times concordantly or discordantly; of these: 954544 mates make up the pairs; of these: 516715 (54.13%) aligned 0 times 209438 (21.94%) aligned exactly 1 time 228391 (23.93%) aligned >1 times 96.99% overall alignment rate Time searching: 00:29:19 Overall time: 00:29:19 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 8 files... [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] 59285 / 8077447 = 0.0073 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 15:38:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.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 15:38:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:38:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:38:35: 1000000 INFO @ Tue, 02 Aug 2022 15:38:47: 2000000 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 15:38:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.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 15:38:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:38:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:38:59: 3000000 INFO @ Tue, 02 Aug 2022 15:39:04: 1000000 INFO @ Tue, 02 Aug 2022 15:39:12: 4000000 INFO @ Tue, 02 Aug 2022 15:39:16: 2000000 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 15:39:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.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 15:39:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:39:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:39:24: 5000000 INFO @ Tue, 02 Aug 2022 15:39:28: 3000000 INFO @ Tue, 02 Aug 2022 15:39:34: 1000000 INFO @ Tue, 02 Aug 2022 15:39:36: 6000000 INFO @ Tue, 02 Aug 2022 15:39:40: 4000000 INFO @ Tue, 02 Aug 2022 15:39:46: 2000000 INFO @ Tue, 02 Aug 2022 15:39:48: 7000000 INFO @ Tue, 02 Aug 2022 15:39:52: 5000000 INFO @ Tue, 02 Aug 2022 15:39:58: 3000000 INFO @ Tue, 02 Aug 2022 15:40:01: 8000000 INFO @ Tue, 02 Aug 2022 15:40:04: 6000000 INFO @ Tue, 02 Aug 2022 15:40:10: 4000000 INFO @ Tue, 02 Aug 2022 15:40:13: 9000000 INFO @ Tue, 02 Aug 2022 15:40:17: 7000000 INFO @ Tue, 02 Aug 2022 15:40:21: 5000000 INFO @ Tue, 02 Aug 2022 15:40:26: 10000000 INFO @ Tue, 02 Aug 2022 15:40:29: 8000000 INFO @ Tue, 02 Aug 2022 15:40:33: 6000000 INFO @ Tue, 02 Aug 2022 15:40:39: 11000000 INFO @ Tue, 02 Aug 2022 15:40:41: 9000000 INFO @ Tue, 02 Aug 2022 15:40:45: 7000000 INFO @ Tue, 02 Aug 2022 15:40:51: 12000000 INFO @ Tue, 02 Aug 2022 15:40:53: 10000000 INFO @ Tue, 02 Aug 2022 15:40:57: 8000000 INFO @ Tue, 02 Aug 2022 15:41:03: 13000000 INFO @ Tue, 02 Aug 2022 15:41:04: 11000000 INFO @ Tue, 02 Aug 2022 15:41:09: 9000000 INFO @ Tue, 02 Aug 2022 15:41:16: 14000000 INFO @ Tue, 02 Aug 2022 15:41:16: 12000000 INFO @ Tue, 02 Aug 2022 15:41:21: 10000000 INFO @ Tue, 02 Aug 2022 15:41:28: 13000000 INFO @ Tue, 02 Aug 2022 15:41:28: 15000000 INFO @ Tue, 02 Aug 2022 15:41:32: 11000000 INFO @ Tue, 02 Aug 2022 15:41:40: 14000000 INFO @ Tue, 02 Aug 2022 15:41:42: 16000000 INFO @ Tue, 02 Aug 2022 15:41:44: 12000000 INFO @ Tue, 02 Aug 2022 15:41:49: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:41:49: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:41:49: #1 total tags in treatment: 7856041 INFO @ Tue, 02 Aug 2022 15:41:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:41:49: #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 15:41:49: #1 tags after filtering in treatment: 7631986 INFO @ Tue, 02 Aug 2022 15:41:49: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:41:49: #1 finished! INFO @ Tue, 02 Aug 2022 15:41:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:41:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:41:50: #2 number of paired peaks: 102 WARNING @ Tue, 02 Aug 2022 15:41:50: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Tue, 02 Aug 2022 15:41:50: start model_add_line... INFO @ Tue, 02 Aug 2022 15:41:50: start X-correlation... INFO @ Tue, 02 Aug 2022 15:41:50: end of X-cor INFO @ Tue, 02 Aug 2022 15:41:50: #2 finished! INFO @ Tue, 02 Aug 2022 15:41:50: #2 predicted fragment length is 152 bps INFO @ Tue, 02 Aug 2022 15:41:50: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 02 Aug 2022 15:41:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.05_model.r INFO @ Tue, 02 Aug 2022 15:41:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:41:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:41:52: 15000000 INFO @ Tue, 02 Aug 2022 15:41:56: 13000000 INFO @ Tue, 02 Aug 2022 15:42:03: 16000000 INFO @ Tue, 02 Aug 2022 15:42:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:42:08: 14000000 INFO @ Tue, 02 Aug 2022 15:42:10: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:42:10: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:42:10: #1 total tags in treatment: 7856041 INFO @ Tue, 02 Aug 2022 15:42:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:42:10: #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 15:42:10: #1 tags after filtering in treatment: 7631986 INFO @ Tue, 02 Aug 2022 15:42:10: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:42:10: #1 finished! INFO @ Tue, 02 Aug 2022 15:42:10: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:42:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:42:11: #2 number of paired peaks: 102 WARNING @ Tue, 02 Aug 2022 15:42:11: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Tue, 02 Aug 2022 15:42:11: start model_add_line... INFO @ Tue, 02 Aug 2022 15:42:11: start X-correlation... INFO @ Tue, 02 Aug 2022 15:42:11: end of X-cor INFO @ Tue, 02 Aug 2022 15:42:11: #2 finished! INFO @ Tue, 02 Aug 2022 15:42:11: #2 predicted fragment length is 152 bps INFO @ Tue, 02 Aug 2022 15:42:11: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 02 Aug 2022 15:42:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.10_model.r INFO @ Tue, 02 Aug 2022 15:42:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:42:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:42:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:42:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:42:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.05_summits.bed INFO @ Tue, 02 Aug 2022 15:42:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1548 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:42:19: 15000000 INFO @ Tue, 02 Aug 2022 15:42:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:42:31: 16000000 INFO @ Tue, 02 Aug 2022 15:42:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:42:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:42:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.10_summits.bed INFO @ Tue, 02 Aug 2022 15:42:33: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (654 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:42:37: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:42:37: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:42:37: #1 total tags in treatment: 7856041 INFO @ Tue, 02 Aug 2022 15:42:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:42:37: #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 15:42:37: #1 tags after filtering in treatment: 7631986 INFO @ Tue, 02 Aug 2022 15:42:37: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:42:37: #1 finished! INFO @ Tue, 02 Aug 2022 15:42:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:42:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:42:38: #2 number of paired peaks: 102 WARNING @ Tue, 02 Aug 2022 15:42:38: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Tue, 02 Aug 2022 15:42:38: start model_add_line... INFO @ Tue, 02 Aug 2022 15:42:38: start X-correlation... INFO @ Tue, 02 Aug 2022 15:42:38: end of X-cor INFO @ Tue, 02 Aug 2022 15:42:38: #2 finished! INFO @ Tue, 02 Aug 2022 15:42:38: #2 predicted fragment length is 152 bps INFO @ Tue, 02 Aug 2022 15:42:38: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 02 Aug 2022 15:42:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.20_model.r INFO @ Tue, 02 Aug 2022 15:42:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:42:38: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:42:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:43:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:43:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:43:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453889/SRX13453889.20_summits.bed INFO @ Tue, 02 Aug 2022 15:43:00: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (272 records, 4 fields): 33 millis CompletedMACS2peakCalling BigWig に変換しました。