Job ID = 16439392 SRX = SRX13453893 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9128238 spots for SRR17276245/SRR17276245.sra Written 9128238 spots for SRR17276245/SRR17276245.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439532 ("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: 00:22:59 9128238 reads; of these: 9128238 (100.00%) were paired; of these: 596783 (6.54%) aligned concordantly 0 times 7005756 (76.75%) aligned concordantly exactly 1 time 1525699 (16.71%) aligned concordantly >1 times ---- 596783 pairs aligned concordantly 0 times; of these: 233062 (39.05%) aligned discordantly 1 time ---- 363721 pairs aligned 0 times concordantly or discordantly; of these: 727442 mates make up the pairs; of these: 366815 (50.43%) aligned 0 times 200947 (27.62%) aligned exactly 1 time 159680 (21.95%) aligned >1 times 97.99% overall alignment rate Time searching: 00:23:00 Overall time: 00:23:00 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] 212901 / 8727012 = 0.0244 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 15:35:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.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 15:35:10: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:35:10: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:35:15: 1000000 INFO @ Tue, 02 Aug 2022 15:35:21: 2000000 INFO @ Tue, 02 Aug 2022 15:35:27: 3000000 INFO @ Tue, 02 Aug 2022 15:35:33: 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 15:35:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.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 15:35:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:35:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:35:39: 5000000 INFO @ Tue, 02 Aug 2022 15:35:45: 1000000 INFO @ Tue, 02 Aug 2022 15:35:46: 6000000 INFO @ Tue, 02 Aug 2022 15:35:51: 2000000 INFO @ Tue, 02 Aug 2022 15:35:53: 7000000 INFO @ Tue, 02 Aug 2022 15:35:57: 3000000 INFO @ Tue, 02 Aug 2022 15:36:00: 8000000 INFO @ Tue, 02 Aug 2022 15:36:05: 4000000 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 15:36:08: 9000000 INFO @ Tue, 02 Aug 2022 15:36:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.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 15:36:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:36:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:36:12: 5000000 INFO @ Tue, 02 Aug 2022 15:36:15: 1000000 INFO @ Tue, 02 Aug 2022 15:36:15: 10000000 INFO @ Tue, 02 Aug 2022 15:36:20: 6000000 INFO @ Tue, 02 Aug 2022 15:36:21: 2000000 INFO @ Tue, 02 Aug 2022 15:36:23: 11000000 INFO @ Tue, 02 Aug 2022 15:36:28: 7000000 INFO @ Tue, 02 Aug 2022 15:36:28: 3000000 INFO @ Tue, 02 Aug 2022 15:36:30: 12000000 INFO @ Tue, 02 Aug 2022 15:36:35: 4000000 INFO @ Tue, 02 Aug 2022 15:36:36: 8000000 INFO @ Tue, 02 Aug 2022 15:36:38: 13000000 INFO @ Tue, 02 Aug 2022 15:36:41: 5000000 INFO @ Tue, 02 Aug 2022 15:36:44: 9000000 INFO @ Tue, 02 Aug 2022 15:36:46: 14000000 INFO @ Tue, 02 Aug 2022 15:36:48: 6000000 INFO @ Tue, 02 Aug 2022 15:36:51: 10000000 INFO @ Tue, 02 Aug 2022 15:36:54: 15000000 INFO @ Tue, 02 Aug 2022 15:36:55: 7000000 INFO @ Tue, 02 Aug 2022 15:37:00: 11000000 INFO @ Tue, 02 Aug 2022 15:37:02: 16000000 INFO @ Tue, 02 Aug 2022 15:37:02: 8000000 INFO @ Tue, 02 Aug 2022 15:37:08: 12000000 INFO @ Tue, 02 Aug 2022 15:37:10: 17000000 INFO @ Tue, 02 Aug 2022 15:37:10: 9000000 INFO @ Tue, 02 Aug 2022 15:37:14: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:37:14: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:37:14: #1 total tags in treatment: 8319531 INFO @ Tue, 02 Aug 2022 15:37:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:37:14: #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 15:37:14: #1 tags after filtering in treatment: 8048842 INFO @ Tue, 02 Aug 2022 15:37:14: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:37:14: #1 finished! INFO @ Tue, 02 Aug 2022 15:37:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:37:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:37:14: #2 number of paired peaks: 177 WARNING @ Tue, 02 Aug 2022 15:37:14: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Tue, 02 Aug 2022 15:37:14: start model_add_line... INFO @ Tue, 02 Aug 2022 15:37:14: start X-correlation... INFO @ Tue, 02 Aug 2022 15:37:14: end of X-cor INFO @ Tue, 02 Aug 2022 15:37:14: #2 finished! INFO @ Tue, 02 Aug 2022 15:37:14: #2 predicted fragment length is 194 bps INFO @ Tue, 02 Aug 2022 15:37:14: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 02 Aug 2022 15:37:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.05_model.r INFO @ Tue, 02 Aug 2022 15:37:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:37:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:37:16: 13000000 INFO @ Tue, 02 Aug 2022 15:37:17: 10000000 INFO @ Tue, 02 Aug 2022 15:37:24: 14000000 INFO @ Tue, 02 Aug 2022 15:37:24: 11000000 INFO @ Tue, 02 Aug 2022 15:37:32: 12000000 INFO @ Tue, 02 Aug 2022 15:37:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:37:32: 15000000 INFO @ Tue, 02 Aug 2022 15:37:39: 13000000 INFO @ Tue, 02 Aug 2022 15:37:41: 16000000 INFO @ Tue, 02 Aug 2022 15:37:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:37:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:37:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.05_summits.bed INFO @ Tue, 02 Aug 2022 15:37:43: Done! pass1 - making usageList (13 chroms): 10 millis pass2 - checking and writing primary data (2403 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:37:47: 14000000 INFO @ Tue, 02 Aug 2022 15:37:49: 17000000 INFO @ Tue, 02 Aug 2022 15:37:53: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:37:53: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:37:53: #1 total tags in treatment: 8319531 INFO @ Tue, 02 Aug 2022 15:37:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:37:53: #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 15:37:53: #1 tags after filtering in treatment: 8048842 INFO @ Tue, 02 Aug 2022 15:37:53: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:37:53: #1 finished! INFO @ Tue, 02 Aug 2022 15:37:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:37:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:37:53: #2 number of paired peaks: 177 WARNING @ Tue, 02 Aug 2022 15:37:53: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Tue, 02 Aug 2022 15:37:53: start model_add_line... INFO @ Tue, 02 Aug 2022 15:37:53: start X-correlation... INFO @ Tue, 02 Aug 2022 15:37:53: end of X-cor INFO @ Tue, 02 Aug 2022 15:37:53: #2 finished! INFO @ Tue, 02 Aug 2022 15:37:53: #2 predicted fragment length is 194 bps INFO @ Tue, 02 Aug 2022 15:37:53: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 02 Aug 2022 15:37:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.10_model.r INFO @ Tue, 02 Aug 2022 15:37:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:37:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:37:55: 15000000 INFO @ Tue, 02 Aug 2022 15:38:02: 16000000 INFO @ Tue, 02 Aug 2022 15:38:09: 17000000 INFO @ Tue, 02 Aug 2022 15:38:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:38:13: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:38:13: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:38:13: #1 total tags in treatment: 8319531 INFO @ Tue, 02 Aug 2022 15:38:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:38:13: #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 15:38:13: #1 tags after filtering in treatment: 8048842 INFO @ Tue, 02 Aug 2022 15:38:13: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:38:13: #1 finished! INFO @ Tue, 02 Aug 2022 15:38:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:38:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:38:14: #2 number of paired peaks: 177 WARNING @ Tue, 02 Aug 2022 15:38:14: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Tue, 02 Aug 2022 15:38:14: start model_add_line... INFO @ Tue, 02 Aug 2022 15:38:14: start X-correlation... INFO @ Tue, 02 Aug 2022 15:38:14: end of X-cor INFO @ Tue, 02 Aug 2022 15:38:14: #2 finished! INFO @ Tue, 02 Aug 2022 15:38:14: #2 predicted fragment length is 194 bps INFO @ Tue, 02 Aug 2022 15:38:14: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 02 Aug 2022 15:38:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.20_model.r INFO @ Tue, 02 Aug 2022 15:38:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:38:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:38:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:38:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:38:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.10_summits.bed INFO @ Tue, 02 Aug 2022 15:38:21: Done! pass1 - making usageList (10 chroms): 11 millis pass2 - checking and writing primary data (845 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:38:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:38:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:38:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:38:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453893/SRX13453893.20_summits.bed INFO @ Tue, 02 Aug 2022 15:38:39: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (286 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。