Job ID = 14168141 SRX = SRX7175245 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19023509 spots for SRR10485685/SRR10485685.sra Written 19023509 spots for SRR10485685/SRR10485685.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169052 ("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: 00:40:00 19023509 reads; of these: 19023509 (100.00%) were paired; of these: 2328011 (12.24%) aligned concordantly 0 times 12504322 (65.73%) aligned concordantly exactly 1 time 4191176 (22.03%) aligned concordantly >1 times ---- 2328011 pairs aligned concordantly 0 times; of these: 154378 (6.63%) aligned discordantly 1 time ---- 2173633 pairs aligned 0 times concordantly or discordantly; of these: 4347266 mates make up the pairs; of these: 3460628 (79.60%) aligned 0 times 486753 (11.20%) aligned exactly 1 time 399885 (9.20%) aligned >1 times 90.90% overall alignment rate Time searching: 00:40:00 Overall time: 00:40:00 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 16 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] 4988149 / 16828735 = 0.2964 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 16:28:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.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 @ Fri, 10 Dec 2021 16:28:35: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:28:35: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:28:40: 1000000 INFO @ Fri, 10 Dec 2021 16:28:45: 2000000 INFO @ Fri, 10 Dec 2021 16:28:50: 3000000 INFO @ Fri, 10 Dec 2021 16:28:54: 4000000 INFO @ Fri, 10 Dec 2021 16:28:59: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 16:29:04: 6000000 INFO @ Fri, 10 Dec 2021 16:29:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.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 @ Fri, 10 Dec 2021 16:29:05: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:29:05: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:29:09: 7000000 INFO @ Fri, 10 Dec 2021 16:29:10: 1000000 INFO @ Fri, 10 Dec 2021 16:29:14: 8000000 INFO @ Fri, 10 Dec 2021 16:29:15: 2000000 INFO @ Fri, 10 Dec 2021 16:29:19: 9000000 INFO @ Fri, 10 Dec 2021 16:29:20: 3000000 INFO @ Fri, 10 Dec 2021 16:29:24: 10000000 INFO @ Fri, 10 Dec 2021 16:29:25: 4000000 INFO @ Fri, 10 Dec 2021 16:29:29: 11000000 INFO @ Fri, 10 Dec 2021 16:29:30: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 16:29:34: 12000000 INFO @ Fri, 10 Dec 2021 16:29:35: 6000000 INFO @ Fri, 10 Dec 2021 16:29:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.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 @ Fri, 10 Dec 2021 16:29:35: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:29:35: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:29:39: 13000000 INFO @ Fri, 10 Dec 2021 16:29:40: 7000000 INFO @ Fri, 10 Dec 2021 16:29:41: 1000000 INFO @ Fri, 10 Dec 2021 16:29:44: 14000000 INFO @ Fri, 10 Dec 2021 16:29:46: 8000000 INFO @ Fri, 10 Dec 2021 16:29:46: 2000000 INFO @ Fri, 10 Dec 2021 16:29:49: 15000000 INFO @ Fri, 10 Dec 2021 16:29:51: 9000000 INFO @ Fri, 10 Dec 2021 16:29:51: 3000000 INFO @ Fri, 10 Dec 2021 16:29:54: 16000000 INFO @ Fri, 10 Dec 2021 16:29:56: 10000000 INFO @ Fri, 10 Dec 2021 16:29:56: 4000000 INFO @ Fri, 10 Dec 2021 16:29:59: 17000000 INFO @ Fri, 10 Dec 2021 16:30:01: 11000000 INFO @ Fri, 10 Dec 2021 16:30:01: 5000000 INFO @ Fri, 10 Dec 2021 16:30:04: 18000000 INFO @ Fri, 10 Dec 2021 16:30:06: 12000000 INFO @ Fri, 10 Dec 2021 16:30:06: 6000000 INFO @ Fri, 10 Dec 2021 16:30:09: 19000000 INFO @ Fri, 10 Dec 2021 16:30:11: 13000000 INFO @ Fri, 10 Dec 2021 16:30:11: 7000000 INFO @ Fri, 10 Dec 2021 16:30:14: 20000000 INFO @ Fri, 10 Dec 2021 16:30:16: 14000000 INFO @ Fri, 10 Dec 2021 16:30:17: 8000000 INFO @ Fri, 10 Dec 2021 16:30:19: 21000000 INFO @ Fri, 10 Dec 2021 16:30:21: 15000000 INFO @ Fri, 10 Dec 2021 16:30:22: 9000000 INFO @ Fri, 10 Dec 2021 16:30:24: 22000000 INFO @ Fri, 10 Dec 2021 16:30:27: 16000000 INFO @ Fri, 10 Dec 2021 16:30:27: 10000000 INFO @ Fri, 10 Dec 2021 16:30:29: 23000000 INFO @ Fri, 10 Dec 2021 16:30:32: 17000000 INFO @ Fri, 10 Dec 2021 16:30:32: 11000000 INFO @ Fri, 10 Dec 2021 16:30:34: 24000000 INFO @ Fri, 10 Dec 2021 16:30:37: 18000000 INFO @ Fri, 10 Dec 2021 16:30:37: 12000000 INFO @ Fri, 10 Dec 2021 16:30:37: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 16:30:37: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 16:30:37: #1 total tags in treatment: 11728476 INFO @ Fri, 10 Dec 2021 16:30:37: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:30:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 16:30:37: #1 tags after filtering in treatment: 11060013 INFO @ Fri, 10 Dec 2021 16:30:37: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 16:30:37: #1 finished! INFO @ Fri, 10 Dec 2021 16:30:37: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:30:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:30:38: #2 number of paired peaks: 374 WARNING @ Fri, 10 Dec 2021 16:30:38: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Fri, 10 Dec 2021 16:30:38: start model_add_line... INFO @ Fri, 10 Dec 2021 16:30:38: start X-correlation... INFO @ Fri, 10 Dec 2021 16:30:38: end of X-cor INFO @ Fri, 10 Dec 2021 16:30:38: #2 finished! INFO @ Fri, 10 Dec 2021 16:30:38: #2 predicted fragment length is 198 bps INFO @ Fri, 10 Dec 2021 16:30:38: #2 alternative fragment length(s) may be 198 bps INFO @ Fri, 10 Dec 2021 16:30:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.05_model.r INFO @ Fri, 10 Dec 2021 16:30:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:30:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:30:42: 19000000 INFO @ Fri, 10 Dec 2021 16:30:42: 13000000 INFO @ Fri, 10 Dec 2021 16:30:47: 14000000 INFO @ Fri, 10 Dec 2021 16:30:47: 20000000 INFO @ Fri, 10 Dec 2021 16:30:52: 15000000 INFO @ Fri, 10 Dec 2021 16:30:52: 21000000 INFO @ Fri, 10 Dec 2021 16:30:57: 16000000 INFO @ Fri, 10 Dec 2021 16:30:58: 22000000 INFO @ Fri, 10 Dec 2021 16:31:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:31:02: 17000000 INFO @ Fri, 10 Dec 2021 16:31:03: 23000000 INFO @ Fri, 10 Dec 2021 16:31:07: 18000000 INFO @ Fri, 10 Dec 2021 16:31:08: 24000000 INFO @ Fri, 10 Dec 2021 16:31:11: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 16:31:11: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 16:31:11: #1 total tags in treatment: 11728476 INFO @ Fri, 10 Dec 2021 16:31:11: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:31:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 16:31:11: #1 tags after filtering in treatment: 11060013 INFO @ Fri, 10 Dec 2021 16:31:11: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 16:31:11: #1 finished! INFO @ Fri, 10 Dec 2021 16:31:11: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:31:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:31:12: #2 number of paired peaks: 374 WARNING @ Fri, 10 Dec 2021 16:31:12: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Fri, 10 Dec 2021 16:31:12: start model_add_line... INFO @ Fri, 10 Dec 2021 16:31:12: start X-correlation... INFO @ Fri, 10 Dec 2021 16:31:12: end of X-cor INFO @ Fri, 10 Dec 2021 16:31:12: #2 finished! INFO @ Fri, 10 Dec 2021 16:31:12: #2 predicted fragment length is 198 bps INFO @ Fri, 10 Dec 2021 16:31:12: #2 alternative fragment length(s) may be 198 bps INFO @ Fri, 10 Dec 2021 16:31:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.10_model.r INFO @ Fri, 10 Dec 2021 16:31:12: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:31:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:31:12: 19000000 INFO @ Fri, 10 Dec 2021 16:31:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:31:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:31:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.05_summits.bed INFO @ Fri, 10 Dec 2021 16:31:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3784 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:31:17: 20000000 INFO @ Fri, 10 Dec 2021 16:31:22: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 16:31:27: 22000000 INFO @ Fri, 10 Dec 2021 16:31:32: 23000000 INFO @ Fri, 10 Dec 2021 16:31:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:31:37: 24000000 INFO @ Fri, 10 Dec 2021 16:31:40: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 16:31:40: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 16:31:40: #1 total tags in treatment: 11728476 INFO @ Fri, 10 Dec 2021 16:31:40: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:31:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 16:31:40: #1 tags after filtering in treatment: 11060013 INFO @ Fri, 10 Dec 2021 16:31:40: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 16:31:40: #1 finished! INFO @ Fri, 10 Dec 2021 16:31:40: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:31:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:31:41: #2 number of paired peaks: 374 WARNING @ Fri, 10 Dec 2021 16:31:41: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Fri, 10 Dec 2021 16:31:41: start model_add_line... INFO @ Fri, 10 Dec 2021 16:31:41: start X-correlation... INFO @ Fri, 10 Dec 2021 16:31:41: end of X-cor INFO @ Fri, 10 Dec 2021 16:31:41: #2 finished! INFO @ Fri, 10 Dec 2021 16:31:41: #2 predicted fragment length is 198 bps INFO @ Fri, 10 Dec 2021 16:31:41: #2 alternative fragment length(s) may be 198 bps INFO @ Fri, 10 Dec 2021 16:31:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.20_model.r INFO @ Fri, 10 Dec 2021 16:31:41: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:31:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:31:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:31:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:31:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.10_summits.bed INFO @ Fri, 10 Dec 2021 16:31:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1849 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:32:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:32:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:32:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:32:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175245/SRX7175245.20_summits.bed INFO @ Fri, 10 Dec 2021 16:32:15: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (734 records, 4 fields): 3 millis CompletedMACS2peakCalling