Job ID = 14172491 SRX = SRX7628898 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14931368 spots for SRR10963260/SRR10963260.sra Written 14931368 spots for SRR10963260/SRR10963260.sra fastq に変換しました。 bowtie でマッピング中... Your job 14173048 ("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: 00:32:03 14931368 reads; of these: 14931368 (100.00%) were paired; of these: 3811273 (25.53%) aligned concordantly 0 times 8341790 (55.87%) aligned concordantly exactly 1 time 2778305 (18.61%) aligned concordantly >1 times ---- 3811273 pairs aligned concordantly 0 times; of these: 71602 (1.88%) aligned discordantly 1 time ---- 3739671 pairs aligned 0 times concordantly or discordantly; of these: 7479342 mates make up the pairs; of these: 6765450 (90.46%) aligned 0 times 316977 (4.24%) aligned exactly 1 time 396915 (5.31%) aligned >1 times 77.34% overall alignment rate Time searching: 00:32:03 Overall time: 00:32:04 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 12 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] 813730 / 11186837 = 0.0727 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 @ Sat, 11 Dec 2021 16:20:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.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 @ Sat, 11 Dec 2021 16:20:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:20:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:20:19: 1000000 INFO @ Sat, 11 Dec 2021 16:20:25: 2000000 INFO @ Sat, 11 Dec 2021 16:20:31: 3000000 INFO @ Sat, 11 Dec 2021 16:20:37: 4000000 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 @ Sat, 11 Dec 2021 16:20:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.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 @ Sat, 11 Dec 2021 16:20:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:20:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:20:43: 5000000 INFO @ Sat, 11 Dec 2021 16:20:49: 6000000 INFO @ Sat, 11 Dec 2021 16:20:50: 1000000 INFO @ Sat, 11 Dec 2021 16:20:56: 7000000 INFO @ Sat, 11 Dec 2021 16:20:58: 2000000 INFO @ Sat, 11 Dec 2021 16:21:02: 8000000 INFO @ Sat, 11 Dec 2021 16:21:06: 3000000 INFO @ Sat, 11 Dec 2021 16:21:08: 9000000 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 @ Sat, 11 Dec 2021 16:21:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.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 @ Sat, 11 Dec 2021 16:21:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:21:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:21:13: 4000000 INFO @ Sat, 11 Dec 2021 16:21:14: 10000000 INFO @ Sat, 11 Dec 2021 16:21:19: 1000000 INFO @ Sat, 11 Dec 2021 16:21:21: 11000000 INFO @ Sat, 11 Dec 2021 16:21:21: 5000000 INFO @ Sat, 11 Dec 2021 16:21:26: 2000000 INFO @ Sat, 11 Dec 2021 16:21:27: 12000000 INFO @ Sat, 11 Dec 2021 16:21:28: 6000000 INFO @ Sat, 11 Dec 2021 16:21:32: 3000000 INFO @ Sat, 11 Dec 2021 16:21:33: 13000000 INFO @ Sat, 11 Dec 2021 16:21:36: 7000000 INFO @ Sat, 11 Dec 2021 16:21:39: 4000000 INFO @ Sat, 11 Dec 2021 16:21:39: 14000000 INFO @ Sat, 11 Dec 2021 16:21:43: 8000000 INFO @ Sat, 11 Dec 2021 16:21:45: 5000000 INFO @ Sat, 11 Dec 2021 16:21:46: 15000000 INFO @ Sat, 11 Dec 2021 16:21:51: 9000000 INFO @ Sat, 11 Dec 2021 16:21:52: 16000000 INFO @ Sat, 11 Dec 2021 16:21:52: 6000000 INFO @ Sat, 11 Dec 2021 16:21:58: 17000000 INFO @ Sat, 11 Dec 2021 16:21:58: 10000000 INFO @ Sat, 11 Dec 2021 16:21:59: 7000000 INFO @ Sat, 11 Dec 2021 16:22:04: 18000000 INFO @ Sat, 11 Dec 2021 16:22:06: 8000000 INFO @ Sat, 11 Dec 2021 16:22:06: 11000000 INFO @ Sat, 11 Dec 2021 16:22:11: 19000000 INFO @ Sat, 11 Dec 2021 16:22:12: 9000000 INFO @ Sat, 11 Dec 2021 16:22:13: 12000000 INFO @ Sat, 11 Dec 2021 16:22:17: 20000000 INFO @ Sat, 11 Dec 2021 16:22:19: 10000000 INFO @ Sat, 11 Dec 2021 16:22:21: 13000000 INFO @ Sat, 11 Dec 2021 16:22:24: 21000000 INFO @ Sat, 11 Dec 2021 16:22:26: 11000000 INFO @ Sat, 11 Dec 2021 16:22:27: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:22:27: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:22:27: #1 total tags in treatment: 10308486 INFO @ Sat, 11 Dec 2021 16:22:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:22:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:22:27: #1 tags after filtering in treatment: 5721936 INFO @ Sat, 11 Dec 2021 16:22:27: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 11 Dec 2021 16:22:27: #1 finished! INFO @ Sat, 11 Dec 2021 16:22:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:22:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:22:28: #2 number of paired peaks: 9564 INFO @ Sat, 11 Dec 2021 16:22:28: start model_add_line... INFO @ Sat, 11 Dec 2021 16:22:28: 14000000 INFO @ Sat, 11 Dec 2021 16:22:28: start X-correlation... INFO @ Sat, 11 Dec 2021 16:22:29: end of X-cor INFO @ Sat, 11 Dec 2021 16:22:29: #2 finished! INFO @ Sat, 11 Dec 2021 16:22:29: #2 predicted fragment length is 183 bps INFO @ Sat, 11 Dec 2021 16:22:29: #2 alternative fragment length(s) may be 183 bps INFO @ Sat, 11 Dec 2021 16:22:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.05_model.r INFO @ Sat, 11 Dec 2021 16:22:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:22:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:22:32: 12000000 INFO @ Sat, 11 Dec 2021 16:22:36: 15000000 INFO @ Sat, 11 Dec 2021 16:22:39: 13000000 INFO @ Sat, 11 Dec 2021 16:22:43: 16000000 INFO @ Sat, 11 Dec 2021 16:22:46: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 16:22:51: 17000000 INFO @ Sat, 11 Dec 2021 16:22:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:22:53: 15000000 INFO @ Sat, 11 Dec 2021 16:22:58: 18000000 INFO @ Sat, 11 Dec 2021 16:23:00: 16000000 INFO @ Sat, 11 Dec 2021 16:23:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.05_peaks.xls INFO @ Sat, 11 Dec 2021 16:23:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:23:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.05_summits.bed INFO @ Sat, 11 Dec 2021 16:23:03: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9326 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:23:06: 19000000 INFO @ Sat, 11 Dec 2021 16:23:06: 17000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 16:23:13: 18000000 INFO @ Sat, 11 Dec 2021 16:23:13: 20000000 INFO @ Sat, 11 Dec 2021 16:23:20: 19000000 INFO @ Sat, 11 Dec 2021 16:23:21: 21000000 INFO @ Sat, 11 Dec 2021 16:23:25: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:23:25: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:23:25: #1 total tags in treatment: 10308486 INFO @ Sat, 11 Dec 2021 16:23:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:23:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:23:25: #1 tags after filtering in treatment: 5721936 INFO @ Sat, 11 Dec 2021 16:23:25: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 11 Dec 2021 16:23:25: #1 finished! INFO @ Sat, 11 Dec 2021 16:23:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:23:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:23:26: #2 number of paired peaks: 9564 INFO @ Sat, 11 Dec 2021 16:23:26: start model_add_line... INFO @ Sat, 11 Dec 2021 16:23:27: 20000000 INFO @ Sat, 11 Dec 2021 16:23:27: start X-correlation... INFO @ Sat, 11 Dec 2021 16:23:27: end of X-cor INFO @ Sat, 11 Dec 2021 16:23:27: #2 finished! INFO @ Sat, 11 Dec 2021 16:23:27: #2 predicted fragment length is 183 bps INFO @ Sat, 11 Dec 2021 16:23:27: #2 alternative fragment length(s) may be 183 bps INFO @ Sat, 11 Dec 2021 16:23:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.10_model.r INFO @ Sat, 11 Dec 2021 16:23:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:23:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:23:33: 21000000 INFO @ Sat, 11 Dec 2021 16:23:36: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:23:36: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:23:36: #1 total tags in treatment: 10308486 INFO @ Sat, 11 Dec 2021 16:23:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:23:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:23:37: #1 tags after filtering in treatment: 5721936 INFO @ Sat, 11 Dec 2021 16:23:37: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 11 Dec 2021 16:23:37: #1 finished! INFO @ Sat, 11 Dec 2021 16:23:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:23:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:23:38: #2 number of paired peaks: 9564 INFO @ Sat, 11 Dec 2021 16:23:38: start model_add_line... INFO @ Sat, 11 Dec 2021 16:23:38: start X-correlation... INFO @ Sat, 11 Dec 2021 16:23:38: end of X-cor INFO @ Sat, 11 Dec 2021 16:23:38: #2 finished! INFO @ Sat, 11 Dec 2021 16:23:38: #2 predicted fragment length is 183 bps INFO @ Sat, 11 Dec 2021 16:23:38: #2 alternative fragment length(s) may be 183 bps INFO @ Sat, 11 Dec 2021 16:23:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.20_model.r INFO @ Sat, 11 Dec 2021 16:23:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:23:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:23:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:23:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.10_peaks.xls INFO @ Sat, 11 Dec 2021 16:23:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:23:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.10_summits.bed INFO @ Sat, 11 Dec 2021 16:23:59: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8441 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:24:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:24:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.20_peaks.xls INFO @ Sat, 11 Dec 2021 16:24:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:24:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628898/SRX7628898.20_summits.bed INFO @ Sat, 11 Dec 2021 16:24:11: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7252 records, 4 fields): 16 millis CompletedMACS2peakCalling