Job ID = 14172177 SRX = SRX9281728 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11065763 spots for SRR12813201/SRR12813201.sra Written 11065763 spots for SRR12813201/SRR12813201.sra Read 10889128 spots for SRR12813202/SRR12813202.sra Written 10889128 spots for SRR12813202/SRR12813202.sra Read 11408334 spots for SRR12813203/SRR12813203.sra Written 11408334 spots for SRR12813203/SRR12813203.sra Read 11138432 spots for SRR12813204/SRR12813204.sra Written 11138432 spots for SRR12813204/SRR12813204.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172697 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:08 44501657 reads; of these: 44501657 (100.00%) were paired; of these: 37622896 (84.54%) aligned concordantly 0 times 5513232 (12.39%) aligned concordantly exactly 1 time 1365529 (3.07%) aligned concordantly >1 times ---- 37622896 pairs aligned concordantly 0 times; of these: 41548 (0.11%) aligned discordantly 1 time ---- 37581348 pairs aligned 0 times concordantly or discordantly; of these: 75162696 mates make up the pairs; of these: 73980583 (98.43%) aligned 0 times 543088 (0.72%) aligned exactly 1 time 639025 (0.85%) aligned >1 times 16.88% overall alignment rate Time searching: 00:14:09 Overall time: 00:14:09 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] 329209 / 6906300 = 0.0477 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 15:00:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.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 15:00:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:00:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:00:31: 1000000 INFO @ Sat, 11 Dec 2021 15:00:36: 2000000 INFO @ Sat, 11 Dec 2021 15:00:40: 3000000 INFO @ Sat, 11 Dec 2021 15:00:45: 4000000 INFO @ Sat, 11 Dec 2021 15:00:49: 5000000 INFO @ Sat, 11 Dec 2021 15:00:54: 6000000 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 15:00:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.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 15:00:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:00:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:00:58: 7000000 INFO @ Sat, 11 Dec 2021 15:01:03: 1000000 INFO @ Sat, 11 Dec 2021 15:01:03: 8000000 INFO @ Sat, 11 Dec 2021 15:01:09: 9000000 INFO @ Sat, 11 Dec 2021 15:01:09: 2000000 INFO @ Sat, 11 Dec 2021 15:01:14: 10000000 INFO @ Sat, 11 Dec 2021 15:01:15: 3000000 INFO @ Sat, 11 Dec 2021 15:01:19: 11000000 INFO @ Sat, 11 Dec 2021 15:01:21: 4000000 INFO @ Sat, 11 Dec 2021 15:01:24: 12000000 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 15:01:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.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 15:01:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:01:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:01:28: 5000000 INFO @ Sat, 11 Dec 2021 15:01:29: 13000000 INFO @ Sat, 11 Dec 2021 15:01:33: 1000000 INFO @ Sat, 11 Dec 2021 15:01:34: 6000000 INFO @ Sat, 11 Dec 2021 15:01:35: 14000000 INFO @ Sat, 11 Dec 2021 15:01:37: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:01:37: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:01:37: #1 total tags in treatment: 6550090 INFO @ Sat, 11 Dec 2021 15:01:37: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:01:37: #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 15:01:37: #1 tags after filtering in treatment: 5953338 INFO @ Sat, 11 Dec 2021 15:01:37: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 15:01:37: #1 finished! INFO @ Sat, 11 Dec 2021 15:01:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:01:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:01:37: #2 number of paired peaks: 1169 INFO @ Sat, 11 Dec 2021 15:01:37: start model_add_line... INFO @ Sat, 11 Dec 2021 15:01:37: start X-correlation... INFO @ Sat, 11 Dec 2021 15:01:37: end of X-cor INFO @ Sat, 11 Dec 2021 15:01:37: #2 finished! INFO @ Sat, 11 Dec 2021 15:01:37: #2 predicted fragment length is 123 bps INFO @ Sat, 11 Dec 2021 15:01:37: #2 alternative fragment length(s) may be 4,123,137,143,591 bps INFO @ Sat, 11 Dec 2021 15:01:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.05_model.r INFO @ Sat, 11 Dec 2021 15:01:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:01:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:01:38: 2000000 INFO @ Sat, 11 Dec 2021 15:01:40: 7000000 INFO @ Sat, 11 Dec 2021 15:01:43: 3000000 INFO @ Sat, 11 Dec 2021 15:01:46: 8000000 INFO @ Sat, 11 Dec 2021 15:01:49: 4000000 INFO @ Sat, 11 Dec 2021 15:01:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:01:52: 9000000 INFO @ Sat, 11 Dec 2021 15:01:54: 5000000 INFO @ Sat, 11 Dec 2021 15:01:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:01:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:01:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.05_summits.bed INFO @ Sat, 11 Dec 2021 15:01:55: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (981 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:01:59: 10000000 INFO @ Sat, 11 Dec 2021 15:01:59: 6000000 INFO @ Sat, 11 Dec 2021 15:02:04: 7000000 INFO @ Sat, 11 Dec 2021 15:02:05: 11000000 INFO @ Sat, 11 Dec 2021 15:02:10: 8000000 INFO @ Sat, 11 Dec 2021 15:02:11: 12000000 INFO @ Sat, 11 Dec 2021 15:02:15: 9000000 INFO @ Sat, 11 Dec 2021 15:02:17: 13000000 INFO @ Sat, 11 Dec 2021 15:02:20: 10000000 INFO @ Sat, 11 Dec 2021 15:02:23: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:02:25: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:02:25: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:02:25: #1 total tags in treatment: 6550090 INFO @ Sat, 11 Dec 2021 15:02:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:02:25: #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 15:02:25: #1 tags after filtering in treatment: 5953338 INFO @ Sat, 11 Dec 2021 15:02:25: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 15:02:25: #1 finished! INFO @ Sat, 11 Dec 2021 15:02:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:02:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:02:25: #2 number of paired peaks: 1169 INFO @ Sat, 11 Dec 2021 15:02:25: start model_add_line... INFO @ Sat, 11 Dec 2021 15:02:25: start X-correlation... INFO @ Sat, 11 Dec 2021 15:02:25: end of X-cor INFO @ Sat, 11 Dec 2021 15:02:25: #2 finished! INFO @ Sat, 11 Dec 2021 15:02:25: #2 predicted fragment length is 123 bps INFO @ Sat, 11 Dec 2021 15:02:25: #2 alternative fragment length(s) may be 4,123,137,143,591 bps INFO @ Sat, 11 Dec 2021 15:02:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.10_model.r INFO @ Sat, 11 Dec 2021 15:02:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:02:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:02:25: 11000000 INFO @ Sat, 11 Dec 2021 15:02:30: 12000000 INFO @ Sat, 11 Dec 2021 15:02:35: 13000000 INFO @ Sat, 11 Dec 2021 15:02:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:02:40: 14000000 INFO @ Sat, 11 Dec 2021 15:02:42: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:02:42: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:02:42: #1 total tags in treatment: 6550090 INFO @ Sat, 11 Dec 2021 15:02:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:02:42: #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 15:02:42: #1 tags after filtering in treatment: 5953338 INFO @ Sat, 11 Dec 2021 15:02:42: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 15:02:42: #1 finished! INFO @ Sat, 11 Dec 2021 15:02:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:02:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:02:43: #2 number of paired peaks: 1169 INFO @ Sat, 11 Dec 2021 15:02:43: start model_add_line... INFO @ Sat, 11 Dec 2021 15:02:43: start X-correlation... INFO @ Sat, 11 Dec 2021 15:02:43: end of X-cor INFO @ Sat, 11 Dec 2021 15:02:43: #2 finished! INFO @ Sat, 11 Dec 2021 15:02:43: #2 predicted fragment length is 123 bps INFO @ Sat, 11 Dec 2021 15:02:43: #2 alternative fragment length(s) may be 4,123,137,143,591 bps INFO @ Sat, 11 Dec 2021 15:02:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.20_model.r INFO @ Sat, 11 Dec 2021 15:02:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:02:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:02:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:02:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:02:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.10_summits.bed INFO @ Sat, 11 Dec 2021 15:02:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (518 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:02:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:03:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:03:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:03:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281728/SRX9281728.20_summits.bed INFO @ Sat, 11 Dec 2021 15:03:01: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (261 records, 4 fields): 2 millis CompletedMACS2peakCalling