Job ID = 14168726 SRX = ERX3978885 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 38836658 spots for ERR3975954/ERR3975954.sra Written 38836658 spots for ERR3975954/ERR3975954.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169925 ("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: 01:43:58 38836658 reads; of these: 38836658 (100.00%) were paired; of these: 5106441 (13.15%) aligned concordantly 0 times 27562508 (70.97%) aligned concordantly exactly 1 time 6167709 (15.88%) aligned concordantly >1 times ---- 5106441 pairs aligned concordantly 0 times; of these: 797792 (15.62%) aligned discordantly 1 time ---- 4308649 pairs aligned 0 times concordantly or discordantly; of these: 8617298 mates make up the pairs; of these: 4155899 (48.23%) aligned 0 times 2402524 (27.88%) aligned exactly 1 time 2058875 (23.89%) aligned >1 times 94.65% overall alignment rate Time searching: 01:43:58 Overall time: 01:43:58 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 32 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] 22581550 / 34358412 = 0.6572 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 21:55:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.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 21:55:55: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:55:55: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:56:00: 1000000 INFO @ Fri, 10 Dec 2021 21:56:06: 2000000 INFO @ Fri, 10 Dec 2021 21:56:11: 3000000 INFO @ Fri, 10 Dec 2021 21:56:16: 4000000 INFO @ Fri, 10 Dec 2021 21:56:22: 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 21:56:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.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 21:56:24: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:56:24: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:56:28: 6000000 INFO @ Fri, 10 Dec 2021 21:56:30: 1000000 INFO @ Fri, 10 Dec 2021 21:56:34: 7000000 INFO @ Fri, 10 Dec 2021 21:56:36: 2000000 INFO @ Fri, 10 Dec 2021 21:56:40: 8000000 INFO @ Fri, 10 Dec 2021 21:56:42: 3000000 INFO @ Fri, 10 Dec 2021 21:56:46: 9000000 INFO @ Fri, 10 Dec 2021 21:56:49: 4000000 BedGraph に変換中... INFO @ Fri, 10 Dec 2021 21:56:52: 10000000 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 21:56:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.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 21:56:54: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:56:54: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:56:55: 5000000 INFO @ Fri, 10 Dec 2021 21:56:59: 11000000 INFO @ Fri, 10 Dec 2021 21:57:01: 1000000 INFO @ Fri, 10 Dec 2021 21:57:01: 6000000 INFO @ Fri, 10 Dec 2021 21:57:05: 12000000 INFO @ Fri, 10 Dec 2021 21:57:07: 7000000 INFO @ Fri, 10 Dec 2021 21:57:07: 2000000 INFO @ Fri, 10 Dec 2021 21:57:12: 13000000 INFO @ Fri, 10 Dec 2021 21:57:13: 8000000 INFO @ Fri, 10 Dec 2021 21:57:13: 3000000 INFO @ Fri, 10 Dec 2021 21:57:18: 14000000 INFO @ Fri, 10 Dec 2021 21:57:19: 9000000 INFO @ Fri, 10 Dec 2021 21:57:20: 4000000 INFO @ Fri, 10 Dec 2021 21:57:24: 15000000 INFO @ Fri, 10 Dec 2021 21:57:25: 10000000 INFO @ Fri, 10 Dec 2021 21:57:26: 5000000 INFO @ Fri, 10 Dec 2021 21:57:31: 16000000 INFO @ Fri, 10 Dec 2021 21:57:32: 11000000 INFO @ Fri, 10 Dec 2021 21:57:33: 6000000 INFO @ Fri, 10 Dec 2021 21:57:37: 17000000 INFO @ Fri, 10 Dec 2021 21:57:38: 12000000 INFO @ Fri, 10 Dec 2021 21:57:39: 7000000 INFO @ Fri, 10 Dec 2021 21:57:43: 18000000 INFO @ Fri, 10 Dec 2021 21:57:44: 13000000 INFO @ Fri, 10 Dec 2021 21:57:45: 8000000 INFO @ Fri, 10 Dec 2021 21:57:50: 14000000 INFO @ Fri, 10 Dec 2021 21:57:50: 19000000 INFO @ Fri, 10 Dec 2021 21:57:52: 9000000 INFO @ Fri, 10 Dec 2021 21:57:56: 15000000 INFO @ Fri, 10 Dec 2021 21:57:56: 20000000 INFO @ Fri, 10 Dec 2021 21:57:58: 10000000 INFO @ Fri, 10 Dec 2021 21:58:02: 16000000 INFO @ Fri, 10 Dec 2021 21:58:03: 21000000 INFO @ Fri, 10 Dec 2021 21:58:04: 11000000 INFO @ Fri, 10 Dec 2021 21:58:08: 17000000 INFO @ Fri, 10 Dec 2021 21:58:09: 22000000 INFO @ Fri, 10 Dec 2021 21:58:11: 12000000 INFO @ Fri, 10 Dec 2021 21:58:15: 18000000 INFO @ Fri, 10 Dec 2021 21:58:16: 23000000 INFO @ Fri, 10 Dec 2021 21:58:17: 13000000 INFO @ Fri, 10 Dec 2021 21:58:21: 19000000 INFO @ Fri, 10 Dec 2021 21:58:22: 24000000 INFO @ Fri, 10 Dec 2021 21:58:24: 14000000 INFO @ Fri, 10 Dec 2021 21:58:27: 20000000 INFO @ Fri, 10 Dec 2021 21:58:29: 25000000 INFO @ Fri, 10 Dec 2021 21:58:30: 15000000 INFO @ Fri, 10 Dec 2021 21:58:33: 21000000 INFO @ Fri, 10 Dec 2021 21:58:35: 26000000 INFO @ Fri, 10 Dec 2021 21:58:36: 16000000 INFO @ Fri, 10 Dec 2021 21:58:40: 22000000 INFO @ Fri, 10 Dec 2021 21:58:42: 27000000 INFO @ Fri, 10 Dec 2021 21:58:43: 17000000 INFO @ Fri, 10 Dec 2021 21:58:46: 23000000 INFO @ Fri, 10 Dec 2021 21:58:48: 28000000 INFO @ Fri, 10 Dec 2021 21:58:49: 18000000 INFO @ Fri, 10 Dec 2021 21:58:50: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 21:58:50: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 21:58:50: #1 total tags in treatment: 11610668 INFO @ Fri, 10 Dec 2021 21:58:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:58:50: #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 21:58:51: #1 tags after filtering in treatment: 10715505 INFO @ Fri, 10 Dec 2021 21:58:51: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 21:58:51: #1 finished! INFO @ Fri, 10 Dec 2021 21:58:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:58:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:58:51: #2 number of paired peaks: 576 WARNING @ Fri, 10 Dec 2021 21:58:51: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Fri, 10 Dec 2021 21:58:51: start model_add_line... INFO @ Fri, 10 Dec 2021 21:58:51: start X-correlation... INFO @ Fri, 10 Dec 2021 21:58:52: end of X-cor INFO @ Fri, 10 Dec 2021 21:58:52: #2 finished! INFO @ Fri, 10 Dec 2021 21:58:52: #2 predicted fragment length is 167 bps INFO @ Fri, 10 Dec 2021 21:58:52: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 10 Dec 2021 21:58:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.05_model.r INFO @ Fri, 10 Dec 2021 21:58:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:58:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:58:52: 24000000 INFO @ Fri, 10 Dec 2021 21:58:56: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 21:58:58: 25000000 INFO @ Fri, 10 Dec 2021 21:59:02: 20000000 INFO @ Fri, 10 Dec 2021 21:59:05: 26000000 INFO @ Fri, 10 Dec 2021 21:59:08: 21000000 INFO @ Fri, 10 Dec 2021 21:59:11: 27000000 INFO @ Fri, 10 Dec 2021 21:59:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:59:14: 22000000 INFO @ Fri, 10 Dec 2021 21:59:17: 28000000 INFO @ Fri, 10 Dec 2021 21:59:19: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 21:59:19: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 21:59:19: #1 total tags in treatment: 11610668 INFO @ Fri, 10 Dec 2021 21:59:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:59:19: #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 21:59:19: #1 tags after filtering in treatment: 10715505 INFO @ Fri, 10 Dec 2021 21:59:19: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 21:59:19: #1 finished! INFO @ Fri, 10 Dec 2021 21:59:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:59:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:59:20: #2 number of paired peaks: 576 WARNING @ Fri, 10 Dec 2021 21:59:20: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Fri, 10 Dec 2021 21:59:20: start model_add_line... INFO @ Fri, 10 Dec 2021 21:59:20: start X-correlation... INFO @ Fri, 10 Dec 2021 21:59:20: end of X-cor INFO @ Fri, 10 Dec 2021 21:59:20: #2 finished! INFO @ Fri, 10 Dec 2021 21:59:20: #2 predicted fragment length is 167 bps INFO @ Fri, 10 Dec 2021 21:59:20: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 10 Dec 2021 21:59:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.10_model.r INFO @ Fri, 10 Dec 2021 21:59:20: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:59:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:59:21: 23000000 INFO @ Fri, 10 Dec 2021 21:59:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.05_peaks.xls INFO @ Fri, 10 Dec 2021 21:59:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:59:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.05_summits.bed INFO @ Fri, 10 Dec 2021 21:59:24: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7929 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:59:27: 24000000 INFO @ Fri, 10 Dec 2021 21:59:33: 25000000 INFO @ Fri, 10 Dec 2021 21:59:39: 26000000 INFO @ Fri, 10 Dec 2021 21:59:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:59:44: 27000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 21:59:50: 28000000 INFO @ Fri, 10 Dec 2021 21:59:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.10_peaks.xls INFO @ Fri, 10 Dec 2021 21:59:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:59:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.10_summits.bed INFO @ Fri, 10 Dec 2021 21:59:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4079 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:59:52: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 21:59:52: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 21:59:52: #1 total tags in treatment: 11610668 INFO @ Fri, 10 Dec 2021 21:59:52: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:59:52: #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 21:59:52: #1 tags after filtering in treatment: 10715505 INFO @ Fri, 10 Dec 2021 21:59:52: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 21:59:52: #1 finished! INFO @ Fri, 10 Dec 2021 21:59:52: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:59:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:59:53: #2 number of paired peaks: 576 WARNING @ Fri, 10 Dec 2021 21:59:53: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Fri, 10 Dec 2021 21:59:53: start model_add_line... INFO @ Fri, 10 Dec 2021 21:59:53: start X-correlation... INFO @ Fri, 10 Dec 2021 21:59:53: end of X-cor INFO @ Fri, 10 Dec 2021 21:59:53: #2 finished! INFO @ Fri, 10 Dec 2021 21:59:53: #2 predicted fragment length is 167 bps INFO @ Fri, 10 Dec 2021 21:59:53: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 10 Dec 2021 21:59:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.20_model.r INFO @ Fri, 10 Dec 2021 21:59:53: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:59:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:00:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:00:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.20_peaks.xls INFO @ Fri, 10 Dec 2021 22:00:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:00:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978885/ERX3978885.20_summits.bed INFO @ Fri, 10 Dec 2021 22:00:25: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1544 records, 4 fields): 4 millis CompletedMACS2peakCalling