Job ID = 14171156 SRX = SRX9986104 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 25873067 spots for SRR13591498/SRR13591498.sra Written 25873067 spots for SRR13591498/SRR13591498.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171636 ("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: 00:09:15 25873067 reads; of these: 25873067 (100.00%) were unpaired; of these: 1078205 (4.17%) aligned 0 times 14640669 (56.59%) aligned exactly 1 time 10154193 (39.25%) aligned >1 times 95.83% overall alignment rate Time searching: 00:09:15 Overall time: 00:09:15 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_rmdupse_core] 8173127 / 24794862 = 0.3296 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 10:26:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.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 10:26:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:26:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:26:54: 1000000 INFO @ Sat, 11 Dec 2021 10:27:00: 2000000 INFO @ Sat, 11 Dec 2021 10:27:07: 3000000 INFO @ Sat, 11 Dec 2021 10:27:13: 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 10:27:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.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 10:27:18: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:27:18: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:27:20: 5000000 INFO @ Sat, 11 Dec 2021 10:27:25: 1000000 INFO @ Sat, 11 Dec 2021 10:27:27: 6000000 INFO @ Sat, 11 Dec 2021 10:27:32: 2000000 INFO @ Sat, 11 Dec 2021 10:27:34: 7000000 INFO @ Sat, 11 Dec 2021 10:27:39: 3000000 INFO @ Sat, 11 Dec 2021 10:27:41: 8000000 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 10:27:46: 4000000 INFO @ Sat, 11 Dec 2021 10:27:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.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 10:27:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:27:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:27:48: 9000000 INFO @ Sat, 11 Dec 2021 10:27:53: 5000000 INFO @ Sat, 11 Dec 2021 10:27:55: 1000000 INFO @ Sat, 11 Dec 2021 10:27:55: 10000000 INFO @ Sat, 11 Dec 2021 10:28:00: 6000000 INFO @ Sat, 11 Dec 2021 10:28:02: 2000000 INFO @ Sat, 11 Dec 2021 10:28:02: 11000000 INFO @ Sat, 11 Dec 2021 10:28:07: 7000000 INFO @ Sat, 11 Dec 2021 10:28:09: 3000000 INFO @ Sat, 11 Dec 2021 10:28:09: 12000000 INFO @ Sat, 11 Dec 2021 10:28:14: 8000000 INFO @ Sat, 11 Dec 2021 10:28:16: 13000000 INFO @ Sat, 11 Dec 2021 10:28:16: 4000000 INFO @ Sat, 11 Dec 2021 10:28:21: 9000000 INFO @ Sat, 11 Dec 2021 10:28:23: 14000000 INFO @ Sat, 11 Dec 2021 10:28:23: 5000000 INFO @ Sat, 11 Dec 2021 10:28:28: 10000000 INFO @ Sat, 11 Dec 2021 10:28:29: 15000000 INFO @ Sat, 11 Dec 2021 10:28:30: 6000000 INFO @ Sat, 11 Dec 2021 10:28:35: 11000000 INFO @ Sat, 11 Dec 2021 10:28:36: 16000000 INFO @ Sat, 11 Dec 2021 10:28:37: 7000000 INFO @ Sat, 11 Dec 2021 10:28:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 10:28:41: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 10:28:41: #1 total tags in treatment: 16621735 INFO @ Sat, 11 Dec 2021 10:28:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:28:41: #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 10:28:41: #1 tags after filtering in treatment: 16621735 INFO @ Sat, 11 Dec 2021 10:28:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:28:41: #1 finished! INFO @ Sat, 11 Dec 2021 10:28:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:28:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:28:42: #2 number of paired peaks: 267 WARNING @ Sat, 11 Dec 2021 10:28:42: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Sat, 11 Dec 2021 10:28:42: start model_add_line... INFO @ Sat, 11 Dec 2021 10:28:42: start X-correlation... INFO @ Sat, 11 Dec 2021 10:28:42: end of X-cor INFO @ Sat, 11 Dec 2021 10:28:42: #2 finished! INFO @ Sat, 11 Dec 2021 10:28:42: #2 predicted fragment length is 168 bps INFO @ Sat, 11 Dec 2021 10:28:42: #2 alternative fragment length(s) may be 168,585 bps INFO @ Sat, 11 Dec 2021 10:28:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.05_model.r INFO @ Sat, 11 Dec 2021 10:28:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:28:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:28:42: 12000000 INFO @ Sat, 11 Dec 2021 10:28:44: 8000000 INFO @ Sat, 11 Dec 2021 10:28:49: 13000000 INFO @ Sat, 11 Dec 2021 10:28:51: 9000000 INFO @ Sat, 11 Dec 2021 10:28:56: 14000000 INFO @ Sat, 11 Dec 2021 10:28:58: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 10:29:03: 15000000 INFO @ Sat, 11 Dec 2021 10:29:05: 11000000 INFO @ Sat, 11 Dec 2021 10:29:10: 16000000 INFO @ Sat, 11 Dec 2021 10:29:11: 12000000 INFO @ Sat, 11 Dec 2021 10:29:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:29:14: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 10:29:14: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 10:29:14: #1 total tags in treatment: 16621735 INFO @ Sat, 11 Dec 2021 10:29:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:29:14: #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 10:29:14: #1 tags after filtering in treatment: 16621735 INFO @ Sat, 11 Dec 2021 10:29:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:29:14: #1 finished! INFO @ Sat, 11 Dec 2021 10:29:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:29:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:29:15: #2 number of paired peaks: 267 WARNING @ Sat, 11 Dec 2021 10:29:15: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Sat, 11 Dec 2021 10:29:15: start model_add_line... INFO @ Sat, 11 Dec 2021 10:29:15: start X-correlation... INFO @ Sat, 11 Dec 2021 10:29:15: end of X-cor INFO @ Sat, 11 Dec 2021 10:29:15: #2 finished! INFO @ Sat, 11 Dec 2021 10:29:15: #2 predicted fragment length is 168 bps INFO @ Sat, 11 Dec 2021 10:29:15: #2 alternative fragment length(s) may be 168,585 bps INFO @ Sat, 11 Dec 2021 10:29:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.10_model.r INFO @ Sat, 11 Dec 2021 10:29:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:29:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:29:18: 13000000 INFO @ Sat, 11 Dec 2021 10:29:24: 14000000 INFO @ Sat, 11 Dec 2021 10:29:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.05_peaks.xls INFO @ Sat, 11 Dec 2021 10:29:31: 15000000 INFO @ Sat, 11 Dec 2021 10:29:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:29:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.05_summits.bed INFO @ Sat, 11 Dec 2021 10:29:31: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (16398 records, 4 fields): 24 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 10:29:37: 16000000 INFO @ Sat, 11 Dec 2021 10:29:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 10:29:41: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 10:29:41: #1 total tags in treatment: 16621735 INFO @ Sat, 11 Dec 2021 10:29:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:29:41: #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 10:29:41: #1 tags after filtering in treatment: 16621735 INFO @ Sat, 11 Dec 2021 10:29:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:29:41: #1 finished! INFO @ Sat, 11 Dec 2021 10:29:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:29:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:29:42: #2 number of paired peaks: 267 WARNING @ Sat, 11 Dec 2021 10:29:42: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Sat, 11 Dec 2021 10:29:42: start model_add_line... INFO @ Sat, 11 Dec 2021 10:29:42: start X-correlation... INFO @ Sat, 11 Dec 2021 10:29:42: end of X-cor INFO @ Sat, 11 Dec 2021 10:29:42: #2 finished! INFO @ Sat, 11 Dec 2021 10:29:42: #2 predicted fragment length is 168 bps INFO @ Sat, 11 Dec 2021 10:29:42: #2 alternative fragment length(s) may be 168,585 bps INFO @ Sat, 11 Dec 2021 10:29:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.20_model.r INFO @ Sat, 11 Dec 2021 10:29:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:29:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:29:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:30:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.10_peaks.xls INFO @ Sat, 11 Dec 2021 10:30:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:30:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.10_summits.bed INFO @ Sat, 11 Dec 2021 10:30:04: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4991 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 10:30:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:30:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.20_peaks.xls INFO @ Sat, 11 Dec 2021 10:30:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:30:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986104/SRX9986104.20_summits.bed INFO @ Sat, 11 Dec 2021 10:30:31: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1058 records, 4 fields): 4 millis CompletedMACS2peakCalling