Job ID = 14171286 SRX = SRX9986138 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 54908870 spots for SRR13591557/SRR13591557.sra Written 54908870 spots for SRR13591557/SRR13591557.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171802 ("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: 00:25:22 54908870 reads; of these: 54908870 (100.00%) were unpaired; of these: 2717458 (4.95%) aligned 0 times 19919783 (36.28%) aligned exactly 1 time 32271629 (58.77%) aligned >1 times 95.05% overall alignment rate Time searching: 00:25:22 Overall time: 00:25:22 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 24 files... [bam_rmdupse_core] 28968154 / 52191412 = 0.5550 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 11:32:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.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 11:32:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:32:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:32:15: 1000000 INFO @ Sat, 11 Dec 2021 11:32:20: 2000000 INFO @ Sat, 11 Dec 2021 11:32:26: 3000000 INFO @ Sat, 11 Dec 2021 11:32:32: 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 11:32:38: 5000000 INFO @ Sat, 11 Dec 2021 11:32:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.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 11:32:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:32:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:32:44: 1000000 INFO @ Sat, 11 Dec 2021 11:32:44: 6000000 INFO @ Sat, 11 Dec 2021 11:32:49: 2000000 INFO @ Sat, 11 Dec 2021 11:32:51: 7000000 INFO @ Sat, 11 Dec 2021 11:32:54: 3000000 INFO @ Sat, 11 Dec 2021 11:32:57: 8000000 INFO @ Sat, 11 Dec 2021 11:32:59: 4000000 INFO @ Sat, 11 Dec 2021 11:33:03: 9000000 INFO @ Sat, 11 Dec 2021 11:33:05: 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 @ Sat, 11 Dec 2021 11:33:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.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 11:33:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:33:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:33:09: 10000000 INFO @ Sat, 11 Dec 2021 11:33:10: 6000000 INFO @ Sat, 11 Dec 2021 11:33:14: 1000000 INFO @ Sat, 11 Dec 2021 11:33:15: 11000000 INFO @ Sat, 11 Dec 2021 11:33:15: 7000000 INFO @ Sat, 11 Dec 2021 11:33:19: 2000000 INFO @ Sat, 11 Dec 2021 11:33:20: 8000000 INFO @ Sat, 11 Dec 2021 11:33:21: 12000000 INFO @ Sat, 11 Dec 2021 11:33:24: 3000000 INFO @ Sat, 11 Dec 2021 11:33:25: 9000000 INFO @ Sat, 11 Dec 2021 11:33:27: 13000000 INFO @ Sat, 11 Dec 2021 11:33:30: 4000000 INFO @ Sat, 11 Dec 2021 11:33:31: 10000000 INFO @ Sat, 11 Dec 2021 11:33:33: 14000000 INFO @ Sat, 11 Dec 2021 11:33:35: 5000000 INFO @ Sat, 11 Dec 2021 11:33:36: 11000000 INFO @ Sat, 11 Dec 2021 11:33:40: 15000000 INFO @ Sat, 11 Dec 2021 11:33:40: 6000000 INFO @ Sat, 11 Dec 2021 11:33:41: 12000000 INFO @ Sat, 11 Dec 2021 11:33:45: 7000000 INFO @ Sat, 11 Dec 2021 11:33:46: 16000000 INFO @ Sat, 11 Dec 2021 11:33:46: 13000000 INFO @ Sat, 11 Dec 2021 11:33:51: 8000000 INFO @ Sat, 11 Dec 2021 11:33:51: 14000000 INFO @ Sat, 11 Dec 2021 11:33:52: 17000000 INFO @ Sat, 11 Dec 2021 11:33:56: 9000000 INFO @ Sat, 11 Dec 2021 11:33:57: 15000000 INFO @ Sat, 11 Dec 2021 11:33:58: 18000000 INFO @ Sat, 11 Dec 2021 11:34:01: 10000000 INFO @ Sat, 11 Dec 2021 11:34:02: 16000000 INFO @ Sat, 11 Dec 2021 11:34:04: 19000000 INFO @ Sat, 11 Dec 2021 11:34:06: 11000000 INFO @ Sat, 11 Dec 2021 11:34:07: 17000000 INFO @ Sat, 11 Dec 2021 11:34:10: 20000000 INFO @ Sat, 11 Dec 2021 11:34:12: 12000000 INFO @ Sat, 11 Dec 2021 11:34:12: 18000000 INFO @ Sat, 11 Dec 2021 11:34:16: 21000000 INFO @ Sat, 11 Dec 2021 11:34:17: 13000000 INFO @ Sat, 11 Dec 2021 11:34:17: 19000000 INFO @ Sat, 11 Dec 2021 11:34:22: 14000000 INFO @ Sat, 11 Dec 2021 11:34:22: 22000000 INFO @ Sat, 11 Dec 2021 11:34:23: 20000000 INFO @ Sat, 11 Dec 2021 11:34:27: 15000000 INFO @ Sat, 11 Dec 2021 11:34:28: 21000000 INFO @ Sat, 11 Dec 2021 11:34:28: 23000000 INFO @ Sat, 11 Dec 2021 11:34:30: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:34:30: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:34:30: #1 total tags in treatment: 23223258 INFO @ Sat, 11 Dec 2021 11:34:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:34:30: #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 11:34:30: #1 tags after filtering in treatment: 23223258 INFO @ Sat, 11 Dec 2021 11:34:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:34:30: #1 finished! INFO @ Sat, 11 Dec 2021 11:34:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:34:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:34:32: #2 number of paired peaks: 406 WARNING @ Sat, 11 Dec 2021 11:34:32: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Sat, 11 Dec 2021 11:34:32: start model_add_line... INFO @ Sat, 11 Dec 2021 11:34:32: start X-correlation... INFO @ Sat, 11 Dec 2021 11:34:32: end of X-cor INFO @ Sat, 11 Dec 2021 11:34:32: #2 finished! INFO @ Sat, 11 Dec 2021 11:34:32: #2 predicted fragment length is 194 bps INFO @ Sat, 11 Dec 2021 11:34:32: #2 alternative fragment length(s) may be 194 bps INFO @ Sat, 11 Dec 2021 11:34:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.05_model.r INFO @ Sat, 11 Dec 2021 11:34:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:34:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:34:32: 16000000 INFO @ Sat, 11 Dec 2021 11:34:33: 22000000 INFO @ Sat, 11 Dec 2021 11:34:37: 17000000 INFO @ Sat, 11 Dec 2021 11:34:38: 23000000 INFO @ Sat, 11 Dec 2021 11:34:39: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:34:39: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:34:39: #1 total tags in treatment: 23223258 INFO @ Sat, 11 Dec 2021 11:34:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:34:39: #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 11:34:40: #1 tags after filtering in treatment: 23223258 INFO @ Sat, 11 Dec 2021 11:34:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:34:40: #1 finished! INFO @ Sat, 11 Dec 2021 11:34:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:34:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:34:41: #2 number of paired peaks: 406 WARNING @ Sat, 11 Dec 2021 11:34:41: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Sat, 11 Dec 2021 11:34:41: start model_add_line... INFO @ Sat, 11 Dec 2021 11:34:41: start X-correlation... INFO @ Sat, 11 Dec 2021 11:34:41: end of X-cor INFO @ Sat, 11 Dec 2021 11:34:41: #2 finished! INFO @ Sat, 11 Dec 2021 11:34:41: #2 predicted fragment length is 194 bps INFO @ Sat, 11 Dec 2021 11:34:41: #2 alternative fragment length(s) may be 194 bps INFO @ Sat, 11 Dec 2021 11:34:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.10_model.r INFO @ Sat, 11 Dec 2021 11:34:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:34:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:34:42: 18000000 INFO @ Sat, 11 Dec 2021 11:34:47: 19000000 INFO @ Sat, 11 Dec 2021 11:34:52: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:34:57: 21000000 INFO @ Sat, 11 Dec 2021 11:35:02: 22000000 INFO @ Sat, 11 Dec 2021 11:35:07: 23000000 INFO @ Sat, 11 Dec 2021 11:35:08: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:35:08: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:35:08: #1 total tags in treatment: 23223258 INFO @ Sat, 11 Dec 2021 11:35:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:35:08: #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 11:35:09: #1 tags after filtering in treatment: 23223258 INFO @ Sat, 11 Dec 2021 11:35:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:35:09: #1 finished! INFO @ Sat, 11 Dec 2021 11:35:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:35:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:35:10: #2 number of paired peaks: 406 WARNING @ Sat, 11 Dec 2021 11:35:10: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Sat, 11 Dec 2021 11:35:10: start model_add_line... INFO @ Sat, 11 Dec 2021 11:35:10: start X-correlation... INFO @ Sat, 11 Dec 2021 11:35:10: end of X-cor INFO @ Sat, 11 Dec 2021 11:35:10: #2 finished! INFO @ Sat, 11 Dec 2021 11:35:10: #2 predicted fragment length is 194 bps INFO @ Sat, 11 Dec 2021 11:35:10: #2 alternative fragment length(s) may be 194 bps INFO @ Sat, 11 Dec 2021 11:35:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.20_model.r INFO @ Sat, 11 Dec 2021 11:35:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:35:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:35:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:35:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:35:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:35:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:35:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.05_summits.bed INFO @ Sat, 11 Dec 2021 11:35:49: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (22080 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:35:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:35:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:35:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.10_summits.bed INFO @ Sat, 11 Dec 2021 11:35:53: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (13851 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:35:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:36:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:36:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:36:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986138/SRX9986138.20_summits.bed INFO @ Sat, 11 Dec 2021 11:36:21: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6806 records, 4 fields): 7 millis CompletedMACS2peakCalling