Job ID = 14170576 SRX = SRX9720894 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12706888 spots for SRR13291884/SRR13291884.sra Written 12706888 spots for SRR13291884/SRR13291884.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170986 ("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: 00:04:16 12706888 reads; of these: 12706888 (100.00%) were unpaired; of these: 1275847 (10.04%) aligned 0 times 7857621 (61.84%) aligned exactly 1 time 3573420 (28.12%) aligned >1 times 89.96% overall alignment rate Time searching: 00:04:16 Overall time: 00:04:16 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 8 files... [bam_rmdupse_core] 1041172 / 11431041 = 0.0911 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 07:26:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.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 07:26:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:26:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:26:29: 1000000 INFO @ Sat, 11 Dec 2021 07:26:35: 2000000 INFO @ Sat, 11 Dec 2021 07:26:40: 3000000 INFO @ Sat, 11 Dec 2021 07:26:45: 4000000 INFO @ Sat, 11 Dec 2021 07:26:50: 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 @ Sat, 11 Dec 2021 07:26:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.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 07:26:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:26:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:26:56: 6000000 INFO @ Sat, 11 Dec 2021 07:27:01: 7000000 INFO @ Sat, 11 Dec 2021 07:27:01: 1000000 INFO @ Sat, 11 Dec 2021 07:27:07: 8000000 INFO @ Sat, 11 Dec 2021 07:27:08: 2000000 INFO @ Sat, 11 Dec 2021 07:27:12: 9000000 INFO @ Sat, 11 Dec 2021 07:27:15: 3000000 INFO @ Sat, 11 Dec 2021 07:27:17: 10000000 INFO @ Sat, 11 Dec 2021 07:27:20: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:27:20: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:27:20: #1 total tags in treatment: 10389869 INFO @ Sat, 11 Dec 2021 07:27:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:27:20: #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 07:27:20: #1 tags after filtering in treatment: 10389869 INFO @ Sat, 11 Dec 2021 07:27:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:27:20: #1 finished! INFO @ Sat, 11 Dec 2021 07:27:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:27:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:27:21: #2 number of paired peaks: 555 WARNING @ Sat, 11 Dec 2021 07:27:21: Fewer paired peaks (555) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 555 pairs to build model! INFO @ Sat, 11 Dec 2021 07:27:21: start model_add_line... INFO @ Sat, 11 Dec 2021 07:27:21: start X-correlation... INFO @ Sat, 11 Dec 2021 07:27:21: end of X-cor INFO @ Sat, 11 Dec 2021 07:27:21: #2 finished! INFO @ Sat, 11 Dec 2021 07:27:21: #2 predicted fragment length is 172 bps INFO @ Sat, 11 Dec 2021 07:27:21: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 11 Dec 2021 07:27:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.05_model.r INFO @ Sat, 11 Dec 2021 07:27:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:27:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:27:21: 4000000 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 07:27:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.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 07:27:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:27:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:27:28: 5000000 INFO @ Sat, 11 Dec 2021 07:27:30: 1000000 INFO @ Sat, 11 Dec 2021 07:27:34: 6000000 INFO @ Sat, 11 Dec 2021 07:27:36: 2000000 INFO @ Sat, 11 Dec 2021 07:27:40: 7000000 INFO @ Sat, 11 Dec 2021 07:27:41: 3000000 INFO @ Sat, 11 Dec 2021 07:27:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:27:46: 8000000 INFO @ Sat, 11 Dec 2021 07:27:47: 4000000 INFO @ Sat, 11 Dec 2021 07:27:52: 5000000 INFO @ Sat, 11 Dec 2021 07:27:53: 9000000 INFO @ Sat, 11 Dec 2021 07:27:58: 6000000 INFO @ Sat, 11 Dec 2021 07:27:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:27:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:27:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.05_summits.bed INFO @ Sat, 11 Dec 2021 07:27:58: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3554 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:27:59: 10000000 INFO @ Sat, 11 Dec 2021 07:28:02: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:28:02: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:28:02: #1 total tags in treatment: 10389869 INFO @ Sat, 11 Dec 2021 07:28:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:28:02: #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 07:28:02: #1 tags after filtering in treatment: 10389869 INFO @ Sat, 11 Dec 2021 07:28:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:28:02: #1 finished! INFO @ Sat, 11 Dec 2021 07:28:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:28:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:28:03: #2 number of paired peaks: 555 WARNING @ Sat, 11 Dec 2021 07:28:03: Fewer paired peaks (555) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 555 pairs to build model! INFO @ Sat, 11 Dec 2021 07:28:03: start model_add_line... INFO @ Sat, 11 Dec 2021 07:28:03: start X-correlation... INFO @ Sat, 11 Dec 2021 07:28:03: end of X-cor INFO @ Sat, 11 Dec 2021 07:28:03: #2 finished! INFO @ Sat, 11 Dec 2021 07:28:03: #2 predicted fragment length is 172 bps INFO @ Sat, 11 Dec 2021 07:28:03: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 11 Dec 2021 07:28:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.10_model.r INFO @ Sat, 11 Dec 2021 07:28:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:28:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:28:03: 7000000 INFO @ Sat, 11 Dec 2021 07:28:10: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:28:18: 9000000 INFO @ Sat, 11 Dec 2021 07:28:25: 10000000 INFO @ Sat, 11 Dec 2021 07:28:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:28:27: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:28:27: #1 total tags in treatment: 10389869 INFO @ Sat, 11 Dec 2021 07:28:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:28:27: #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 07:28:28: #1 tags after filtering in treatment: 10389869 INFO @ Sat, 11 Dec 2021 07:28:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:28:28: #1 finished! INFO @ Sat, 11 Dec 2021 07:28:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:28:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:28:28: #2 number of paired peaks: 555 WARNING @ Sat, 11 Dec 2021 07:28:28: Fewer paired peaks (555) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 555 pairs to build model! INFO @ Sat, 11 Dec 2021 07:28:28: start model_add_line... INFO @ Sat, 11 Dec 2021 07:28:28: start X-correlation... INFO @ Sat, 11 Dec 2021 07:28:28: end of X-cor INFO @ Sat, 11 Dec 2021 07:28:28: #2 finished! INFO @ Sat, 11 Dec 2021 07:28:28: #2 predicted fragment length is 172 bps INFO @ Sat, 11 Dec 2021 07:28:28: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 11 Dec 2021 07:28:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.20_model.r INFO @ Sat, 11 Dec 2021 07:28:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:28:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:28:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:28:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:28:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:28:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.10_summits.bed INFO @ Sat, 11 Dec 2021 07:28:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2329 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:28:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:29:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:29:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:29:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720894/SRX9720894.20_summits.bed INFO @ Sat, 11 Dec 2021 07:29:07: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1319 records, 4 fields): 3 millis CompletedMACS2peakCalling