Job ID = 14167023 SRX = SRX9717950 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14908425 spots for SRR13288857/SRR13288857.sra Written 14908425 spots for SRR13288857/SRR13288857.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167391 ("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: 00:14:58 14908425 reads; of these: 14908425 (100.00%) were paired; of these: 7534266 (50.54%) aligned concordantly 0 times 5231768 (35.09%) aligned concordantly exactly 1 time 2142391 (14.37%) aligned concordantly >1 times ---- 7534266 pairs aligned concordantly 0 times; of these: 751059 (9.97%) aligned discordantly 1 time ---- 6783207 pairs aligned 0 times concordantly or discordantly; of these: 13566414 mates make up the pairs; of these: 12022086 (88.62%) aligned 0 times 558211 (4.11%) aligned exactly 1 time 986117 (7.27%) aligned >1 times 59.68% overall alignment rate Time searching: 00:14:58 Overall time: 00:14:58 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 8 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] 3782028 / 8070735 = 0.4686 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 09:13:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.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 09:13:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:13:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:13:08: 1000000 INFO @ Fri, 10 Dec 2021 09:13:13: 2000000 INFO @ Fri, 10 Dec 2021 09:13:17: 3000000 INFO @ Fri, 10 Dec 2021 09:13:22: 4000000 INFO @ Fri, 10 Dec 2021 09:13:26: 5000000 INFO @ Fri, 10 Dec 2021 09:13:31: 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 @ Fri, 10 Dec 2021 09:13:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.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 09:13:33: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:13:33: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:13:36: 7000000 INFO @ Fri, 10 Dec 2021 09:13:38: 1000000 INFO @ Fri, 10 Dec 2021 09:13:41: 8000000 INFO @ Fri, 10 Dec 2021 09:13:44: 2000000 INFO @ Fri, 10 Dec 2021 09:13:46: 9000000 INFO @ Fri, 10 Dec 2021 09:13:49: 3000000 INFO @ Fri, 10 Dec 2021 09:13:51: 10000000 INFO @ Fri, 10 Dec 2021 09:13:52: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 09:13:52: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 09:13:52: #1 total tags in treatment: 3924327 INFO @ Fri, 10 Dec 2021 09:13:52: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:13:52: #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 09:13:52: #1 tags after filtering in treatment: 3569952 INFO @ Fri, 10 Dec 2021 09:13:52: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 09:13:52: #1 finished! INFO @ Fri, 10 Dec 2021 09:13:52: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:13:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:13:52: #2 number of paired peaks: 433 WARNING @ Fri, 10 Dec 2021 09:13:52: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Fri, 10 Dec 2021 09:13:52: start model_add_line... INFO @ Fri, 10 Dec 2021 09:13:52: start X-correlation... INFO @ Fri, 10 Dec 2021 09:13:52: end of X-cor INFO @ Fri, 10 Dec 2021 09:13:52: #2 finished! INFO @ Fri, 10 Dec 2021 09:13:52: #2 predicted fragment length is 86 bps INFO @ Fri, 10 Dec 2021 09:13:52: #2 alternative fragment length(s) may be 86 bps INFO @ Fri, 10 Dec 2021 09:13:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.05_model.r INFO @ Fri, 10 Dec 2021 09:13:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:13:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:13:54: 4000000 INFO @ Fri, 10 Dec 2021 09:13:58: 5000000 INFO @ Fri, 10 Dec 2021 09:14:00: #3 Call peaks for each chromosome... 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 @ Fri, 10 Dec 2021 09:14:03: 6000000 INFO @ Fri, 10 Dec 2021 09:14:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.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 09:14:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:14:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:14:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.05_peaks.xls INFO @ Fri, 10 Dec 2021 09:14:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:14:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.05_summits.bed INFO @ Fri, 10 Dec 2021 09:14:04: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1442 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 09:14:08: 7000000 INFO @ Fri, 10 Dec 2021 09:14:09: 1000000 INFO @ Fri, 10 Dec 2021 09:14:13: 8000000 INFO @ Fri, 10 Dec 2021 09:14:14: 2000000 INFO @ Fri, 10 Dec 2021 09:14:18: 9000000 INFO @ Fri, 10 Dec 2021 09:14:19: 3000000 INFO @ Fri, 10 Dec 2021 09:14:23: 10000000 INFO @ Fri, 10 Dec 2021 09:14:24: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 09:14:24: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 09:14:24: #1 total tags in treatment: 3924327 INFO @ Fri, 10 Dec 2021 09:14:24: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:14:24: #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 09:14:24: #1 tags after filtering in treatment: 3569952 INFO @ Fri, 10 Dec 2021 09:14:24: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 09:14:24: #1 finished! INFO @ Fri, 10 Dec 2021 09:14:24: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:14:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:14:24: 4000000 INFO @ Fri, 10 Dec 2021 09:14:25: #2 number of paired peaks: 433 WARNING @ Fri, 10 Dec 2021 09:14:25: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Fri, 10 Dec 2021 09:14:25: start model_add_line... INFO @ Fri, 10 Dec 2021 09:14:25: start X-correlation... INFO @ Fri, 10 Dec 2021 09:14:25: end of X-cor INFO @ Fri, 10 Dec 2021 09:14:25: #2 finished! INFO @ Fri, 10 Dec 2021 09:14:25: #2 predicted fragment length is 86 bps INFO @ Fri, 10 Dec 2021 09:14:25: #2 alternative fragment length(s) may be 86 bps INFO @ Fri, 10 Dec 2021 09:14:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.10_model.r INFO @ Fri, 10 Dec 2021 09:14:25: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:14:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:14:29: 5000000 INFO @ Fri, 10 Dec 2021 09:14:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:14:34: 6000000 INFO @ Fri, 10 Dec 2021 09:14:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.10_peaks.xls INFO @ Fri, 10 Dec 2021 09:14:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:14:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.10_summits.bed INFO @ Fri, 10 Dec 2021 09:14:36: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (535 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 09:14:38: 7000000 INFO @ Fri, 10 Dec 2021 09:14:43: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 09:14:48: 9000000 INFO @ Fri, 10 Dec 2021 09:14:52: 10000000 INFO @ Fri, 10 Dec 2021 09:14:53: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 09:14:53: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 09:14:53: #1 total tags in treatment: 3924327 INFO @ Fri, 10 Dec 2021 09:14:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:14:53: #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 09:14:53: #1 tags after filtering in treatment: 3569952 INFO @ Fri, 10 Dec 2021 09:14:53: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 09:14:53: #1 finished! INFO @ Fri, 10 Dec 2021 09:14:53: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:14:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:14:53: #2 number of paired peaks: 433 WARNING @ Fri, 10 Dec 2021 09:14:53: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Fri, 10 Dec 2021 09:14:53: start model_add_line... INFO @ Fri, 10 Dec 2021 09:14:54: start X-correlation... INFO @ Fri, 10 Dec 2021 09:14:54: end of X-cor INFO @ Fri, 10 Dec 2021 09:14:54: #2 finished! INFO @ Fri, 10 Dec 2021 09:14:54: #2 predicted fragment length is 86 bps INFO @ Fri, 10 Dec 2021 09:14:54: #2 alternative fragment length(s) may be 86 bps INFO @ Fri, 10 Dec 2021 09:14:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.20_model.r INFO @ Fri, 10 Dec 2021 09:14:54: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:14:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:15:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:15:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.20_peaks.xls INFO @ Fri, 10 Dec 2021 09:15:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:15:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9717950/SRX9717950.20_summits.bed INFO @ Fri, 10 Dec 2021 09:15:05: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (204 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。