Job ID = 14167286 SRX = SRX8076977 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20353336 spots for SRR11504849/SRR11504849.sra Written 20353336 spots for SRR11504849/SRR11504849.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167960 ("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: 00:18:54 20353336 reads; of these: 20353336 (100.00%) were paired; of these: 10250410 (50.36%) aligned concordantly 0 times 7645658 (37.56%) aligned concordantly exactly 1 time 2457268 (12.07%) aligned concordantly >1 times ---- 10250410 pairs aligned concordantly 0 times; of these: 387310 (3.78%) aligned discordantly 1 time ---- 9863100 pairs aligned 0 times concordantly or discordantly; of these: 19726200 mates make up the pairs; of these: 18741520 (95.01%) aligned 0 times 613537 (3.11%) aligned exactly 1 time 371143 (1.88%) aligned >1 times 53.96% overall alignment rate Time searching: 00:18:55 Overall time: 00:18:55 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_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] 904181 / 10479156 = 0.0863 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 12:02:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.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 12:02:15: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:02:15: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:02:20: 1000000 INFO @ Fri, 10 Dec 2021 12:02:25: 2000000 INFO @ Fri, 10 Dec 2021 12:02:29: 3000000 INFO @ Fri, 10 Dec 2021 12:02:34: 4000000 INFO @ Fri, 10 Dec 2021 12:02:38: 5000000 INFO @ Fri, 10 Dec 2021 12:02:43: 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 12:02:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.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 12:02:45: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:02:45: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:02:48: 7000000 INFO @ Fri, 10 Dec 2021 12:02:51: 1000000 INFO @ Fri, 10 Dec 2021 12:02:53: 8000000 INFO @ Fri, 10 Dec 2021 12:02:56: 2000000 INFO @ Fri, 10 Dec 2021 12:02:58: 9000000 INFO @ Fri, 10 Dec 2021 12:03:01: 3000000 INFO @ Fri, 10 Dec 2021 12:03:04: 10000000 INFO @ Fri, 10 Dec 2021 12:03:06: 4000000 INFO @ Fri, 10 Dec 2021 12:03:09: 11000000 INFO @ Fri, 10 Dec 2021 12:03:12: 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 @ Fri, 10 Dec 2021 12:03:14: 12000000 INFO @ Fri, 10 Dec 2021 12:03:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.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 12:03:15: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:03:15: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:03:17: 6000000 INFO @ Fri, 10 Dec 2021 12:03:20: 13000000 INFO @ Fri, 10 Dec 2021 12:03:21: 1000000 INFO @ Fri, 10 Dec 2021 12:03:23: 7000000 INFO @ Fri, 10 Dec 2021 12:03:25: 14000000 INFO @ Fri, 10 Dec 2021 12:03:27: 2000000 INFO @ Fri, 10 Dec 2021 12:03:28: 8000000 INFO @ Fri, 10 Dec 2021 12:03:31: 15000000 INFO @ Fri, 10 Dec 2021 12:03:33: 3000000 INFO @ Fri, 10 Dec 2021 12:03:34: 9000000 INFO @ Fri, 10 Dec 2021 12:03:37: 16000000 INFO @ Fri, 10 Dec 2021 12:03:40: 10000000 INFO @ Fri, 10 Dec 2021 12:03:40: 4000000 INFO @ Fri, 10 Dec 2021 12:03:42: 17000000 INFO @ Fri, 10 Dec 2021 12:03:45: 11000000 INFO @ Fri, 10 Dec 2021 12:03:46: 5000000 INFO @ Fri, 10 Dec 2021 12:03:48: 18000000 INFO @ Fri, 10 Dec 2021 12:03:51: 12000000 INFO @ Fri, 10 Dec 2021 12:03:52: 6000000 INFO @ Fri, 10 Dec 2021 12:03:54: 19000000 INFO @ Fri, 10 Dec 2021 12:03:57: 13000000 INFO @ Fri, 10 Dec 2021 12:03:59: 7000000 INFO @ Fri, 10 Dec 2021 12:04:00: 20000000 INFO @ Fri, 10 Dec 2021 12:04:00: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 12:04:00: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 12:04:00: #1 total tags in treatment: 9225375 INFO @ Fri, 10 Dec 2021 12:04:00: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:04:00: #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 12:04:01: #1 tags after filtering in treatment: 8907773 INFO @ Fri, 10 Dec 2021 12:04:01: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 12:04:01: #1 finished! INFO @ Fri, 10 Dec 2021 12:04:01: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:04:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:04:01: #2 number of paired peaks: 113 WARNING @ Fri, 10 Dec 2021 12:04:01: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Fri, 10 Dec 2021 12:04:01: start model_add_line... INFO @ Fri, 10 Dec 2021 12:04:01: start X-correlation... INFO @ Fri, 10 Dec 2021 12:04:01: end of X-cor INFO @ Fri, 10 Dec 2021 12:04:01: #2 finished! INFO @ Fri, 10 Dec 2021 12:04:01: #2 predicted fragment length is 138 bps INFO @ Fri, 10 Dec 2021 12:04:01: #2 alternative fragment length(s) may be 138 bps INFO @ Fri, 10 Dec 2021 12:04:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.05_model.r INFO @ Fri, 10 Dec 2021 12:04:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:04:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:04:02: 14000000 INFO @ Fri, 10 Dec 2021 12:04:06: 8000000 INFO @ Fri, 10 Dec 2021 12:04:08: 15000000 INFO @ Fri, 10 Dec 2021 12:04:12: 9000000 INFO @ Fri, 10 Dec 2021 12:04:14: 16000000 INFO @ Fri, 10 Dec 2021 12:04:18: 10000000 INFO @ Fri, 10 Dec 2021 12:04:19: 17000000 INFO @ Fri, 10 Dec 2021 12:04:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:04:25: 11000000 INFO @ Fri, 10 Dec 2021 12:04:25: 18000000 INFO @ Fri, 10 Dec 2021 12:04:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:04:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:04:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.05_summits.bed INFO @ Fri, 10 Dec 2021 12:04:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (623 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:04:31: 19000000 INFO @ Fri, 10 Dec 2021 12:04:31: 12000000 INFO @ Fri, 10 Dec 2021 12:04:37: 20000000 INFO @ Fri, 10 Dec 2021 12:04:38: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 12:04:38: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 12:04:38: #1 total tags in treatment: 9225375 INFO @ Fri, 10 Dec 2021 12:04:38: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:04:38: #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 12:04:38: #1 tags after filtering in treatment: 8907773 INFO @ Fri, 10 Dec 2021 12:04:38: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 12:04:38: #1 finished! INFO @ Fri, 10 Dec 2021 12:04:38: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:04:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:04:38: 13000000 INFO @ Fri, 10 Dec 2021 12:04:38: #2 number of paired peaks: 113 WARNING @ Fri, 10 Dec 2021 12:04:38: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Fri, 10 Dec 2021 12:04:38: start model_add_line... INFO @ Fri, 10 Dec 2021 12:04:38: start X-correlation... INFO @ Fri, 10 Dec 2021 12:04:38: end of X-cor INFO @ Fri, 10 Dec 2021 12:04:38: #2 finished! INFO @ Fri, 10 Dec 2021 12:04:38: #2 predicted fragment length is 138 bps INFO @ Fri, 10 Dec 2021 12:04:38: #2 alternative fragment length(s) may be 138 bps INFO @ Fri, 10 Dec 2021 12:04:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.10_model.r INFO @ Fri, 10 Dec 2021 12:04:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:04:38: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:04:44: 14000000 INFO @ Fri, 10 Dec 2021 12:04:50: 15000000 INFO @ Fri, 10 Dec 2021 12:04:55: 16000000 INFO @ Fri, 10 Dec 2021 12:04:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:05:01: 17000000 INFO @ Fri, 10 Dec 2021 12:05:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:05:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:05:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.10_summits.bed INFO @ Fri, 10 Dec 2021 12:05:05: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (411 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:05:07: 18000000 INFO @ Fri, 10 Dec 2021 12:05:13: 19000000 INFO @ Fri, 10 Dec 2021 12:05:19: 20000000 INFO @ Fri, 10 Dec 2021 12:05:19: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 12:05:19: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 12:05:19: #1 total tags in treatment: 9225375 INFO @ Fri, 10 Dec 2021 12:05:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:05:19: #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 12:05:20: #1 tags after filtering in treatment: 8907773 INFO @ Fri, 10 Dec 2021 12:05:20: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 12:05:20: #1 finished! INFO @ Fri, 10 Dec 2021 12:05:20: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:05:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:05:20: #2 number of paired peaks: 113 WARNING @ Fri, 10 Dec 2021 12:05:20: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Fri, 10 Dec 2021 12:05:20: start model_add_line... INFO @ Fri, 10 Dec 2021 12:05:20: start X-correlation... INFO @ Fri, 10 Dec 2021 12:05:20: end of X-cor INFO @ Fri, 10 Dec 2021 12:05:20: #2 finished! INFO @ Fri, 10 Dec 2021 12:05:20: #2 predicted fragment length is 138 bps INFO @ Fri, 10 Dec 2021 12:05:20: #2 alternative fragment length(s) may be 138 bps INFO @ Fri, 10 Dec 2021 12:05:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.20_model.r INFO @ Fri, 10 Dec 2021 12:05:20: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:05:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:05:38: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:05:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:05:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:05:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076977/SRX8076977.20_summits.bed INFO @ Fri, 10 Dec 2021 12:05:47: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (237 records, 4 fields): 1 millis CompletedMACS2peakCalling