Job ID = 14171530 SRX = SRX10386205 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14431833 spots for SRR14009270/SRR14009270.sra Written 14431833 spots for SRR14009270/SRR14009270.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172047 ("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: 00:17:04 14431833 reads; of these: 14431833 (100.00%) were paired; of these: 6263086 (43.40%) aligned concordantly 0 times 5877049 (40.72%) aligned concordantly exactly 1 time 2291698 (15.88%) aligned concordantly >1 times ---- 6263086 pairs aligned concordantly 0 times; of these: 969985 (15.49%) aligned discordantly 1 time ---- 5293101 pairs aligned 0 times concordantly or discordantly; of these: 10586202 mates make up the pairs; of these: 9451468 (89.28%) aligned 0 times 449877 (4.25%) aligned exactly 1 time 684857 (6.47%) aligned >1 times 67.25% overall alignment rate Time searching: 00:17:04 Overall time: 00:17:04 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] 1680982 / 9093136 = 0.1849 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 12:18:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.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 12:18:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:18:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:18:59: 1000000 INFO @ Sat, 11 Dec 2021 12:19:06: 2000000 INFO @ Sat, 11 Dec 2021 12:19:13: 3000000 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 12:19:20: 4000000 INFO @ Sat, 11 Dec 2021 12:19:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.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 12:19:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:19:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:19:27: 5000000 INFO @ Sat, 11 Dec 2021 12:19:29: 1000000 INFO @ Sat, 11 Dec 2021 12:19:35: 6000000 INFO @ Sat, 11 Dec 2021 12:19:36: 2000000 INFO @ Sat, 11 Dec 2021 12:19:43: 3000000 INFO @ Sat, 11 Dec 2021 12:19:44: 7000000 BedGraph に変換中... INFO @ Sat, 11 Dec 2021 12:19:50: 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 12:19:52: 8000000 INFO @ Sat, 11 Dec 2021 12:19:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.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 12:19:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:19:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:19:57: 5000000 INFO @ Sat, 11 Dec 2021 12:19:59: 1000000 INFO @ Sat, 11 Dec 2021 12:20:00: 9000000 INFO @ Sat, 11 Dec 2021 12:20:04: 6000000 INFO @ Sat, 11 Dec 2021 12:20:06: 2000000 INFO @ Sat, 11 Dec 2021 12:20:08: 10000000 INFO @ Sat, 11 Dec 2021 12:20:11: 7000000 INFO @ Sat, 11 Dec 2021 12:20:13: 3000000 INFO @ Sat, 11 Dec 2021 12:20:16: 11000000 INFO @ Sat, 11 Dec 2021 12:20:18: 8000000 INFO @ Sat, 11 Dec 2021 12:20:20: 4000000 INFO @ Sat, 11 Dec 2021 12:20:24: 12000000 INFO @ Sat, 11 Dec 2021 12:20:25: 9000000 INFO @ Sat, 11 Dec 2021 12:20:27: 5000000 INFO @ Sat, 11 Dec 2021 12:20:32: 13000000 INFO @ Sat, 11 Dec 2021 12:20:32: 10000000 INFO @ Sat, 11 Dec 2021 12:20:34: 6000000 INFO @ Sat, 11 Dec 2021 12:20:39: 11000000 INFO @ Sat, 11 Dec 2021 12:20:40: 14000000 INFO @ Sat, 11 Dec 2021 12:20:41: 7000000 INFO @ Sat, 11 Dec 2021 12:20:46: 12000000 INFO @ Sat, 11 Dec 2021 12:20:48: 8000000 INFO @ Sat, 11 Dec 2021 12:20:48: 15000000 INFO @ Sat, 11 Dec 2021 12:20:53: 13000000 INFO @ Sat, 11 Dec 2021 12:20:55: 9000000 INFO @ Sat, 11 Dec 2021 12:20:56: 16000000 INFO @ Sat, 11 Dec 2021 12:20:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:20:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:20:56: #1 total tags in treatment: 6591185 INFO @ Sat, 11 Dec 2021 12:20:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:20:56: #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 12:20:56: #1 tags after filtering in treatment: 6010254 INFO @ Sat, 11 Dec 2021 12:20:56: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 12:20:56: #1 finished! INFO @ Sat, 11 Dec 2021 12:20:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:20:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:20:57: #2 number of paired peaks: 223 WARNING @ Sat, 11 Dec 2021 12:20:57: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Sat, 11 Dec 2021 12:20:57: start model_add_line... INFO @ Sat, 11 Dec 2021 12:20:57: start X-correlation... INFO @ Sat, 11 Dec 2021 12:20:57: end of X-cor INFO @ Sat, 11 Dec 2021 12:20:57: #2 finished! INFO @ Sat, 11 Dec 2021 12:20:57: #2 predicted fragment length is 104 bps INFO @ Sat, 11 Dec 2021 12:20:57: #2 alternative fragment length(s) may be 104 bps INFO @ Sat, 11 Dec 2021 12:20:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.05_model.r INFO @ Sat, 11 Dec 2021 12:20:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:20:57: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:21:00: 14000000 INFO @ Sat, 11 Dec 2021 12:21:02: 10000000 INFO @ Sat, 11 Dec 2021 12:21:07: 15000000 INFO @ Sat, 11 Dec 2021 12:21:08: 11000000 INFO @ Sat, 11 Dec 2021 12:21:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:21:14: 16000000 INFO @ Sat, 11 Dec 2021 12:21:14: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:21:14: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:21:14: #1 total tags in treatment: 6591185 INFO @ Sat, 11 Dec 2021 12:21:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:21:14: #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 12:21:14: #1 tags after filtering in treatment: 6010254 INFO @ Sat, 11 Dec 2021 12:21:14: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 12:21:14: #1 finished! INFO @ Sat, 11 Dec 2021 12:21:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:21:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:21:15: #2 number of paired peaks: 223 WARNING @ Sat, 11 Dec 2021 12:21:15: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Sat, 11 Dec 2021 12:21:15: start model_add_line... INFO @ Sat, 11 Dec 2021 12:21:15: start X-correlation... INFO @ Sat, 11 Dec 2021 12:21:15: end of X-cor INFO @ Sat, 11 Dec 2021 12:21:15: #2 finished! INFO @ Sat, 11 Dec 2021 12:21:15: #2 predicted fragment length is 104 bps INFO @ Sat, 11 Dec 2021 12:21:15: #2 alternative fragment length(s) may be 104 bps INFO @ Sat, 11 Dec 2021 12:21:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.10_model.r INFO @ Sat, 11 Dec 2021 12:21:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:21:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:21:15: 12000000 INFO @ Sat, 11 Dec 2021 12:21:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:21:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:21:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.05_summits.bed INFO @ Sat, 11 Dec 2021 12:21:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (947 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:21:21: 13000000 INFO @ Sat, 11 Dec 2021 12:21:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:21:28: 14000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:21:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:21:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:21:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.10_summits.bed INFO @ Sat, 11 Dec 2021 12:21:33: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (631 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:21:34: 15000000 INFO @ Sat, 11 Dec 2021 12:21:40: 16000000 INFO @ Sat, 11 Dec 2021 12:21:40: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:21:40: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:21:40: #1 total tags in treatment: 6591185 INFO @ Sat, 11 Dec 2021 12:21:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:21:40: #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 12:21:40: #1 tags after filtering in treatment: 6010254 INFO @ Sat, 11 Dec 2021 12:21:40: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 12:21:40: #1 finished! INFO @ Sat, 11 Dec 2021 12:21:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:21:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:21:41: #2 number of paired peaks: 223 WARNING @ Sat, 11 Dec 2021 12:21:41: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Sat, 11 Dec 2021 12:21:41: start model_add_line... INFO @ Sat, 11 Dec 2021 12:21:41: start X-correlation... INFO @ Sat, 11 Dec 2021 12:21:41: end of X-cor INFO @ Sat, 11 Dec 2021 12:21:41: #2 finished! INFO @ Sat, 11 Dec 2021 12:21:41: #2 predicted fragment length is 104 bps INFO @ Sat, 11 Dec 2021 12:21:41: #2 alternative fragment length(s) may be 104 bps INFO @ Sat, 11 Dec 2021 12:21:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.20_model.r INFO @ Sat, 11 Dec 2021 12:21:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:21:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:21:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:21:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:21:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:21:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386205/SRX10386205.20_summits.bed INFO @ Sat, 11 Dec 2021 12:21:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (317 records, 4 fields): 1 millis CompletedMACS2peakCalling