Job ID = 14171434 SRX = SRX9555286 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3683228 spots for SRR13110715/SRR13110715.sra Written 3683228 spots for SRR13110715/SRR13110715.sra Read 3557915 spots for SRR13110716/SRR13110716.sra Written 3557915 spots for SRR13110716/SRR13110716.sra Read 3721582 spots for SRR13110717/SRR13110717.sra Written 3721582 spots for SRR13110717/SRR13110717.sra Read 3619738 spots for SRR13110718/SRR13110718.sra Written 3619738 spots for SRR13110718/SRR13110718.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171916 ("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: 00:02:21 14582463 reads; of these: 14582463 (100.00%) were paired; of these: 14248575 (97.71%) aligned concordantly 0 times 245717 (1.69%) aligned concordantly exactly 1 time 88171 (0.60%) aligned concordantly >1 times ---- 14248575 pairs aligned concordantly 0 times; of these: 1295 (0.01%) aligned discordantly 1 time ---- 14247280 pairs aligned 0 times concordantly or discordantly; of these: 28494560 mates make up the pairs; of these: 28199388 (98.96%) aligned 0 times 115299 (0.40%) aligned exactly 1 time 179873 (0.63%) aligned >1 times 3.31% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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_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] 7543 / 334131 = 0.0226 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 11:43:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.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 11:43:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:43:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:43:14: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:43:14: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:43:14: #1 total tags in treatment: 326355 INFO @ Sat, 11 Dec 2021 11:43:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:43:14: #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 11:43:14: #1 tags after filtering in treatment: 323226 INFO @ Sat, 11 Dec 2021 11:43:14: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:43:14: #1 finished! INFO @ Sat, 11 Dec 2021 11:43:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:43:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:43:14: #2 number of paired peaks: 827 WARNING @ Sat, 11 Dec 2021 11:43:14: Fewer paired peaks (827) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 827 pairs to build model! INFO @ Sat, 11 Dec 2021 11:43:14: start model_add_line... INFO @ Sat, 11 Dec 2021 11:43:14: start X-correlation... INFO @ Sat, 11 Dec 2021 11:43:14: end of X-cor INFO @ Sat, 11 Dec 2021 11:43:14: #2 finished! INFO @ Sat, 11 Dec 2021 11:43:14: #2 predicted fragment length is 94 bps INFO @ Sat, 11 Dec 2021 11:43:14: #2 alternative fragment length(s) may be 94,515 bps INFO @ Sat, 11 Dec 2021 11:43:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.05_model.r INFO @ Sat, 11 Dec 2021 11:43:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:43:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:43:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:43:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:43:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:43:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.05_summits.bed INFO @ Sat, 11 Dec 2021 11:43:15: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (77 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 11:43:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.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 11:43:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:43:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:43:44: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:43:44: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:43:44: #1 total tags in treatment: 326355 INFO @ Sat, 11 Dec 2021 11:43:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:43:44: #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 11:43:44: #1 tags after filtering in treatment: 323226 INFO @ Sat, 11 Dec 2021 11:43:44: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:43:44: #1 finished! INFO @ Sat, 11 Dec 2021 11:43:44: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:43:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:43:44: #2 number of paired peaks: 827 WARNING @ Sat, 11 Dec 2021 11:43:44: Fewer paired peaks (827) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 827 pairs to build model! INFO @ Sat, 11 Dec 2021 11:43:44: start model_add_line... INFO @ Sat, 11 Dec 2021 11:43:44: start X-correlation... INFO @ Sat, 11 Dec 2021 11:43:44: end of X-cor INFO @ Sat, 11 Dec 2021 11:43:44: #2 finished! INFO @ Sat, 11 Dec 2021 11:43:44: #2 predicted fragment length is 94 bps INFO @ Sat, 11 Dec 2021 11:43:44: #2 alternative fragment length(s) may be 94,515 bps INFO @ Sat, 11 Dec 2021 11:43:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.10_model.r INFO @ Sat, 11 Dec 2021 11:43:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:43:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:43:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:43:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:43:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:43:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.10_summits.bed INFO @ Sat, 11 Dec 2021 11:43:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (45 records, 4 fields): 427 millis CompletedMACS2peakCalling 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 11:44:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.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 11:44:10: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:44:10: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:44:14: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:44:14: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:44:14: #1 total tags in treatment: 326355 INFO @ Sat, 11 Dec 2021 11:44:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:44:14: #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 11:44:14: #1 tags after filtering in treatment: 323226 INFO @ Sat, 11 Dec 2021 11:44:14: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:44:14: #1 finished! INFO @ Sat, 11 Dec 2021 11:44:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:44:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:44:15: #2 number of paired peaks: 827 WARNING @ Sat, 11 Dec 2021 11:44:15: Fewer paired peaks (827) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 827 pairs to build model! INFO @ Sat, 11 Dec 2021 11:44:15: start model_add_line... INFO @ Sat, 11 Dec 2021 11:44:15: start X-correlation... INFO @ Sat, 11 Dec 2021 11:44:15: end of X-cor INFO @ Sat, 11 Dec 2021 11:44:15: #2 finished! INFO @ Sat, 11 Dec 2021 11:44:15: #2 predicted fragment length is 94 bps INFO @ Sat, 11 Dec 2021 11:44:15: #2 alternative fragment length(s) may be 94,515 bps INFO @ Sat, 11 Dec 2021 11:44:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.20_model.r INFO @ Sat, 11 Dec 2021 11:44:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:44:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:44:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:44:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:44:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:44:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555286/SRX9555286.20_summits.bed INFO @ Sat, 11 Dec 2021 11:44:16: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (22 records, 4 fields): 6 millis CompletedMACS2peakCalling