Job ID = 14172311 SRX = SRX9281762 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2078877 spots for SRR12813527/SRR12813527.sra Written 2078877 spots for SRR12813527/SRR12813527.sra Read 2065799 spots for SRR12813528/SRR12813528.sra Written 2065799 spots for SRR12813528/SRR12813528.sra Read 2113786 spots for SRR12813529/SRR12813529.sra Written 2113786 spots for SRR12813529/SRR12813529.sra Read 2097526 spots for SRR12813530/SRR12813530.sra Written 2097526 spots for SRR12813530/SRR12813530.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172759 ("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: 00:01:13 8355988 reads; of these: 8355988 (100.00%) were paired; of these: 8127582 (97.27%) aligned concordantly 0 times 165453 (1.98%) aligned concordantly exactly 1 time 62953 (0.75%) aligned concordantly >1 times ---- 8127582 pairs aligned concordantly 0 times; of these: 362 (0.00%) aligned discordantly 1 time ---- 8127220 pairs aligned 0 times concordantly or discordantly; of these: 16254440 mates make up the pairs; of these: 16206955 (99.71%) aligned 0 times 14924 (0.09%) aligned exactly 1 time 32561 (0.20%) aligned >1 times 3.02% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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] 4502 / 228613 = 0.0197 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 15:08:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.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 15:08:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:08:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:08:04: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:08:04: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:08:04: #1 total tags in treatment: 223909 INFO @ Sat, 11 Dec 2021 15:08:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:08:04: #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 15:08:04: #1 tags after filtering in treatment: 221547 INFO @ Sat, 11 Dec 2021 15:08:04: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:08:04: #1 finished! INFO @ Sat, 11 Dec 2021 15:08:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:08:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:08:04: #2 number of paired peaks: 856 WARNING @ Sat, 11 Dec 2021 15:08:04: Fewer paired peaks (856) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 856 pairs to build model! INFO @ Sat, 11 Dec 2021 15:08:04: start model_add_line... INFO @ Sat, 11 Dec 2021 15:08:04: start X-correlation... INFO @ Sat, 11 Dec 2021 15:08:04: end of X-cor INFO @ Sat, 11 Dec 2021 15:08:04: #2 finished! INFO @ Sat, 11 Dec 2021 15:08:04: #2 predicted fragment length is 90 bps INFO @ Sat, 11 Dec 2021 15:08:04: #2 alternative fragment length(s) may be 90,203,256,564 bps INFO @ Sat, 11 Dec 2021 15:08:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.05_model.r INFO @ Sat, 11 Dec 2021 15:08:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:08:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:08:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:08:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:08:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:08:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.05_summits.bed INFO @ Sat, 11 Dec 2021 15:08:05: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (51 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 15:08:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.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 15:08:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:08:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:08:34: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:08:34: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:08:34: #1 total tags in treatment: 223909 INFO @ Sat, 11 Dec 2021 15:08:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:08:34: #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 15:08:34: #1 tags after filtering in treatment: 221547 INFO @ Sat, 11 Dec 2021 15:08:34: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:08:34: #1 finished! INFO @ Sat, 11 Dec 2021 15:08:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:08:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:08:34: #2 number of paired peaks: 856 WARNING @ Sat, 11 Dec 2021 15:08:34: Fewer paired peaks (856) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 856 pairs to build model! INFO @ Sat, 11 Dec 2021 15:08:34: start model_add_line... INFO @ Sat, 11 Dec 2021 15:08:34: start X-correlation... INFO @ Sat, 11 Dec 2021 15:08:34: end of X-cor INFO @ Sat, 11 Dec 2021 15:08:34: #2 finished! INFO @ Sat, 11 Dec 2021 15:08:34: #2 predicted fragment length is 90 bps INFO @ Sat, 11 Dec 2021 15:08:34: #2 alternative fragment length(s) may be 90,203,256,564 bps INFO @ Sat, 11 Dec 2021 15:08:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.10_model.r INFO @ Sat, 11 Dec 2021 15:08:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:08:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:08:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:08:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:08:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:08:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.10_summits.bed INFO @ Sat, 11 Dec 2021 15:08:36: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 1 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 15:09:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.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 15:09:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:09:02: #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 15:09:04: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:09:04: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:09:04: #1 total tags in treatment: 223909 INFO @ Sat, 11 Dec 2021 15:09:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:09:04: #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 15:09:04: #1 tags after filtering in treatment: 221547 INFO @ Sat, 11 Dec 2021 15:09:04: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:09:04: #1 finished! INFO @ Sat, 11 Dec 2021 15:09:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:09:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:09:04: #2 number of paired peaks: 856 WARNING @ Sat, 11 Dec 2021 15:09:04: Fewer paired peaks (856) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 856 pairs to build model! INFO @ Sat, 11 Dec 2021 15:09:04: start model_add_line... INFO @ Sat, 11 Dec 2021 15:09:04: start X-correlation... INFO @ Sat, 11 Dec 2021 15:09:04: end of X-cor INFO @ Sat, 11 Dec 2021 15:09:04: #2 finished! INFO @ Sat, 11 Dec 2021 15:09:04: #2 predicted fragment length is 90 bps INFO @ Sat, 11 Dec 2021 15:09:04: #2 alternative fragment length(s) may be 90,203,256,564 bps INFO @ Sat, 11 Dec 2021 15:09:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.20_model.r INFO @ Sat, 11 Dec 2021 15:09:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:09:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:09:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:09:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:09:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:09:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281762/SRX9281762.20_summits.bed INFO @ Sat, 11 Dec 2021 15:09:05: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (27 records, 4 fields): 62 millis CompletedMACS2peakCalling