Job ID = 14172221 SRX = SRX9281736 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10851205 spots for SRR12813233/SRR12813233.sra Written 10851205 spots for SRR12813233/SRR12813233.sra Read 10853352 spots for SRR12813234/SRR12813234.sra Written 10853352 spots for SRR12813234/SRR12813234.sra Read 11249119 spots for SRR12813235/SRR12813235.sra Written 11249119 spots for SRR12813235/SRR12813235.sra Read 10274164 spots for SRR12813236/SRR12813236.sra Written 10274164 spots for SRR12813236/SRR12813236.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172734 ("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: 00:11:09 43227840 reads; of these: 43227840 (100.00%) were paired; of these: 39864635 (92.22%) aligned concordantly 0 times 2520806 (5.83%) aligned concordantly exactly 1 time 842399 (1.95%) aligned concordantly >1 times ---- 39864635 pairs aligned concordantly 0 times; of these: 13514 (0.03%) aligned discordantly 1 time ---- 39851121 pairs aligned 0 times concordantly or discordantly; of these: 79702242 mates make up the pairs; of these: 78548025 (98.55%) aligned 0 times 360193 (0.45%) aligned exactly 1 time 794024 (1.00%) aligned >1 times 9.15% overall alignment rate Time searching: 00:11:09 Overall time: 00:11:09 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] 142113 / 3370815 = 0.0422 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 15:05:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.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 15:05:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:05:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:05:58: 1000000 INFO @ Sat, 11 Dec 2021 15:06:04: 2000000 INFO @ Sat, 11 Dec 2021 15:06:10: 3000000 INFO @ Sat, 11 Dec 2021 15:06:17: 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 15:06:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.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 15:06:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:06:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:06:23: 5000000 INFO @ Sat, 11 Dec 2021 15:06:28: 1000000 INFO @ Sat, 11 Dec 2021 15:06:30: 6000000 INFO @ Sat, 11 Dec 2021 15:06:35: 2000000 INFO @ Sat, 11 Dec 2021 15:06:37: 7000000 INFO @ Sat, 11 Dec 2021 15:06:41: 3000000 INFO @ Sat, 11 Dec 2021 15:06:41: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:06:41: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:06:41: #1 total tags in treatment: 3221294 INFO @ Sat, 11 Dec 2021 15:06:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:06:41: #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 15:06:41: #1 tags after filtering in treatment: 3060723 INFO @ Sat, 11 Dec 2021 15:06:41: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 15:06:41: #1 finished! INFO @ Sat, 11 Dec 2021 15:06:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:06:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:06:42: #2 number of paired peaks: 706 WARNING @ Sat, 11 Dec 2021 15:06:42: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Sat, 11 Dec 2021 15:06:42: start model_add_line... INFO @ Sat, 11 Dec 2021 15:06:42: start X-correlation... INFO @ Sat, 11 Dec 2021 15:06:42: end of X-cor INFO @ Sat, 11 Dec 2021 15:06:42: #2 finished! INFO @ Sat, 11 Dec 2021 15:06:42: #2 predicted fragment length is 103 bps INFO @ Sat, 11 Dec 2021 15:06:42: #2 alternative fragment length(s) may be 103,594 bps INFO @ Sat, 11 Dec 2021 15:06:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.05_model.r INFO @ Sat, 11 Dec 2021 15:06:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:06:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:06:47: 4000000 INFO @ Sat, 11 Dec 2021 15:06:48: #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 @ Sat, 11 Dec 2021 15:06:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.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 15:06:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:06:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:06:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:06:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:06:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.05_summits.bed INFO @ Sat, 11 Dec 2021 15:06:52: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (421 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:06:52: 5000000 INFO @ Sat, 11 Dec 2021 15:06:58: 1000000 INFO @ Sat, 11 Dec 2021 15:06:58: 6000000 INFO @ Sat, 11 Dec 2021 15:07:04: 2000000 INFO @ Sat, 11 Dec 2021 15:07:04: 7000000 INFO @ Sat, 11 Dec 2021 15:07:08: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:07:08: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:07:08: #1 total tags in treatment: 3221294 INFO @ Sat, 11 Dec 2021 15:07:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:07:08: #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 15:07:08: #1 tags after filtering in treatment: 3060723 INFO @ Sat, 11 Dec 2021 15:07:08: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 15:07:08: #1 finished! INFO @ Sat, 11 Dec 2021 15:07:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:07:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:07:08: #2 number of paired peaks: 706 WARNING @ Sat, 11 Dec 2021 15:07:08: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Sat, 11 Dec 2021 15:07:08: start model_add_line... INFO @ Sat, 11 Dec 2021 15:07:08: start X-correlation... INFO @ Sat, 11 Dec 2021 15:07:08: end of X-cor INFO @ Sat, 11 Dec 2021 15:07:08: #2 finished! INFO @ Sat, 11 Dec 2021 15:07:08: #2 predicted fragment length is 103 bps INFO @ Sat, 11 Dec 2021 15:07:08: #2 alternative fragment length(s) may be 103,594 bps INFO @ Sat, 11 Dec 2021 15:07:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.10_model.r INFO @ Sat, 11 Dec 2021 15:07:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:07:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:07:10: 3000000 INFO @ Sat, 11 Dec 2021 15:07:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:07:15: 4000000 INFO @ Sat, 11 Dec 2021 15:07:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:07:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:07:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.10_summits.bed INFO @ Sat, 11 Dec 2021 15:07:18: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (207 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:07:20: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:07:25: 6000000 INFO @ Sat, 11 Dec 2021 15:07:29: 7000000 INFO @ Sat, 11 Dec 2021 15:07:32: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:07:32: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:07:32: #1 total tags in treatment: 3221294 INFO @ Sat, 11 Dec 2021 15:07:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:07:32: #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 15:07:32: #1 tags after filtering in treatment: 3060723 INFO @ Sat, 11 Dec 2021 15:07:32: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 15:07:32: #1 finished! INFO @ Sat, 11 Dec 2021 15:07:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:07:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:07:33: #2 number of paired peaks: 706 WARNING @ Sat, 11 Dec 2021 15:07:33: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Sat, 11 Dec 2021 15:07:33: start model_add_line... INFO @ Sat, 11 Dec 2021 15:07:33: start X-correlation... INFO @ Sat, 11 Dec 2021 15:07:33: end of X-cor INFO @ Sat, 11 Dec 2021 15:07:33: #2 finished! INFO @ Sat, 11 Dec 2021 15:07:33: #2 predicted fragment length is 103 bps INFO @ Sat, 11 Dec 2021 15:07:33: #2 alternative fragment length(s) may be 103,594 bps INFO @ Sat, 11 Dec 2021 15:07:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.20_model.r INFO @ Sat, 11 Dec 2021 15:07:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:07:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:07:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:07:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:07:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:07:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281736/SRX9281736.20_summits.bed INFO @ Sat, 11 Dec 2021 15:07:43: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (90 records, 4 fields): 1 millis CompletedMACS2peakCalling