Job ID = 14167279 SRX = SRX8076970 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16827256 spots for SRR11504842/SRR11504842.sra Written 16827256 spots for SRR11504842/SRR11504842.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167927 ("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: 00:10:28 16827256 reads; of these: 16827256 (100.00%) were paired; of these: 10931410 (64.96%) aligned concordantly 0 times 5127127 (30.47%) aligned concordantly exactly 1 time 768719 (4.57%) aligned concordantly >1 times ---- 10931410 pairs aligned concordantly 0 times; of these: 495479 (4.53%) aligned discordantly 1 time ---- 10435931 pairs aligned 0 times concordantly or discordantly; of these: 20871862 mates make up the pairs; of these: 20264137 (97.09%) aligned 0 times 390318 (1.87%) aligned exactly 1 time 217407 (1.04%) aligned >1 times 39.79% overall alignment rate Time searching: 00:10:28 Overall time: 00:10:28 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] 897179 / 6387709 = 0.1405 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 11:47:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.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 11:47:59: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:47:59: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:48:04: 1000000 INFO @ Fri, 10 Dec 2021 11:48:10: 2000000 INFO @ Fri, 10 Dec 2021 11:48:15: 3000000 INFO @ Fri, 10 Dec 2021 11:48:20: 4000000 INFO @ Fri, 10 Dec 2021 11:48:26: 5000000 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 11:48:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.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 11:48:28: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:48:28: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:48:32: 6000000 INFO @ Fri, 10 Dec 2021 11:48:35: 1000000 INFO @ Fri, 10 Dec 2021 11:48:38: 7000000 INFO @ Fri, 10 Dec 2021 11:48:41: 2000000 INFO @ Fri, 10 Dec 2021 11:48:45: 8000000 INFO @ Fri, 10 Dec 2021 11:48:47: 3000000 INFO @ Fri, 10 Dec 2021 11:48:51: 9000000 INFO @ Fri, 10 Dec 2021 11:48:54: 4000000 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 11:48:57: 10000000 INFO @ Fri, 10 Dec 2021 11:48:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.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 11:48:58: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:48:58: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:49:00: 5000000 INFO @ Fri, 10 Dec 2021 11:49:04: 11000000 INFO @ Fri, 10 Dec 2021 11:49:04: 1000000 INFO @ Fri, 10 Dec 2021 11:49:07: 6000000 INFO @ Fri, 10 Dec 2021 11:49:07: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 11:49:07: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 11:49:07: #1 total tags in treatment: 5050809 INFO @ Fri, 10 Dec 2021 11:49:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:49:07: #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 11:49:08: #1 tags after filtering in treatment: 4942207 INFO @ Fri, 10 Dec 2021 11:49:08: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:49:08: #1 finished! INFO @ Fri, 10 Dec 2021 11:49:08: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:49:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:49:08: #2 number of paired peaks: 382 WARNING @ Fri, 10 Dec 2021 11:49:08: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Fri, 10 Dec 2021 11:49:08: start model_add_line... INFO @ Fri, 10 Dec 2021 11:49:08: start X-correlation... INFO @ Fri, 10 Dec 2021 11:49:08: end of X-cor INFO @ Fri, 10 Dec 2021 11:49:08: #2 finished! INFO @ Fri, 10 Dec 2021 11:49:08: #2 predicted fragment length is 235 bps INFO @ Fri, 10 Dec 2021 11:49:08: #2 alternative fragment length(s) may be 184,201,235 bps INFO @ Fri, 10 Dec 2021 11:49:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.05_model.r INFO @ Fri, 10 Dec 2021 11:49:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:49:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:49:11: 2000000 INFO @ Fri, 10 Dec 2021 11:49:13: 7000000 INFO @ Fri, 10 Dec 2021 11:49:17: 3000000 INFO @ Fri, 10 Dec 2021 11:49:19: 8000000 INFO @ Fri, 10 Dec 2021 11:49:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:49:23: 4000000 INFO @ Fri, 10 Dec 2021 11:49:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:49:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:49:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.05_summits.bed INFO @ Fri, 10 Dec 2021 11:49:25: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (998 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:49:26: 9000000 INFO @ Fri, 10 Dec 2021 11:49:30: 5000000 INFO @ Fri, 10 Dec 2021 11:49:32: 10000000 INFO @ Fri, 10 Dec 2021 11:49:36: 6000000 INFO @ Fri, 10 Dec 2021 11:49:38: 11000000 INFO @ Fri, 10 Dec 2021 11:49:42: 7000000 INFO @ Fri, 10 Dec 2021 11:49:42: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 11:49:42: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 11:49:42: #1 total tags in treatment: 5050809 INFO @ Fri, 10 Dec 2021 11:49:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:49:42: #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 11:49:42: #1 tags after filtering in treatment: 4942207 INFO @ Fri, 10 Dec 2021 11:49:42: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:49:42: #1 finished! INFO @ Fri, 10 Dec 2021 11:49:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:49:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:49:42: #2 number of paired peaks: 382 WARNING @ Fri, 10 Dec 2021 11:49:42: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Fri, 10 Dec 2021 11:49:42: start model_add_line... INFO @ Fri, 10 Dec 2021 11:49:43: start X-correlation... INFO @ Fri, 10 Dec 2021 11:49:43: end of X-cor INFO @ Fri, 10 Dec 2021 11:49:43: #2 finished! INFO @ Fri, 10 Dec 2021 11:49:43: #2 predicted fragment length is 235 bps INFO @ Fri, 10 Dec 2021 11:49:43: #2 alternative fragment length(s) may be 184,201,235 bps INFO @ Fri, 10 Dec 2021 11:49:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.10_model.r INFO @ Fri, 10 Dec 2021 11:49:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:49:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:49:48: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:49:53: 9000000 INFO @ Fri, 10 Dec 2021 11:49:53: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:49:59: 10000000 INFO @ Fri, 10 Dec 2021 11:49:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:49:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:49:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.10_summits.bed INFO @ Fri, 10 Dec 2021 11:49:59: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (155 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:50:04: 11000000 INFO @ Fri, 10 Dec 2021 11:50:07: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 11:50:07: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 11:50:07: #1 total tags in treatment: 5050809 INFO @ Fri, 10 Dec 2021 11:50:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:50:07: #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 11:50:07: #1 tags after filtering in treatment: 4942207 INFO @ Fri, 10 Dec 2021 11:50:07: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:50:07: #1 finished! INFO @ Fri, 10 Dec 2021 11:50:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:50:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:50:08: #2 number of paired peaks: 382 WARNING @ Fri, 10 Dec 2021 11:50:08: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Fri, 10 Dec 2021 11:50:08: start model_add_line... INFO @ Fri, 10 Dec 2021 11:50:08: start X-correlation... INFO @ Fri, 10 Dec 2021 11:50:08: end of X-cor INFO @ Fri, 10 Dec 2021 11:50:08: #2 finished! INFO @ Fri, 10 Dec 2021 11:50:08: #2 predicted fragment length is 235 bps INFO @ Fri, 10 Dec 2021 11:50:08: #2 alternative fragment length(s) may be 184,201,235 bps INFO @ Fri, 10 Dec 2021 11:50:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.20_model.r INFO @ Fri, 10 Dec 2021 11:50:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:50:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:50:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:50:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:50:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:50:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076970/SRX8076970.20_summits.bed INFO @ Fri, 10 Dec 2021 11:50:24: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (23 records, 4 fields): 1 millis CompletedMACS2peakCalling