Job ID = 14170556 SRX = SRX9372357 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16818510 spots for SRR12907634/SRR12907634.sra Written 16818510 spots for SRR12907634/SRR12907634.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170997 ("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: 00:14:08 16818510 reads; of these: 16818510 (100.00%) were paired; of these: 8178130 (48.63%) aligned concordantly 0 times 7526832 (44.75%) aligned concordantly exactly 1 time 1113548 (6.62%) aligned concordantly >1 times ---- 8178130 pairs aligned concordantly 0 times; of these: 548720 (6.71%) aligned discordantly 1 time ---- 7629410 pairs aligned 0 times concordantly or discordantly; of these: 15258820 mates make up the pairs; of these: 14621653 (95.82%) aligned 0 times 388563 (2.55%) aligned exactly 1 time 248604 (1.63%) aligned >1 times 56.53% overall alignment rate Time searching: 00:14:08 Overall time: 00:14:08 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] 983111 / 9178172 = 0.1071 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 07:32:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.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 07:32:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:32:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:32:43: 1000000 INFO @ Sat, 11 Dec 2021 07:32:51: 2000000 INFO @ Sat, 11 Dec 2021 07:32:58: 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 07:33:05: 4000000 INFO @ Sat, 11 Dec 2021 07:33:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.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 07:33:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:33:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:33:12: 5000000 INFO @ Sat, 11 Dec 2021 07:33:14: 1000000 INFO @ Sat, 11 Dec 2021 07:33:20: 6000000 INFO @ Sat, 11 Dec 2021 07:33:21: 2000000 INFO @ Sat, 11 Dec 2021 07:33:27: 7000000 INFO @ Sat, 11 Dec 2021 07:33:29: 3000000 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 07:33:35: 8000000 INFO @ Sat, 11 Dec 2021 07:33:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.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 07:33:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:33:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:33:37: 4000000 INFO @ Sat, 11 Dec 2021 07:33:43: 9000000 INFO @ Sat, 11 Dec 2021 07:33:44: 1000000 INFO @ Sat, 11 Dec 2021 07:33:45: 5000000 INFO @ Sat, 11 Dec 2021 07:33:51: 10000000 INFO @ Sat, 11 Dec 2021 07:33:52: 2000000 INFO @ Sat, 11 Dec 2021 07:33:53: 6000000 INFO @ Sat, 11 Dec 2021 07:33:59: 3000000 INFO @ Sat, 11 Dec 2021 07:33:59: 11000000 INFO @ Sat, 11 Dec 2021 07:34:01: 7000000 INFO @ Sat, 11 Dec 2021 07:34:07: 4000000 INFO @ Sat, 11 Dec 2021 07:34:08: 12000000 INFO @ Sat, 11 Dec 2021 07:34:10: 8000000 INFO @ Sat, 11 Dec 2021 07:34:15: 5000000 INFO @ Sat, 11 Dec 2021 07:34:16: 13000000 INFO @ Sat, 11 Dec 2021 07:34:18: 9000000 INFO @ Sat, 11 Dec 2021 07:34:23: 6000000 INFO @ Sat, 11 Dec 2021 07:34:24: 14000000 INFO @ Sat, 11 Dec 2021 07:34:26: 10000000 INFO @ Sat, 11 Dec 2021 07:34:30: 7000000 INFO @ Sat, 11 Dec 2021 07:34:32: 15000000 INFO @ Sat, 11 Dec 2021 07:34:34: 11000000 INFO @ Sat, 11 Dec 2021 07:34:38: 8000000 INFO @ Sat, 11 Dec 2021 07:34:41: 16000000 INFO @ Sat, 11 Dec 2021 07:34:42: 12000000 INFO @ Sat, 11 Dec 2021 07:34:45: 9000000 INFO @ Sat, 11 Dec 2021 07:34:49: 17000000 INFO @ Sat, 11 Dec 2021 07:34:49: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 07:34:49: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 07:34:49: #1 total tags in treatment: 7699586 INFO @ Sat, 11 Dec 2021 07:34:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:34:49: #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 07:34:49: #1 tags after filtering in treatment: 7443411 INFO @ Sat, 11 Dec 2021 07:34:49: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 07:34:49: #1 finished! INFO @ Sat, 11 Dec 2021 07:34:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:34:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:34:50: #2 number of paired peaks: 529 WARNING @ Sat, 11 Dec 2021 07:34:50: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Sat, 11 Dec 2021 07:34:50: start model_add_line... INFO @ Sat, 11 Dec 2021 07:34:50: start X-correlation... INFO @ Sat, 11 Dec 2021 07:34:50: end of X-cor INFO @ Sat, 11 Dec 2021 07:34:50: #2 finished! INFO @ Sat, 11 Dec 2021 07:34:50: #2 predicted fragment length is 271 bps INFO @ Sat, 11 Dec 2021 07:34:50: #2 alternative fragment length(s) may be 3,159,221,240,271,291 bps INFO @ Sat, 11 Dec 2021 07:34:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.05_model.r INFO @ Sat, 11 Dec 2021 07:34:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:34:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:34:50: 13000000 INFO @ Sat, 11 Dec 2021 07:34:54: 10000000 INFO @ Sat, 11 Dec 2021 07:34:58: 14000000 INFO @ Sat, 11 Dec 2021 07:35:02: 11000000 INFO @ Sat, 11 Dec 2021 07:35:05: 15000000 INFO @ Sat, 11 Dec 2021 07:35:07: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:35:10: 12000000 INFO @ Sat, 11 Dec 2021 07:35:13: 16000000 INFO @ Sat, 11 Dec 2021 07:35:17: 13000000 INFO @ Sat, 11 Dec 2021 07:35:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:35:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:35:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.05_summits.bed INFO @ Sat, 11 Dec 2021 07:35:18: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3516 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:35:20: 17000000 INFO @ Sat, 11 Dec 2021 07:35:20: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 07:35:20: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 07:35:20: #1 total tags in treatment: 7699586 INFO @ Sat, 11 Dec 2021 07:35:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:35:20: #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 07:35:20: #1 tags after filtering in treatment: 7443411 INFO @ Sat, 11 Dec 2021 07:35:20: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 07:35:20: #1 finished! INFO @ Sat, 11 Dec 2021 07:35:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:35:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:35:21: #2 number of paired peaks: 529 WARNING @ Sat, 11 Dec 2021 07:35:21: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Sat, 11 Dec 2021 07:35:21: start model_add_line... INFO @ Sat, 11 Dec 2021 07:35:21: start X-correlation... INFO @ Sat, 11 Dec 2021 07:35:21: end of X-cor INFO @ Sat, 11 Dec 2021 07:35:21: #2 finished! INFO @ Sat, 11 Dec 2021 07:35:21: #2 predicted fragment length is 271 bps INFO @ Sat, 11 Dec 2021 07:35:21: #2 alternative fragment length(s) may be 3,159,221,240,271,291 bps INFO @ Sat, 11 Dec 2021 07:35:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.10_model.r INFO @ Sat, 11 Dec 2021 07:35:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:35:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:35:24: 14000000 INFO @ Sat, 11 Dec 2021 07:35:31: 15000000 INFO @ Sat, 11 Dec 2021 07:35:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:35:38: 16000000 INFO @ Sat, 11 Dec 2021 07:35:45: 17000000 INFO @ Sat, 11 Dec 2021 07:35:45: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 07:35:45: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 07:35:45: #1 total tags in treatment: 7699586 INFO @ Sat, 11 Dec 2021 07:35:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:35:45: #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 07:35:46: #1 tags after filtering in treatment: 7443411 INFO @ Sat, 11 Dec 2021 07:35:46: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 07:35:46: #1 finished! INFO @ Sat, 11 Dec 2021 07:35:46: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:35:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:35:46: #2 number of paired peaks: 529 WARNING @ Sat, 11 Dec 2021 07:35:46: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Sat, 11 Dec 2021 07:35:46: start model_add_line... INFO @ Sat, 11 Dec 2021 07:35:46: start X-correlation... INFO @ Sat, 11 Dec 2021 07:35:46: end of X-cor INFO @ Sat, 11 Dec 2021 07:35:46: #2 finished! INFO @ Sat, 11 Dec 2021 07:35:46: #2 predicted fragment length is 271 bps INFO @ Sat, 11 Dec 2021 07:35:46: #2 alternative fragment length(s) may be 3,159,221,240,271,291 bps INFO @ Sat, 11 Dec 2021 07:35:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.20_model.r INFO @ Sat, 11 Dec 2021 07:35:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:35:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:35:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:35:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:35:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.10_summits.bed INFO @ Sat, 11 Dec 2021 07:35:48: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (763 records, 4 fields): 40 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:36:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:36:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:36:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:36:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9372357/SRX9372357.20_summits.bed INFO @ Sat, 11 Dec 2021 07:36:13: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (69 records, 4 fields): 2 millis CompletedMACS2peakCalling