Job ID = 14171473 SRX = SRX10971111 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-11T02:46:10 prefetch.2.10.7: 1) Downloading 'SRR14631235'... 2021-12-11T02:46:10 prefetch.2.10.7: Downloading via HTTPS... 2021-12-11T02:47:19 prefetch.2.10.7: HTTPS download succeed 2021-12-11T02:47:19 prefetch.2.10.7: 1) 'SRR14631235' was downloaded successfully 2021-12-11T02:47:19 prefetch.2.10.7: 'SRR14631235' has 0 unresolved dependencies Read 17225755 spots for SRR14631235/SRR14631235.sra Written 17225755 spots for SRR14631235/SRR14631235.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172242 ("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: 01:11:14 17225755 reads; of these: 17225755 (100.00%) were paired; of these: 1558459 (9.05%) aligned concordantly 0 times 13268635 (77.03%) aligned concordantly exactly 1 time 2398661 (13.92%) aligned concordantly >1 times ---- 1558459 pairs aligned concordantly 0 times; of these: 127563 (8.19%) aligned discordantly 1 time ---- 1430896 pairs aligned 0 times concordantly or discordantly; of these: 2861792 mates make up the pairs; of these: 1872044 (65.42%) aligned 0 times 470441 (16.44%) aligned exactly 1 time 519307 (18.15%) aligned >1 times 94.57% overall alignment rate Time searching: 01:11:14 Overall time: 01:11:14 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 16 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] 2417076 / 15701338 = 0.1539 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 13:15:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.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 13:15:10: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:15:10: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:15:17: 1000000 INFO @ Sat, 11 Dec 2021 13:15:25: 2000000 INFO @ Sat, 11 Dec 2021 13:15:32: 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 13:15:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.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 13:15:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:15:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:15:40: 4000000 INFO @ Sat, 11 Dec 2021 13:15:47: 1000000 INFO @ Sat, 11 Dec 2021 13:15:48: 5000000 INFO @ Sat, 11 Dec 2021 13:15:55: 2000000 INFO @ Sat, 11 Dec 2021 13:15:56: 6000000 INFO @ Sat, 11 Dec 2021 13:16:04: 3000000 INFO @ Sat, 11 Dec 2021 13:16:04: 7000000 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 13:16:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.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 13:16:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:16:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:16:12: 4000000 INFO @ Sat, 11 Dec 2021 13:16:12: 8000000 INFO @ Sat, 11 Dec 2021 13:16:18: 1000000 INFO @ Sat, 11 Dec 2021 13:16:19: 5000000 INFO @ Sat, 11 Dec 2021 13:16:21: 9000000 INFO @ Sat, 11 Dec 2021 13:16:27: 2000000 INFO @ Sat, 11 Dec 2021 13:16:28: 6000000 INFO @ Sat, 11 Dec 2021 13:16:29: 10000000 INFO @ Sat, 11 Dec 2021 13:16:36: 7000000 INFO @ Sat, 11 Dec 2021 13:16:36: 3000000 INFO @ Sat, 11 Dec 2021 13:16:37: 11000000 INFO @ Sat, 11 Dec 2021 13:16:44: 8000000 INFO @ Sat, 11 Dec 2021 13:16:45: 12000000 INFO @ Sat, 11 Dec 2021 13:16:45: 4000000 INFO @ Sat, 11 Dec 2021 13:16:52: 9000000 INFO @ Sat, 11 Dec 2021 13:16:53: 13000000 INFO @ Sat, 11 Dec 2021 13:16:54: 5000000 INFO @ Sat, 11 Dec 2021 13:17:00: 10000000 INFO @ Sat, 11 Dec 2021 13:17:01: 14000000 INFO @ Sat, 11 Dec 2021 13:17:03: 6000000 INFO @ Sat, 11 Dec 2021 13:17:08: 11000000 INFO @ Sat, 11 Dec 2021 13:17:09: 15000000 INFO @ Sat, 11 Dec 2021 13:17:12: 7000000 INFO @ Sat, 11 Dec 2021 13:17:16: 12000000 INFO @ Sat, 11 Dec 2021 13:17:17: 16000000 INFO @ Sat, 11 Dec 2021 13:17:20: 8000000 INFO @ Sat, 11 Dec 2021 13:17:24: 13000000 INFO @ Sat, 11 Dec 2021 13:17:25: 17000000 INFO @ Sat, 11 Dec 2021 13:17:29: 9000000 INFO @ Sat, 11 Dec 2021 13:17:33: 14000000 INFO @ Sat, 11 Dec 2021 13:17:34: 18000000 INFO @ Sat, 11 Dec 2021 13:17:38: 10000000 INFO @ Sat, 11 Dec 2021 13:17:41: 15000000 INFO @ Sat, 11 Dec 2021 13:17:41: 19000000 INFO @ Sat, 11 Dec 2021 13:17:47: 11000000 INFO @ Sat, 11 Dec 2021 13:17:50: 16000000 INFO @ Sat, 11 Dec 2021 13:17:50: 20000000 INFO @ Sat, 11 Dec 2021 13:17:56: 12000000 INFO @ Sat, 11 Dec 2021 13:17:57: 17000000 INFO @ Sat, 11 Dec 2021 13:17:58: 21000000 INFO @ Sat, 11 Dec 2021 13:18:05: 13000000 INFO @ Sat, 11 Dec 2021 13:18:05: 18000000 INFO @ Sat, 11 Dec 2021 13:18:06: 22000000 INFO @ Sat, 11 Dec 2021 13:18:13: 19000000 INFO @ Sat, 11 Dec 2021 13:18:13: 14000000 INFO @ Sat, 11 Dec 2021 13:18:14: 23000000 INFO @ Sat, 11 Dec 2021 13:18:21: 20000000 INFO @ Sat, 11 Dec 2021 13:18:22: 24000000 INFO @ Sat, 11 Dec 2021 13:18:22: 15000000 INFO @ Sat, 11 Dec 2021 13:18:29: 21000000 INFO @ Sat, 11 Dec 2021 13:18:30: 25000000 INFO @ Sat, 11 Dec 2021 13:18:31: 16000000 INFO @ Sat, 11 Dec 2021 13:18:37: 22000000 INFO @ Sat, 11 Dec 2021 13:18:38: 26000000 INFO @ Sat, 11 Dec 2021 13:18:40: 17000000 INFO @ Sat, 11 Dec 2021 13:18:45: 23000000 INFO @ Sat, 11 Dec 2021 13:18:46: 27000000 INFO @ Sat, 11 Dec 2021 13:18:48: 18000000 INFO @ Sat, 11 Dec 2021 13:18:52: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 13:18:52: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 13:18:52: #1 total tags in treatment: 13258454 INFO @ Sat, 11 Dec 2021 13:18:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:18:52: #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 13:18:52: #1 tags after filtering in treatment: 12665512 INFO @ Sat, 11 Dec 2021 13:18:52: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 13:18:52: #1 finished! INFO @ Sat, 11 Dec 2021 13:18:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:18:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:18:53: 24000000 INFO @ Sat, 11 Dec 2021 13:18:53: #2 number of paired peaks: 269 WARNING @ Sat, 11 Dec 2021 13:18:53: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Sat, 11 Dec 2021 13:18:53: start model_add_line... INFO @ Sat, 11 Dec 2021 13:18:53: start X-correlation... INFO @ Sat, 11 Dec 2021 13:18:53: end of X-cor INFO @ Sat, 11 Dec 2021 13:18:53: #2 finished! INFO @ Sat, 11 Dec 2021 13:18:53: #2 predicted fragment length is 235 bps INFO @ Sat, 11 Dec 2021 13:18:53: #2 alternative fragment length(s) may be 235 bps INFO @ Sat, 11 Dec 2021 13:18:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.05_model.r INFO @ Sat, 11 Dec 2021 13:18:55: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:18:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:18:57: 19000000 INFO @ Sat, 11 Dec 2021 13:19:00: 25000000 INFO @ Sat, 11 Dec 2021 13:19:06: 20000000 INFO @ Sat, 11 Dec 2021 13:19:08: 26000000 INFO @ Sat, 11 Dec 2021 13:19:14: 21000000 INFO @ Sat, 11 Dec 2021 13:19:16: 27000000 INFO @ Sat, 11 Dec 2021 13:19:22: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 13:19:22: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 13:19:22: #1 total tags in treatment: 13258454 INFO @ Sat, 11 Dec 2021 13:19:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:19:22: #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 13:19:22: #1 tags after filtering in treatment: 12665512 INFO @ Sat, 11 Dec 2021 13:19:22: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 13:19:22: #1 finished! INFO @ Sat, 11 Dec 2021 13:19:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:19:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:19:23: #2 number of paired peaks: 269 WARNING @ Sat, 11 Dec 2021 13:19:23: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Sat, 11 Dec 2021 13:19:23: start model_add_line... INFO @ Sat, 11 Dec 2021 13:19:23: start X-correlation... INFO @ Sat, 11 Dec 2021 13:19:23: end of X-cor INFO @ Sat, 11 Dec 2021 13:19:23: #2 finished! INFO @ Sat, 11 Dec 2021 13:19:23: #2 predicted fragment length is 235 bps INFO @ Sat, 11 Dec 2021 13:19:23: #2 alternative fragment length(s) may be 235 bps INFO @ Sat, 11 Dec 2021 13:19:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.10_model.r INFO @ Sat, 11 Dec 2021 13:19:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:19:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:19:23: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:19:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:19:32: 23000000 INFO @ Sat, 11 Dec 2021 13:19:40: 24000000 INFO @ Sat, 11 Dec 2021 13:19:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:19:49: 25000000 INFO @ Sat, 11 Dec 2021 13:19:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:19:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.05_summits.bed INFO @ Sat, 11 Dec 2021 13:19:53: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (916 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:19:58: 26000000 INFO @ Sat, 11 Dec 2021 13:19:59: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:20:06: 27000000 INFO @ Sat, 11 Dec 2021 13:20:13: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 13:20:13: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 13:20:13: #1 total tags in treatment: 13258454 INFO @ Sat, 11 Dec 2021 13:20:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:20:13: #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 13:20:13: #1 tags after filtering in treatment: 12665512 INFO @ Sat, 11 Dec 2021 13:20:13: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 13:20:13: #1 finished! INFO @ Sat, 11 Dec 2021 13:20:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:20:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:20:14: #2 number of paired peaks: 269 WARNING @ Sat, 11 Dec 2021 13:20:14: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Sat, 11 Dec 2021 13:20:14: start model_add_line... INFO @ Sat, 11 Dec 2021 13:20:14: start X-correlation... INFO @ Sat, 11 Dec 2021 13:20:14: end of X-cor INFO @ Sat, 11 Dec 2021 13:20:14: #2 finished! INFO @ Sat, 11 Dec 2021 13:20:14: #2 predicted fragment length is 235 bps INFO @ Sat, 11 Dec 2021 13:20:14: #2 alternative fragment length(s) may be 235 bps INFO @ Sat, 11 Dec 2021 13:20:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.20_model.r INFO @ Sat, 11 Dec 2021 13:20:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:20:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:20:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:20:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:20:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.10_summits.bed INFO @ Sat, 11 Dec 2021 13:20:17: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (629 records, 4 fields): 52 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:20:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:21:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:21:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:21:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971111/SRX10971111.20_summits.bed INFO @ Sat, 11 Dec 2021 13:21:08: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (428 records, 4 fields): 53 millis CompletedMACS2peakCalling