Job ID = 14171697 SRX = SRX10386221 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24179473 spots for SRR14009286/SRR14009286.sra Written 24179473 spots for SRR14009286/SRR14009286.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172270 ("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: 00:34:14 24179473 reads; of these: 24179473 (100.00%) were paired; of these: 8203722 (33.93%) aligned concordantly 0 times 11014401 (45.55%) aligned concordantly exactly 1 time 4961350 (20.52%) aligned concordantly >1 times ---- 8203722 pairs aligned concordantly 0 times; of these: 407567 (4.97%) aligned discordantly 1 time ---- 7796155 pairs aligned 0 times concordantly or discordantly; of these: 15592310 mates make up the pairs; of these: 14610787 (93.71%) aligned 0 times 477971 (3.07%) aligned exactly 1 time 503552 (3.23%) aligned >1 times 69.79% overall alignment rate Time searching: 00:34:14 Overall time: 00:34:14 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] 1992078 / 16357617 = 0.1218 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 13:14:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.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 13:14:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:14:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:14:09: 1000000 INFO @ Sat, 11 Dec 2021 13:14:15: 2000000 INFO @ Sat, 11 Dec 2021 13:14:20: 3000000 INFO @ Sat, 11 Dec 2021 13:14:25: 4000000 INFO @ Sat, 11 Dec 2021 13:14:30: 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 @ Sat, 11 Dec 2021 13:14:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.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 13:14:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:14:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:14:36: 6000000 INFO @ Sat, 11 Dec 2021 13:14:40: 1000000 INFO @ Sat, 11 Dec 2021 13:14:42: 7000000 INFO @ Sat, 11 Dec 2021 13:14:46: 2000000 INFO @ Sat, 11 Dec 2021 13:14:48: 8000000 INFO @ Sat, 11 Dec 2021 13:14:52: 3000000 INFO @ Sat, 11 Dec 2021 13:14:55: 9000000 INFO @ Sat, 11 Dec 2021 13:14:59: 4000000 INFO @ Sat, 11 Dec 2021 13:15:01: 10000000 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 13:15:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.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 13:15:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:15:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:15:05: 5000000 INFO @ Sat, 11 Dec 2021 13:15:07: 11000000 INFO @ Sat, 11 Dec 2021 13:15:12: 1000000 INFO @ Sat, 11 Dec 2021 13:15:12: 6000000 INFO @ Sat, 11 Dec 2021 13:15:14: 12000000 INFO @ Sat, 11 Dec 2021 13:15:19: 7000000 INFO @ Sat, 11 Dec 2021 13:15:19: 2000000 INFO @ Sat, 11 Dec 2021 13:15:21: 13000000 INFO @ Sat, 11 Dec 2021 13:15:26: 8000000 INFO @ Sat, 11 Dec 2021 13:15:27: 3000000 INFO @ Sat, 11 Dec 2021 13:15:29: 14000000 INFO @ Sat, 11 Dec 2021 13:15:33: 9000000 INFO @ Sat, 11 Dec 2021 13:15:34: 4000000 INFO @ Sat, 11 Dec 2021 13:15:36: 15000000 INFO @ Sat, 11 Dec 2021 13:15:40: 10000000 INFO @ Sat, 11 Dec 2021 13:15:42: 5000000 INFO @ Sat, 11 Dec 2021 13:15:43: 16000000 INFO @ Sat, 11 Dec 2021 13:15:47: 11000000 INFO @ Sat, 11 Dec 2021 13:15:49: 6000000 INFO @ Sat, 11 Dec 2021 13:15:50: 17000000 INFO @ Sat, 11 Dec 2021 13:15:54: 12000000 INFO @ Sat, 11 Dec 2021 13:15:57: 18000000 INFO @ Sat, 11 Dec 2021 13:15:57: 7000000 INFO @ Sat, 11 Dec 2021 13:16:02: 13000000 INFO @ Sat, 11 Dec 2021 13:16:04: 19000000 INFO @ Sat, 11 Dec 2021 13:16:05: 8000000 INFO @ Sat, 11 Dec 2021 13:16:09: 14000000 INFO @ Sat, 11 Dec 2021 13:16:11: 20000000 INFO @ Sat, 11 Dec 2021 13:16:12: 9000000 INFO @ Sat, 11 Dec 2021 13:16:16: 15000000 INFO @ Sat, 11 Dec 2021 13:16:18: 21000000 INFO @ Sat, 11 Dec 2021 13:16:20: 10000000 INFO @ Sat, 11 Dec 2021 13:16:23: 16000000 INFO @ Sat, 11 Dec 2021 13:16:26: 22000000 INFO @ Sat, 11 Dec 2021 13:16:27: 11000000 INFO @ Sat, 11 Dec 2021 13:16:30: 17000000 INFO @ Sat, 11 Dec 2021 13:16:33: 23000000 INFO @ Sat, 11 Dec 2021 13:16:35: 12000000 INFO @ Sat, 11 Dec 2021 13:16:37: 18000000 INFO @ Sat, 11 Dec 2021 13:16:40: 24000000 INFO @ Sat, 11 Dec 2021 13:16:42: 13000000 INFO @ Sat, 11 Dec 2021 13:16:44: 19000000 INFO @ Sat, 11 Dec 2021 13:16:47: 25000000 INFO @ Sat, 11 Dec 2021 13:16:49: 14000000 INFO @ Sat, 11 Dec 2021 13:16:52: 20000000 INFO @ Sat, 11 Dec 2021 13:16:55: 26000000 INFO @ Sat, 11 Dec 2021 13:16:57: 15000000 INFO @ Sat, 11 Dec 2021 13:16:59: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:17:02: 27000000 INFO @ Sat, 11 Dec 2021 13:17:04: 16000000 INFO @ Sat, 11 Dec 2021 13:17:06: 22000000 INFO @ Sat, 11 Dec 2021 13:17:09: 28000000 INFO @ Sat, 11 Dec 2021 13:17:12: 17000000 INFO @ Sat, 11 Dec 2021 13:17:13: 23000000 INFO @ Sat, 11 Dec 2021 13:17:16: 29000000 INFO @ Sat, 11 Dec 2021 13:17:19: 18000000 INFO @ Sat, 11 Dec 2021 13:17:21: 24000000 INFO @ Sat, 11 Dec 2021 13:17:22: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:17:22: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:17:22: #1 total tags in treatment: 13996306 INFO @ Sat, 11 Dec 2021 13:17:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:17:22: #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 13:17:22: #1 tags after filtering in treatment: 12004372 INFO @ Sat, 11 Dec 2021 13:17:22: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 13:17:22: #1 finished! INFO @ Sat, 11 Dec 2021 13:17:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:17:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:17:23: #2 number of paired peaks: 126 WARNING @ Sat, 11 Dec 2021 13:17:23: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sat, 11 Dec 2021 13:17:23: start model_add_line... INFO @ Sat, 11 Dec 2021 13:17:23: start X-correlation... INFO @ Sat, 11 Dec 2021 13:17:23: end of X-cor INFO @ Sat, 11 Dec 2021 13:17:23: #2 finished! INFO @ Sat, 11 Dec 2021 13:17:23: #2 predicted fragment length is 114 bps INFO @ Sat, 11 Dec 2021 13:17:23: #2 alternative fragment length(s) may be 114 bps INFO @ Sat, 11 Dec 2021 13:17:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.05_model.r INFO @ Sat, 11 Dec 2021 13:17:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:17:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:17:27: 19000000 INFO @ Sat, 11 Dec 2021 13:17:27: 25000000 INFO @ Sat, 11 Dec 2021 13:17:34: 20000000 INFO @ Sat, 11 Dec 2021 13:17:34: 26000000 INFO @ Sat, 11 Dec 2021 13:17:41: 27000000 INFO @ Sat, 11 Dec 2021 13:17:42: 21000000 INFO @ Sat, 11 Dec 2021 13:17:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:17:48: 28000000 INFO @ Sat, 11 Dec 2021 13:17:49: 22000000 INFO @ Sat, 11 Dec 2021 13:17:55: 29000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:17:57: 23000000 INFO @ Sat, 11 Dec 2021 13:17:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:17:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:17:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.05_summits.bed INFO @ Sat, 11 Dec 2021 13:17:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1366 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:18:00: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:18:00: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:18:00: #1 total tags in treatment: 13996306 INFO @ Sat, 11 Dec 2021 13:18:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:18:00: #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 13:18:01: #1 tags after filtering in treatment: 12004372 INFO @ Sat, 11 Dec 2021 13:18:01: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 13:18:01: #1 finished! INFO @ Sat, 11 Dec 2021 13:18:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:18:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:18:01: #2 number of paired peaks: 126 WARNING @ Sat, 11 Dec 2021 13:18:01: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sat, 11 Dec 2021 13:18:01: start model_add_line... INFO @ Sat, 11 Dec 2021 13:18:01: start X-correlation... INFO @ Sat, 11 Dec 2021 13:18:01: end of X-cor INFO @ Sat, 11 Dec 2021 13:18:01: #2 finished! INFO @ Sat, 11 Dec 2021 13:18:01: #2 predicted fragment length is 114 bps INFO @ Sat, 11 Dec 2021 13:18:01: #2 alternative fragment length(s) may be 114 bps INFO @ Sat, 11 Dec 2021 13:18:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.10_model.r INFO @ Sat, 11 Dec 2021 13:18:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:18:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:18:04: 24000000 INFO @ Sat, 11 Dec 2021 13:18:10: 25000000 INFO @ Sat, 11 Dec 2021 13:18:17: 26000000 INFO @ Sat, 11 Dec 2021 13:18:24: 27000000 INFO @ Sat, 11 Dec 2021 13:18:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:18:30: 28000000 INFO @ Sat, 11 Dec 2021 13:18:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:18:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:18:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.10_summits.bed INFO @ Sat, 11 Dec 2021 13:18:36: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (897 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:18:37: 29000000 INFO @ Sat, 11 Dec 2021 13:18:42: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:18:42: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:18:42: #1 total tags in treatment: 13996306 INFO @ Sat, 11 Dec 2021 13:18:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:18:42: #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 13:18:42: #1 tags after filtering in treatment: 12004372 INFO @ Sat, 11 Dec 2021 13:18:42: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 13:18:42: #1 finished! INFO @ Sat, 11 Dec 2021 13:18:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:18:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:18:43: #2 number of paired peaks: 126 WARNING @ Sat, 11 Dec 2021 13:18:43: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sat, 11 Dec 2021 13:18:43: start model_add_line... INFO @ Sat, 11 Dec 2021 13:18:43: start X-correlation... INFO @ Sat, 11 Dec 2021 13:18:43: end of X-cor INFO @ Sat, 11 Dec 2021 13:18:43: #2 finished! INFO @ Sat, 11 Dec 2021 13:18:43: #2 predicted fragment length is 114 bps INFO @ Sat, 11 Dec 2021 13:18:43: #2 alternative fragment length(s) may be 114 bps INFO @ Sat, 11 Dec 2021 13:18:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.20_model.r INFO @ Sat, 11 Dec 2021 13:18:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:18:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:19:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:19:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:19:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:19:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386221/SRX10386221.20_summits.bed INFO @ Sat, 11 Dec 2021 13:19:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (563 records, 4 fields): 1 millis CompletedMACS2peakCalling