Job ID = 14171347 SRX = SRX9005682 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 1023943 READS because READLEN < 1 Read 15188844 spots for SRR12515083/SRR12515083.sra Written 15188844 spots for SRR12515083/SRR12515083.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172009 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) 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 20 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] 1 unmatched pairs [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 1 unmatched pairs [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] 1 unmatched pairs [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] 1 unmatched pairs [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] 1 unmatched pairs [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] 23 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2500493 / 12925676 = 0.1935 in library ' ' awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted 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 12:14:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.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 12:14:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:14:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:15:04: 1000000 INFO @ Sat, 11 Dec 2021 12:15:13: 2000000 INFO @ Sat, 11 Dec 2021 12:15:21: 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 12:15:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.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 12:15:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:15:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:15:29: 4000000 INFO @ Sat, 11 Dec 2021 12:15:35: 1000000 INFO @ Sat, 11 Dec 2021 12:15:38: 5000000 INFO @ Sat, 11 Dec 2021 12:15:43: 2000000 INFO @ Sat, 11 Dec 2021 12:15:47: 6000000 INFO @ Sat, 11 Dec 2021 12:15:51: 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 12:15:56: 7000000 INFO @ Sat, 11 Dec 2021 12:15:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.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 12:15:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:15:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:15:59: 4000000 INFO @ Sat, 11 Dec 2021 12:16:05: 8000000 INFO @ Sat, 11 Dec 2021 12:16:06: 1000000 INFO @ Sat, 11 Dec 2021 12:16:07: 5000000 INFO @ Sat, 11 Dec 2021 12:16:14: 9000000 INFO @ Sat, 11 Dec 2021 12:16:15: 2000000 INFO @ Sat, 11 Dec 2021 12:16:15: 6000000 INFO @ Sat, 11 Dec 2021 12:16:23: 10000000 INFO @ Sat, 11 Dec 2021 12:16:24: 7000000 INFO @ Sat, 11 Dec 2021 12:16:24: 3000000 INFO @ Sat, 11 Dec 2021 12:16:32: 8000000 INFO @ Sat, 11 Dec 2021 12:16:32: 11000000 INFO @ Sat, 11 Dec 2021 12:16:34: 4000000 INFO @ Sat, 11 Dec 2021 12:16:40: 9000000 INFO @ Sat, 11 Dec 2021 12:16:41: 12000000 INFO @ Sat, 11 Dec 2021 12:16:43: 5000000 INFO @ Sat, 11 Dec 2021 12:16:48: 10000000 INFO @ Sat, 11 Dec 2021 12:16:49: 13000000 INFO @ Sat, 11 Dec 2021 12:16:52: 6000000 INFO @ Sat, 11 Dec 2021 12:16:56: 11000000 INFO @ Sat, 11 Dec 2021 12:16:58: 14000000 INFO @ Sat, 11 Dec 2021 12:17:02: 7000000 INFO @ Sat, 11 Dec 2021 12:17:04: 12000000 INFO @ Sat, 11 Dec 2021 12:17:07: 15000000 INFO @ Sat, 11 Dec 2021 12:17:11: 8000000 INFO @ Sat, 11 Dec 2021 12:17:13: 13000000 INFO @ Sat, 11 Dec 2021 12:17:16: 16000000 INFO @ Sat, 11 Dec 2021 12:17:20: 9000000 INFO @ Sat, 11 Dec 2021 12:17:21: 14000000 INFO @ Sat, 11 Dec 2021 12:17:26: 17000000 INFO @ Sat, 11 Dec 2021 12:17:29: 15000000 INFO @ Sat, 11 Dec 2021 12:17:30: 10000000 INFO @ Sat, 11 Dec 2021 12:17:35: 18000000 INFO @ Sat, 11 Dec 2021 12:17:37: 16000000 INFO @ Sat, 11 Dec 2021 12:17:39: 11000000 INFO @ Sat, 11 Dec 2021 12:17:44: 19000000 INFO @ Sat, 11 Dec 2021 12:17:45: 17000000 INFO @ Sat, 11 Dec 2021 12:17:48: 12000000 INFO @ Sat, 11 Dec 2021 12:17:53: 20000000 INFO @ Sat, 11 Dec 2021 12:17:54: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:17:57: 13000000 INFO @ Sat, 11 Dec 2021 12:18:02: 19000000 INFO @ Sat, 11 Dec 2021 12:18:02: 21000000 INFO @ Sat, 11 Dec 2021 12:18:06: 14000000 INFO @ Sat, 11 Dec 2021 12:18:11: 20000000 INFO @ Sat, 11 Dec 2021 12:18:12: 22000000 INFO @ Sat, 11 Dec 2021 12:18:14: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 12:18:14: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 12:18:14: #1 total tags in treatment: 10358191 INFO @ Sat, 11 Dec 2021 12:18:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:18:14: #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 12:18:14: #1 tags after filtering in treatment: 9698484 INFO @ Sat, 11 Dec 2021 12:18:14: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 12:18:14: #1 finished! INFO @ Sat, 11 Dec 2021 12:18:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:18:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:18:15: #2 number of paired peaks: 639 WARNING @ Sat, 11 Dec 2021 12:18:15: Fewer paired peaks (639) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 639 pairs to build model! INFO @ Sat, 11 Dec 2021 12:18:15: start model_add_line... INFO @ Sat, 11 Dec 2021 12:18:15: start X-correlation... INFO @ Sat, 11 Dec 2021 12:18:15: end of X-cor INFO @ Sat, 11 Dec 2021 12:18:15: #2 finished! INFO @ Sat, 11 Dec 2021 12:18:15: #2 predicted fragment length is 255 bps INFO @ Sat, 11 Dec 2021 12:18:15: #2 alternative fragment length(s) may be 255 bps INFO @ Sat, 11 Dec 2021 12:18:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.05_model.r INFO @ Sat, 11 Dec 2021 12:18:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:18:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:18:16: 15000000 INFO @ Sat, 11 Dec 2021 12:18:19: 21000000 INFO @ Sat, 11 Dec 2021 12:18:24: 16000000 INFO @ Sat, 11 Dec 2021 12:18:27: 22000000 INFO @ Sat, 11 Dec 2021 12:18:29: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 12:18:29: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 12:18:29: #1 total tags in treatment: 10358191 INFO @ Sat, 11 Dec 2021 12:18:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:18:29: #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 12:18:29: #1 tags after filtering in treatment: 9698484 INFO @ Sat, 11 Dec 2021 12:18:29: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 12:18:29: #1 finished! INFO @ Sat, 11 Dec 2021 12:18:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:18:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:18:30: #2 number of paired peaks: 639 WARNING @ Sat, 11 Dec 2021 12:18:30: Fewer paired peaks (639) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 639 pairs to build model! INFO @ Sat, 11 Dec 2021 12:18:30: start model_add_line... INFO @ Sat, 11 Dec 2021 12:18:30: start X-correlation... INFO @ Sat, 11 Dec 2021 12:18:30: end of X-cor INFO @ Sat, 11 Dec 2021 12:18:30: #2 finished! INFO @ Sat, 11 Dec 2021 12:18:30: #2 predicted fragment length is 255 bps INFO @ Sat, 11 Dec 2021 12:18:30: #2 alternative fragment length(s) may be 255 bps INFO @ Sat, 11 Dec 2021 12:18:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.10_model.r INFO @ Sat, 11 Dec 2021 12:18:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:18:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:18:33: 17000000 INFO @ Sat, 11 Dec 2021 12:18:35: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:18:42: 18000000 INFO @ Sat, 11 Dec 2021 12:18:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:18:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:18:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.05_summits.bed INFO @ Sat, 11 Dec 2021 12:18:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4635 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:18:50: 19000000 INFO @ Sat, 11 Dec 2021 12:18:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:18:58: 20000000 INFO @ Sat, 11 Dec 2021 12:19:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:19:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:19:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.10_summits.bed INFO @ Sat, 11 Dec 2021 12:19:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2593 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:19:07: 21000000 INFO @ Sat, 11 Dec 2021 12:19:16: 22000000 INFO @ Sat, 11 Dec 2021 12:19:18: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 12:19:18: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 12:19:18: #1 total tags in treatment: 10358191 INFO @ Sat, 11 Dec 2021 12:19:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:19:18: #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 12:19:18: #1 tags after filtering in treatment: 9698484 INFO @ Sat, 11 Dec 2021 12:19:18: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 12:19:18: #1 finished! INFO @ Sat, 11 Dec 2021 12:19:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:19:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:19:18: #2 number of paired peaks: 639 WARNING @ Sat, 11 Dec 2021 12:19:18: Fewer paired peaks (639) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 639 pairs to build model! INFO @ Sat, 11 Dec 2021 12:19:18: start model_add_line... INFO @ Sat, 11 Dec 2021 12:19:18: start X-correlation... INFO @ Sat, 11 Dec 2021 12:19:18: end of X-cor INFO @ Sat, 11 Dec 2021 12:19:18: #2 finished! INFO @ Sat, 11 Dec 2021 12:19:18: #2 predicted fragment length is 255 bps INFO @ Sat, 11 Dec 2021 12:19:18: #2 alternative fragment length(s) may be 255 bps INFO @ Sat, 11 Dec 2021 12:19:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.20_model.r INFO @ Sat, 11 Dec 2021 12:19:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:19:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:19:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:19:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:19:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:19:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005682/SRX9005682.20_summits.bed INFO @ Sat, 11 Dec 2021 12:19:49: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1283 records, 4 fields): 3 millis CompletedMACS2peakCalling