Job ID = 14171455 SRX = SRX10971695 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-11T02:42:53 prefetch.2.10.7: 1) Downloading 'SRR14631846'... 2021-12-11T02:42:53 prefetch.2.10.7: Downloading via HTTPS... 2021-12-11T02:43:14 prefetch.2.10.7: HTTPS download succeed 2021-12-11T02:43:15 prefetch.2.10.7: 'SRR14631846' is valid 2021-12-11T02:43:15 prefetch.2.10.7: 1) 'SRR14631846' was downloaded successfully 2021-12-11T02:43:15 prefetch.2.10.7: 'SRR14631846' has 0 unresolved dependencies Rejected 389771 READS because READLEN < 1 Read 3487930 spots for SRR14631846/SRR14631846.sra Written 3487930 spots for SRR14631846/SRR14631846.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171951 ("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_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] 2 unmatched pairs [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] 1 unmatched pairs [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 274285 / 2837503 = 0.0967 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 11:52:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.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 11:52:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:52:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:52:56: 1000000 INFO @ Sat, 11 Dec 2021 11:53:04: 2000000 INFO @ Sat, 11 Dec 2021 11:53:11: 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 11:53:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.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 11:53:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:53:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:53:19: 4000000 INFO @ Sat, 11 Dec 2021 11:53:28: 1000000 INFO @ Sat, 11 Dec 2021 11:53:28: 5000000 INFO @ Sat, 11 Dec 2021 11:53:34: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:53:34: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:53:34: #1 total tags in treatment: 2297875 INFO @ Sat, 11 Dec 2021 11:53:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:53:34: #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 11:53:34: #1 tags after filtering in treatment: 2275124 INFO @ Sat, 11 Dec 2021 11:53:34: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:53:34: #1 finished! INFO @ Sat, 11 Dec 2021 11:53:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:53:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:53:34: #2 number of paired peaks: 122 WARNING @ Sat, 11 Dec 2021 11:53:34: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sat, 11 Dec 2021 11:53:34: start model_add_line... INFO @ Sat, 11 Dec 2021 11:53:34: start X-correlation... INFO @ Sat, 11 Dec 2021 11:53:34: end of X-cor INFO @ Sat, 11 Dec 2021 11:53:34: #2 finished! INFO @ Sat, 11 Dec 2021 11:53:34: #2 predicted fragment length is 262 bps INFO @ Sat, 11 Dec 2021 11:53:34: #2 alternative fragment length(s) may be 244,262,277 bps INFO @ Sat, 11 Dec 2021 11:53:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.05_model.r INFO @ Sat, 11 Dec 2021 11:53:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:53:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:53:37: 2000000 INFO @ Sat, 11 Dec 2021 11:53:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:53:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:53:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:53:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.05_summits.bed INFO @ Sat, 11 Dec 2021 11:53:41: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (110 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:53:45: 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 11:53:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.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 11:53:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:53:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:53:54: 4000000 INFO @ Sat, 11 Dec 2021 11:53:58: 1000000 INFO @ Sat, 11 Dec 2021 11:54:03: 5000000 INFO @ Sat, 11 Dec 2021 11:54:06: 2000000 INFO @ Sat, 11 Dec 2021 11:54:08: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:54:08: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:54:08: #1 total tags in treatment: 2297875 INFO @ Sat, 11 Dec 2021 11:54:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:54:08: #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 11:54:08: #1 tags after filtering in treatment: 2275124 INFO @ Sat, 11 Dec 2021 11:54:08: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:54:08: #1 finished! INFO @ Sat, 11 Dec 2021 11:54:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:54:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:54:08: #2 number of paired peaks: 122 WARNING @ Sat, 11 Dec 2021 11:54:08: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sat, 11 Dec 2021 11:54:08: start model_add_line... INFO @ Sat, 11 Dec 2021 11:54:08: start X-correlation... INFO @ Sat, 11 Dec 2021 11:54:08: end of X-cor INFO @ Sat, 11 Dec 2021 11:54:08: #2 finished! INFO @ Sat, 11 Dec 2021 11:54:08: #2 predicted fragment length is 262 bps INFO @ Sat, 11 Dec 2021 11:54:08: #2 alternative fragment length(s) may be 244,262,277 bps INFO @ Sat, 11 Dec 2021 11:54:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.10_model.r INFO @ Sat, 11 Dec 2021 11:54:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:54:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:54:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:54:15: 3000000 INFO @ Sat, 11 Dec 2021 11:54:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:54:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:54:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.10_summits.bed INFO @ Sat, 11 Dec 2021 11:54:15: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (53 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:54:23: 4000000 INFO @ Sat, 11 Dec 2021 11:54:31: 5000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:54:36: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:54:36: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:54:36: #1 total tags in treatment: 2297875 INFO @ Sat, 11 Dec 2021 11:54:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:54:36: #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 11:54:36: #1 tags after filtering in treatment: 2275124 INFO @ Sat, 11 Dec 2021 11:54:36: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:54:36: #1 finished! INFO @ Sat, 11 Dec 2021 11:54:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:54:36: #2 number of paired peaks: 122 WARNING @ Sat, 11 Dec 2021 11:54:36: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sat, 11 Dec 2021 11:54:36: start model_add_line... INFO @ Sat, 11 Dec 2021 11:54:36: start X-correlation... INFO @ Sat, 11 Dec 2021 11:54:36: end of X-cor INFO @ Sat, 11 Dec 2021 11:54:36: #2 finished! INFO @ Sat, 11 Dec 2021 11:54:36: #2 predicted fragment length is 262 bps INFO @ Sat, 11 Dec 2021 11:54:36: #2 alternative fragment length(s) may be 244,262,277 bps INFO @ Sat, 11 Dec 2021 11:54:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.20_model.r INFO @ Sat, 11 Dec 2021 11:54:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:54:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:54:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:54:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:54:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:54:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971695/SRX10971695.20_summits.bed INFO @ Sat, 11 Dec 2021 11:54:43: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (24 records, 4 fields): 1 millis CompletedMACS2peakCalling