Job ID = 14167145 SRX = SRX10340454 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 985216 READS because READLEN < 1 Read 8197319 spots for SRR13962463/SRR13962463.sra Written 8197319 spots for SRR13962463/SRR13962463.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167679 ("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 8 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] 6 unmatched pairs [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] 8 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] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] 2 unmatched pairs [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1599492 / 6189162 = 0.2584 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 @ Fri, 10 Dec 2021 10:53:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.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 @ Fri, 10 Dec 2021 10:53:32: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:53:32: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:53:39: 1000000 INFO @ Fri, 10 Dec 2021 10:53:46: 2000000 INFO @ Fri, 10 Dec 2021 10:53:53: 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 @ Fri, 10 Dec 2021 10:54:00: 4000000 INFO @ Fri, 10 Dec 2021 10:54:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.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 @ Fri, 10 Dec 2021 10:54:02: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:54:02: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:54:07: 5000000 INFO @ Fri, 10 Dec 2021 10:54:09: 1000000 INFO @ Fri, 10 Dec 2021 10:54:15: 6000000 INFO @ Fri, 10 Dec 2021 10:54:17: 2000000 INFO @ Fri, 10 Dec 2021 10:54:22: 7000000 INFO @ Fri, 10 Dec 2021 10:54:25: 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 @ Fri, 10 Dec 2021 10:54:30: 8000000 INFO @ Fri, 10 Dec 2021 10:54:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.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 @ Fri, 10 Dec 2021 10:54:32: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:54:32: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:54:33: 4000000 INFO @ Fri, 10 Dec 2021 10:54:38: 9000000 INFO @ Fri, 10 Dec 2021 10:54:40: 1000000 INFO @ Fri, 10 Dec 2021 10:54:41: 5000000 INFO @ Fri, 10 Dec 2021 10:54:46: 10000000 INFO @ Fri, 10 Dec 2021 10:54:47: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 10:54:47: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 10:54:47: #1 total tags in treatment: 4331000 INFO @ Fri, 10 Dec 2021 10:54:47: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:54:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:54:47: #1 tags after filtering in treatment: 4265396 INFO @ Fri, 10 Dec 2021 10:54:47: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 10:54:47: #1 finished! INFO @ Fri, 10 Dec 2021 10:54:47: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:54:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:54:48: #2 number of paired peaks: 215 WARNING @ Fri, 10 Dec 2021 10:54:48: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Fri, 10 Dec 2021 10:54:48: start model_add_line... INFO @ Fri, 10 Dec 2021 10:54:48: start X-correlation... INFO @ Fri, 10 Dec 2021 10:54:48: end of X-cor INFO @ Fri, 10 Dec 2021 10:54:48: #2 finished! INFO @ Fri, 10 Dec 2021 10:54:48: #2 predicted fragment length is 278 bps INFO @ Fri, 10 Dec 2021 10:54:48: #2 alternative fragment length(s) may be 278 bps INFO @ Fri, 10 Dec 2021 10:54:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.05_model.r INFO @ Fri, 10 Dec 2021 10:54:48: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:54:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:54:48: 2000000 INFO @ Fri, 10 Dec 2021 10:54:49: 6000000 INFO @ Fri, 10 Dec 2021 10:54:56: 3000000 INFO @ Fri, 10 Dec 2021 10:54:56: 7000000 INFO @ Fri, 10 Dec 2021 10:54:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:55:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:55:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:55:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.05_summits.bed INFO @ Fri, 10 Dec 2021 10:55:02: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1057 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:55:04: 4000000 INFO @ Fri, 10 Dec 2021 10:55:04: 8000000 INFO @ Fri, 10 Dec 2021 10:55:11: 5000000 INFO @ Fri, 10 Dec 2021 10:55:12: 9000000 INFO @ Fri, 10 Dec 2021 10:55:19: 6000000 INFO @ Fri, 10 Dec 2021 10:55:20: 10000000 INFO @ Fri, 10 Dec 2021 10:55:21: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 10:55:21: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 10:55:21: #1 total tags in treatment: 4331000 INFO @ Fri, 10 Dec 2021 10:55:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:55:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:55:21: #1 tags after filtering in treatment: 4265396 INFO @ Fri, 10 Dec 2021 10:55:21: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 10:55:21: #1 finished! INFO @ Fri, 10 Dec 2021 10:55:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:55:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:55:22: #2 number of paired peaks: 215 WARNING @ Fri, 10 Dec 2021 10:55:22: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Fri, 10 Dec 2021 10:55:22: start model_add_line... INFO @ Fri, 10 Dec 2021 10:55:22: start X-correlation... INFO @ Fri, 10 Dec 2021 10:55:22: end of X-cor INFO @ Fri, 10 Dec 2021 10:55:22: #2 finished! INFO @ Fri, 10 Dec 2021 10:55:22: #2 predicted fragment length is 278 bps INFO @ Fri, 10 Dec 2021 10:55:22: #2 alternative fragment length(s) may be 278 bps INFO @ Fri, 10 Dec 2021 10:55:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.10_model.r INFO @ Fri, 10 Dec 2021 10:55:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:55:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:55:26: 7000000 INFO @ Fri, 10 Dec 2021 10:55:31: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:55:34: 8000000 INFO @ Fri, 10 Dec 2021 10:55:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:55:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:55:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.10_summits.bed INFO @ Fri, 10 Dec 2021 10:55:36: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (486 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:55:41: 9000000 INFO @ Fri, 10 Dec 2021 10:55:48: 10000000 INFO @ Fri, 10 Dec 2021 10:55:48: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 10:55:48: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 10:55:48: #1 total tags in treatment: 4331000 INFO @ Fri, 10 Dec 2021 10:55:48: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:55:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:55:49: #1 tags after filtering in treatment: 4265396 INFO @ Fri, 10 Dec 2021 10:55:49: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 10:55:49: #1 finished! INFO @ Fri, 10 Dec 2021 10:55:49: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:55:49: #2 number of paired peaks: 215 WARNING @ Fri, 10 Dec 2021 10:55:49: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Fri, 10 Dec 2021 10:55:49: start model_add_line... INFO @ Fri, 10 Dec 2021 10:55:49: start X-correlation... INFO @ Fri, 10 Dec 2021 10:55:49: end of X-cor INFO @ Fri, 10 Dec 2021 10:55:49: #2 finished! INFO @ Fri, 10 Dec 2021 10:55:49: #2 predicted fragment length is 278 bps INFO @ Fri, 10 Dec 2021 10:55:49: #2 alternative fragment length(s) may be 278 bps INFO @ Fri, 10 Dec 2021 10:55:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.20_model.r INFO @ Fri, 10 Dec 2021 10:55:49: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:55:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:55:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:56:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:56:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:56:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340454/SRX10340454.20_summits.bed INFO @ Fri, 10 Dec 2021 10:56:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (174 records, 4 fields): 1 millis CompletedMACS2peakCalling