Job ID = 14171351 SRX = SRX9005686 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 1266681 READS because READLEN < 1 Read 9733181 spots for SRR12515087/SRR12515087.sra Written 9733181 spots for SRR12515087/SRR12515087.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171867 ("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] 1 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] 5 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 87618 / 298962 = 0.2931 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 11:37:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.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 11:37:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:37:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:38:04: 1000000 INFO @ Sat, 11 Dec 2021 11:38:18: 2000000 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 11:38:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.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 11:38:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:38:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:38:30: #1 tag size is determined as 97 bps INFO @ Sat, 11 Dec 2021 11:38:30: #1 tag size = 97 INFO @ Sat, 11 Dec 2021 11:38:30: #1 total tags in treatment: 202834 INFO @ Sat, 11 Dec 2021 11:38:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:38:30: #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 11:38:30: #1 tags after filtering in treatment: 188598 INFO @ Sat, 11 Dec 2021 11:38:30: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 11:38:30: #1 finished! INFO @ Sat, 11 Dec 2021 11:38:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:38:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:38:30: #2 number of paired peaks: 4614 INFO @ Sat, 11 Dec 2021 11:38:30: start model_add_line... INFO @ Sat, 11 Dec 2021 11:38:30: start X-correlation... INFO @ Sat, 11 Dec 2021 11:38:30: end of X-cor INFO @ Sat, 11 Dec 2021 11:38:30: #2 finished! INFO @ Sat, 11 Dec 2021 11:38:30: #2 predicted fragment length is 295 bps INFO @ Sat, 11 Dec 2021 11:38:30: #2 alternative fragment length(s) may be 295 bps INFO @ Sat, 11 Dec 2021 11:38:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.05_model.r INFO @ Sat, 11 Dec 2021 11:38:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:38:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:38:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:38:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:38:31: 1000000 INFO @ Sat, 11 Dec 2021 11:38:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:38:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.05_summits.bed INFO @ Sat, 11 Dec 2021 11:38:39: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (127 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:38:40: 2000000 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 11:38:49: #1 tag size is determined as 97 bps INFO @ Sat, 11 Dec 2021 11:38:49: #1 tag size = 97 INFO @ Sat, 11 Dec 2021 11:38:49: #1 total tags in treatment: 202834 INFO @ Sat, 11 Dec 2021 11:38:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:38:49: #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 11:38:49: #1 tags after filtering in treatment: 188598 INFO @ Sat, 11 Dec 2021 11:38:49: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 11:38:49: #1 finished! INFO @ Sat, 11 Dec 2021 11:38:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:38:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:38:49: #2 number of paired peaks: 4614 INFO @ Sat, 11 Dec 2021 11:38:49: start model_add_line... INFO @ Sat, 11 Dec 2021 11:38:49: start X-correlation... INFO @ Sat, 11 Dec 2021 11:38:49: end of X-cor INFO @ Sat, 11 Dec 2021 11:38:49: #2 finished! INFO @ Sat, 11 Dec 2021 11:38:49: #2 predicted fragment length is 295 bps INFO @ Sat, 11 Dec 2021 11:38:49: #2 alternative fragment length(s) may be 295 bps INFO @ Sat, 11 Dec 2021 11:38:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.10_model.r INFO @ Sat, 11 Dec 2021 11:38:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:38:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:38:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:38:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:38:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:38:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.10_summits.bed INFO @ Sat, 11 Dec 2021 11:38:50: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (50 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:38:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.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 11:38:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:38:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:39:05: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:39:20: 2000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:39:31: #1 tag size is determined as 97 bps INFO @ Sat, 11 Dec 2021 11:39:31: #1 tag size = 97 INFO @ Sat, 11 Dec 2021 11:39:31: #1 total tags in treatment: 202834 INFO @ Sat, 11 Dec 2021 11:39:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:39:31: #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 11:39:31: #1 tags after filtering in treatment: 188598 INFO @ Sat, 11 Dec 2021 11:39:31: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 11:39:31: #1 finished! INFO @ Sat, 11 Dec 2021 11:39:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:39:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:39:32: #2 number of paired peaks: 4614 INFO @ Sat, 11 Dec 2021 11:39:32: start model_add_line... INFO @ Sat, 11 Dec 2021 11:39:32: start X-correlation... INFO @ Sat, 11 Dec 2021 11:39:32: end of X-cor INFO @ Sat, 11 Dec 2021 11:39:32: #2 finished! INFO @ Sat, 11 Dec 2021 11:39:32: #2 predicted fragment length is 295 bps INFO @ Sat, 11 Dec 2021 11:39:32: #2 alternative fragment length(s) may be 295 bps INFO @ Sat, 11 Dec 2021 11:39:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.20_model.r INFO @ Sat, 11 Dec 2021 11:39:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:39:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:39:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:39:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:39:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:39:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005686/SRX9005686.20_summits.bed INFO @ Sat, 11 Dec 2021 11:39:33: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling