Job ID = 14171381 SRX = SRX9005692 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 1584181 READS because READLEN < 1 Read 7577772 spots for SRR12515093/SRR12515093.sra Written 7577772 spots for SRR12515093/SRR12515093.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171876 ("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] 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] 24 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 65656 / 165403 = 0.3969 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 11:37:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.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 11:37:53: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:37:53: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:37:59: 1000000 INFO @ Sat, 11 Dec 2021 11:38:04: #1 tag size is determined as 97 bps INFO @ Sat, 11 Dec 2021 11:38:04: #1 tag size = 97 INFO @ Sat, 11 Dec 2021 11:38:04: #1 total tags in treatment: 94050 INFO @ Sat, 11 Dec 2021 11:38:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:38:04: #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 11:38:04: #1 tags after filtering in treatment: 90507 INFO @ Sat, 11 Dec 2021 11:38:04: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 11:38:04: #1 finished! INFO @ Sat, 11 Dec 2021 11:38:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:38:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:38:04: #2 number of paired peaks: 4760 INFO @ Sat, 11 Dec 2021 11:38:04: start model_add_line... INFO @ Sat, 11 Dec 2021 11:38:04: start X-correlation... INFO @ Sat, 11 Dec 2021 11:38:04: end of X-cor INFO @ Sat, 11 Dec 2021 11:38:04: #2 finished! INFO @ Sat, 11 Dec 2021 11:38:04: #2 predicted fragment length is 193 bps INFO @ Sat, 11 Dec 2021 11:38:04: #2 alternative fragment length(s) may be 193,292 bps INFO @ Sat, 11 Dec 2021 11:38:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.05_model.r WARNING @ Sat, 11 Dec 2021 11:38:04: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:38:04: #2 You may need to consider one of the other alternative d(s): 193,292 WARNING @ Sat, 11 Dec 2021 11:38:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:38:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:38:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:38:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:38:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:38:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:38:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.05_summits.bed INFO @ Sat, 11 Dec 2021 11:38:04: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (20 records, 4 fields): 12 millis CompletedMACS2peakCalling 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 11:38:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.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 11:38:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:38:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:38:31: 1000000 INFO @ Sat, 11 Dec 2021 11:38:36: #1 tag size is determined as 97 bps INFO @ Sat, 11 Dec 2021 11:38:36: #1 tag size = 97 INFO @ Sat, 11 Dec 2021 11:38:36: #1 total tags in treatment: 94050 INFO @ Sat, 11 Dec 2021 11:38:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:38:36: #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 11:38:36: #1 tags after filtering in treatment: 90507 INFO @ Sat, 11 Dec 2021 11:38:36: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 11:38:36: #1 finished! INFO @ Sat, 11 Dec 2021 11:38:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:38:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:38:37: #2 number of paired peaks: 4760 INFO @ Sat, 11 Dec 2021 11:38:37: start model_add_line... INFO @ Sat, 11 Dec 2021 11:38:37: start X-correlation... INFO @ Sat, 11 Dec 2021 11:38:37: end of X-cor INFO @ Sat, 11 Dec 2021 11:38:37: #2 finished! INFO @ Sat, 11 Dec 2021 11:38:37: #2 predicted fragment length is 193 bps INFO @ Sat, 11 Dec 2021 11:38:37: #2 alternative fragment length(s) may be 193,292 bps INFO @ Sat, 11 Dec 2021 11:38:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.10_model.r WARNING @ Sat, 11 Dec 2021 11:38:37: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:38:37: #2 You may need to consider one of the other alternative d(s): 193,292 WARNING @ Sat, 11 Dec 2021 11:38:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:38:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:38:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:38:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:38:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:38:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:38:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.10_summits.bed INFO @ Sat, 11 Dec 2021 11:38:37: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 9 millis CompletedMACS2peakCalling 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 11:38:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.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 11:38:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:38:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:38:59: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:39:04: #1 tag size is determined as 97 bps INFO @ Sat, 11 Dec 2021 11:39:04: #1 tag size = 97 INFO @ Sat, 11 Dec 2021 11:39:04: #1 total tags in treatment: 94050 INFO @ Sat, 11 Dec 2021 11:39:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:39:04: #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 11:39:04: #1 tags after filtering in treatment: 90507 INFO @ Sat, 11 Dec 2021 11:39:04: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 11:39:04: #1 finished! INFO @ Sat, 11 Dec 2021 11:39:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:39:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:39:04: #2 number of paired peaks: 4760 INFO @ Sat, 11 Dec 2021 11:39:04: start model_add_line... INFO @ Sat, 11 Dec 2021 11:39:04: start X-correlation... INFO @ Sat, 11 Dec 2021 11:39:04: end of X-cor INFO @ Sat, 11 Dec 2021 11:39:04: #2 finished! INFO @ Sat, 11 Dec 2021 11:39:04: #2 predicted fragment length is 193 bps INFO @ Sat, 11 Dec 2021 11:39:04: #2 alternative fragment length(s) may be 193,292 bps INFO @ Sat, 11 Dec 2021 11:39:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.20_model.r WARNING @ Sat, 11 Dec 2021 11:39:04: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:39:04: #2 You may need to consider one of the other alternative d(s): 193,292 WARNING @ Sat, 11 Dec 2021 11:39:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:39:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:39:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:39:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:39:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:39:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:39:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005692/SRX9005692.20_summits.bed INFO @ Sat, 11 Dec 2021 11:39:04: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling