Job ID = 14171009 SRX = SRX9005704 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 1215984 READS because READLEN < 1 Read 9866663 spots for SRR12515105/SRR12515105.sra Written 9866663 spots for SRR12515105/SRR12515105.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171527 ("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 12 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] 2 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] 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] 9 unmatched pairs [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] 1534347 / 7084797 = 0.2166 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 09:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.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 09:42:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:42:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:42:25: 1000000 INFO @ Sat, 11 Dec 2021 09:42:32: 2000000 INFO @ Sat, 11 Dec 2021 09:42:39: 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 09:42:46: 4000000 INFO @ Sat, 11 Dec 2021 09:42:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.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 09:42:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:42:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:42:54: 5000000 INFO @ Sat, 11 Dec 2021 09:42:56: 1000000 INFO @ Sat, 11 Dec 2021 09:43:02: 6000000 INFO @ Sat, 11 Dec 2021 09:43:05: 2000000 INFO @ Sat, 11 Dec 2021 09:43:10: 7000000 INFO @ Sat, 11 Dec 2021 09:43:13: 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 09:43:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.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 09:43:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:43:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:43:18: 8000000 INFO @ Sat, 11 Dec 2021 09:43:22: 4000000 INFO @ Sat, 11 Dec 2021 09:43:27: 1000000 INFO @ Sat, 11 Dec 2021 09:43:27: 9000000 INFO @ Sat, 11 Dec 2021 09:43:31: 5000000 INFO @ Sat, 11 Dec 2021 09:43:36: 10000000 INFO @ Sat, 11 Dec 2021 09:43:37: 2000000 INFO @ Sat, 11 Dec 2021 09:43:40: 6000000 INFO @ Sat, 11 Dec 2021 09:43:46: 11000000 INFO @ Sat, 11 Dec 2021 09:43:46: 3000000 INFO @ Sat, 11 Dec 2021 09:43:50: 7000000 INFO @ Sat, 11 Dec 2021 09:43:55: 12000000 INFO @ Sat, 11 Dec 2021 09:43:56: 4000000 INFO @ Sat, 11 Dec 2021 09:43:58: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 09:43:58: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 09:43:58: #1 total tags in treatment: 5395573 INFO @ Sat, 11 Dec 2021 09:43:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:43:58: #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 09:43:58: #1 tags after filtering in treatment: 4861958 INFO @ Sat, 11 Dec 2021 09:43:58: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 09:43:58: #1 finished! INFO @ Sat, 11 Dec 2021 09:43:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:43:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:43:58: #2 number of paired peaks: 4571 INFO @ Sat, 11 Dec 2021 09:43:58: start model_add_line... INFO @ Sat, 11 Dec 2021 09:43:58: start X-correlation... INFO @ Sat, 11 Dec 2021 09:43:59: end of X-cor INFO @ Sat, 11 Dec 2021 09:43:59: #2 finished! INFO @ Sat, 11 Dec 2021 09:43:59: #2 predicted fragment length is 220 bps INFO @ Sat, 11 Dec 2021 09:43:59: #2 alternative fragment length(s) may be 220 bps INFO @ Sat, 11 Dec 2021 09:43:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.05_model.r WARNING @ Sat, 11 Dec 2021 09:43:59: #2 Since the d (220) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:43:59: #2 You may need to consider one of the other alternative d(s): 220 WARNING @ Sat, 11 Dec 2021 09:43:59: #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 09:43:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:43:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:43:59: 8000000 INFO @ Sat, 11 Dec 2021 09:44:06: 5000000 INFO @ Sat, 11 Dec 2021 09:44:08: 9000000 INFO @ Sat, 11 Dec 2021 09:44:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:44:16: 6000000 INFO @ Sat, 11 Dec 2021 09:44:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:44:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:44:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.05_summits.bed INFO @ Sat, 11 Dec 2021 09:44:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6419 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:44:17: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:44:26: 7000000 INFO @ Sat, 11 Dec 2021 09:44:27: 11000000 INFO @ Sat, 11 Dec 2021 09:44:35: 8000000 INFO @ Sat, 11 Dec 2021 09:44:36: 12000000 INFO @ Sat, 11 Dec 2021 09:44:39: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 09:44:39: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 09:44:39: #1 total tags in treatment: 5395573 INFO @ Sat, 11 Dec 2021 09:44:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:44:39: #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 09:44:39: #1 tags after filtering in treatment: 4861958 INFO @ Sat, 11 Dec 2021 09:44:39: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 09:44:39: #1 finished! INFO @ Sat, 11 Dec 2021 09:44:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:44:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:44:40: #2 number of paired peaks: 4571 INFO @ Sat, 11 Dec 2021 09:44:40: start model_add_line... INFO @ Sat, 11 Dec 2021 09:44:40: start X-correlation... INFO @ Sat, 11 Dec 2021 09:44:40: end of X-cor INFO @ Sat, 11 Dec 2021 09:44:40: #2 finished! INFO @ Sat, 11 Dec 2021 09:44:40: #2 predicted fragment length is 220 bps INFO @ Sat, 11 Dec 2021 09:44:40: #2 alternative fragment length(s) may be 220 bps INFO @ Sat, 11 Dec 2021 09:44:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.10_model.r WARNING @ Sat, 11 Dec 2021 09:44:40: #2 Since the d (220) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:44:40: #2 You may need to consider one of the other alternative d(s): 220 WARNING @ Sat, 11 Dec 2021 09:44:40: #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 09:44:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:44:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:44:45: 9000000 INFO @ Sat, 11 Dec 2021 09:44:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:44:54: 10000000 INFO @ Sat, 11 Dec 2021 09:45:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:45:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:45:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.10_summits.bed INFO @ Sat, 11 Dec 2021 09:45:00: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4369 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:45:03: 11000000 INFO @ Sat, 11 Dec 2021 09:45:12: 12000000 INFO @ Sat, 11 Dec 2021 09:45:15: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 09:45:15: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 09:45:15: #1 total tags in treatment: 5395573 INFO @ Sat, 11 Dec 2021 09:45:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:45:15: #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 09:45:15: #1 tags after filtering in treatment: 4861958 INFO @ Sat, 11 Dec 2021 09:45:15: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 09:45:15: #1 finished! INFO @ Sat, 11 Dec 2021 09:45:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:45:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:45:16: #2 number of paired peaks: 4571 INFO @ Sat, 11 Dec 2021 09:45:16: start model_add_line... INFO @ Sat, 11 Dec 2021 09:45:16: start X-correlation... INFO @ Sat, 11 Dec 2021 09:45:16: end of X-cor INFO @ Sat, 11 Dec 2021 09:45:16: #2 finished! INFO @ Sat, 11 Dec 2021 09:45:16: #2 predicted fragment length is 220 bps INFO @ Sat, 11 Dec 2021 09:45:16: #2 alternative fragment length(s) may be 220 bps INFO @ Sat, 11 Dec 2021 09:45:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.20_model.r WARNING @ Sat, 11 Dec 2021 09:45:16: #2 Since the d (220) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:45:16: #2 You may need to consider one of the other alternative d(s): 220 WARNING @ Sat, 11 Dec 2021 09:45:16: #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 09:45:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:45:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:45:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:45:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:45:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:45:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005704/SRX9005704.20_summits.bed INFO @ Sat, 11 Dec 2021 09:45:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2655 records, 4 fields): 5 millis CompletedMACS2peakCalling