Job ID = 14171007 SRX = SRX9005703 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 1073229 READS because READLEN < 1 Read 8897610 spots for SRR12515104/SRR12515104.sra Written 8897610 spots for SRR12515104/SRR12515104.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171516 ("srTdm6") has been submitted Time loading reference: 00:00:01 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] 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] 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] 3 unmatched pairs [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] 1630547 / 6709957 = 0.2430 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 09:37:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.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 09:37:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:37:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:37:34: 1000000 INFO @ Sat, 11 Dec 2021 09:37:41: 2000000 INFO @ Sat, 11 Dec 2021 09:37:49: 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 09:37:56: 4000000 INFO @ Sat, 11 Dec 2021 09:37:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.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 09:37:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:37:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:38:03: 1000000 INFO @ Sat, 11 Dec 2021 09:38:04: 5000000 INFO @ Sat, 11 Dec 2021 09:38:09: 2000000 INFO @ Sat, 11 Dec 2021 09:38:11: 6000000 INFO @ Sat, 11 Dec 2021 09:38:16: 3000000 INFO @ Sat, 11 Dec 2021 09:38:19: 7000000 INFO @ Sat, 11 Dec 2021 09:38:22: 4000000 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 09:38:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.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 09:38:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:38:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:38:26: 8000000 INFO @ Sat, 11 Dec 2021 09:38:29: 5000000 INFO @ Sat, 11 Dec 2021 09:38:33: 1000000 INFO @ Sat, 11 Dec 2021 09:38:34: 9000000 INFO @ Sat, 11 Dec 2021 09:38:35: 6000000 INFO @ Sat, 11 Dec 2021 09:38:39: 2000000 INFO @ Sat, 11 Dec 2021 09:38:42: 7000000 INFO @ Sat, 11 Dec 2021 09:38:42: 10000000 INFO @ Sat, 11 Dec 2021 09:38:46: 3000000 INFO @ Sat, 11 Dec 2021 09:38:48: 8000000 INFO @ Sat, 11 Dec 2021 09:38:50: 11000000 INFO @ Sat, 11 Dec 2021 09:38:52: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 09:38:52: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 09:38:52: #1 total tags in treatment: 5004145 INFO @ Sat, 11 Dec 2021 09:38:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:38:52: #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 09:38:52: #1 tags after filtering in treatment: 4322339 INFO @ Sat, 11 Dec 2021 09:38:52: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 09:38:52: #1 finished! INFO @ Sat, 11 Dec 2021 09:38:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:38:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:38:52: #2 number of paired peaks: 5294 INFO @ Sat, 11 Dec 2021 09:38:52: start model_add_line... INFO @ Sat, 11 Dec 2021 09:38:52: 4000000 INFO @ Sat, 11 Dec 2021 09:38:52: start X-correlation... INFO @ Sat, 11 Dec 2021 09:38:52: end of X-cor INFO @ Sat, 11 Dec 2021 09:38:52: #2 finished! INFO @ Sat, 11 Dec 2021 09:38:52: #2 predicted fragment length is 221 bps INFO @ Sat, 11 Dec 2021 09:38:52: #2 alternative fragment length(s) may be 221 bps INFO @ Sat, 11 Dec 2021 09:38:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.05_model.r WARNING @ Sat, 11 Dec 2021 09:38:52: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:38:52: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Sat, 11 Dec 2021 09:38:52: #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 09:38:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:38:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:38:55: 9000000 INFO @ Sat, 11 Dec 2021 09:38:59: 5000000 INFO @ Sat, 11 Dec 2021 09:39:01: 10000000 INFO @ Sat, 11 Dec 2021 09:39:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:39:05: 6000000 INFO @ Sat, 11 Dec 2021 09:39:07: 11000000 INFO @ Sat, 11 Dec 2021 09:39:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:39:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:39:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.05_summits.bed INFO @ Sat, 11 Dec 2021 09:39:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6425 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:39:09: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 09:39:09: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 09:39:09: #1 total tags in treatment: 5004145 INFO @ Sat, 11 Dec 2021 09:39:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:39:09: #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 09:39:09: #1 tags after filtering in treatment: 4322339 INFO @ Sat, 11 Dec 2021 09:39:09: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 09:39:09: #1 finished! INFO @ Sat, 11 Dec 2021 09:39:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:39:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:39:10: #2 number of paired peaks: 5294 INFO @ Sat, 11 Dec 2021 09:39:10: start model_add_line... INFO @ Sat, 11 Dec 2021 09:39:10: start X-correlation... INFO @ Sat, 11 Dec 2021 09:39:10: end of X-cor INFO @ Sat, 11 Dec 2021 09:39:10: #2 finished! INFO @ Sat, 11 Dec 2021 09:39:10: #2 predicted fragment length is 221 bps INFO @ Sat, 11 Dec 2021 09:39:10: #2 alternative fragment length(s) may be 221 bps INFO @ Sat, 11 Dec 2021 09:39:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.10_model.r WARNING @ Sat, 11 Dec 2021 09:39:10: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:39:10: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Sat, 11 Dec 2021 09:39:10: #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 09:39:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:39:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:39:11: 7000000 INFO @ Sat, 11 Dec 2021 09:39:17: 8000000 INFO @ Sat, 11 Dec 2021 09:39:21: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:39:23: 9000000 INFO @ Sat, 11 Dec 2021 09:39:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:39:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:39:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.10_summits.bed INFO @ Sat, 11 Dec 2021 09:39:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4707 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:39:30: 10000000 INFO @ Sat, 11 Dec 2021 09:39:36: 11000000 INFO @ Sat, 11 Dec 2021 09:39:37: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 09:39:37: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 09:39:37: #1 total tags in treatment: 5004145 INFO @ Sat, 11 Dec 2021 09:39:37: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:39:37: #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 09:39:37: #1 tags after filtering in treatment: 4322339 INFO @ Sat, 11 Dec 2021 09:39:37: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 09:39:37: #1 finished! INFO @ Sat, 11 Dec 2021 09:39:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:39:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:39:38: #2 number of paired peaks: 5294 INFO @ Sat, 11 Dec 2021 09:39:38: start model_add_line... INFO @ Sat, 11 Dec 2021 09:39:38: start X-correlation... INFO @ Sat, 11 Dec 2021 09:39:38: end of X-cor INFO @ Sat, 11 Dec 2021 09:39:38: #2 finished! INFO @ Sat, 11 Dec 2021 09:39:38: #2 predicted fragment length is 221 bps INFO @ Sat, 11 Dec 2021 09:39:38: #2 alternative fragment length(s) may be 221 bps INFO @ Sat, 11 Dec 2021 09:39:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.20_model.r WARNING @ Sat, 11 Dec 2021 09:39:38: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:39:38: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Sat, 11 Dec 2021 09:39:38: #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 09:39:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:39:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:39:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:39:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:39:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:39:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005703/SRX9005703.20_summits.bed INFO @ Sat, 11 Dec 2021 09:39:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3178 records, 4 fields): 5 millis CompletedMACS2peakCalling