Job ID = 14171320 SRX = SRX9005671 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 1411608 READS because READLEN < 1 Read 11020444 spots for SRR12515072/SRR12515072.sra Written 11020444 spots for SRR12515072/SRR12515072.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171884 ("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] 2 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] 1 unmatched pairs [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] 14 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1792270 / 8208613 = 0.2183 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 11:47:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.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 11:47:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:47:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:47:33: 1000000 INFO @ Sat, 11 Dec 2021 11:47:43: 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 11:47:52: 3000000 INFO @ Sat, 11 Dec 2021 11:47:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.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 11:47:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:47:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:48:03: 4000000 INFO @ Sat, 11 Dec 2021 11:48:05: 1000000 INFO @ Sat, 11 Dec 2021 11:48:13: 5000000 INFO @ Sat, 11 Dec 2021 11:48:16: 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 11:48:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.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 11:48:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:48:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:48:24: 6000000 INFO @ Sat, 11 Dec 2021 11:48:27: 3000000 INFO @ Sat, 11 Dec 2021 11:48:35: 1000000 INFO @ Sat, 11 Dec 2021 11:48:35: 7000000 INFO @ Sat, 11 Dec 2021 11:48:38: 4000000 INFO @ Sat, 11 Dec 2021 11:48:45: 2000000 INFO @ Sat, 11 Dec 2021 11:48:46: 8000000 INFO @ Sat, 11 Dec 2021 11:48:48: 5000000 INFO @ Sat, 11 Dec 2021 11:48:55: 3000000 INFO @ Sat, 11 Dec 2021 11:48:56: 9000000 INFO @ Sat, 11 Dec 2021 11:48:58: 6000000 INFO @ Sat, 11 Dec 2021 11:49:06: 4000000 INFO @ Sat, 11 Dec 2021 11:49:06: 10000000 INFO @ Sat, 11 Dec 2021 11:49:09: 7000000 INFO @ Sat, 11 Dec 2021 11:49:16: 5000000 INFO @ Sat, 11 Dec 2021 11:49:16: 11000000 INFO @ Sat, 11 Dec 2021 11:49:19: 8000000 INFO @ Sat, 11 Dec 2021 11:49:26: 6000000 INFO @ Sat, 11 Dec 2021 11:49:26: 12000000 INFO @ Sat, 11 Dec 2021 11:49:29: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:49:37: 13000000 INFO @ Sat, 11 Dec 2021 11:49:37: 7000000 INFO @ Sat, 11 Dec 2021 11:49:40: 10000000 INFO @ Sat, 11 Dec 2021 11:49:48: 8000000 INFO @ Sat, 11 Dec 2021 11:49:48: 14000000 INFO @ Sat, 11 Dec 2021 11:49:51: 11000000 INFO @ Sat, 11 Dec 2021 11:49:51: #1 tag size is determined as 124 bps INFO @ Sat, 11 Dec 2021 11:49:51: #1 tag size = 124 INFO @ Sat, 11 Dec 2021 11:49:51: #1 total tags in treatment: 6320425 INFO @ Sat, 11 Dec 2021 11:49:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:49:51: #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 11:49:51: #1 tags after filtering in treatment: 5346051 INFO @ Sat, 11 Dec 2021 11:49:51: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 11:49:51: #1 finished! INFO @ Sat, 11 Dec 2021 11:49:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:49:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:49:52: #2 number of paired peaks: 7295 INFO @ Sat, 11 Dec 2021 11:49:52: start model_add_line... INFO @ Sat, 11 Dec 2021 11:49:52: start X-correlation... INFO @ Sat, 11 Dec 2021 11:49:52: end of X-cor INFO @ Sat, 11 Dec 2021 11:49:52: #2 finished! INFO @ Sat, 11 Dec 2021 11:49:52: #2 predicted fragment length is 232 bps INFO @ Sat, 11 Dec 2021 11:49:52: #2 alternative fragment length(s) may be 232 bps INFO @ Sat, 11 Dec 2021 11:49:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.05_model.r WARNING @ Sat, 11 Dec 2021 11:49:52: #2 Since the d (232) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:49:52: #2 You may need to consider one of the other alternative d(s): 232 WARNING @ Sat, 11 Dec 2021 11:49:52: #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 11:49:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:49:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:49:58: 9000000 INFO @ Sat, 11 Dec 2021 11:50:02: 12000000 INFO @ Sat, 11 Dec 2021 11:50:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:50:08: 10000000 INFO @ Sat, 11 Dec 2021 11:50:13: 13000000 INFO @ Sat, 11 Dec 2021 11:50:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:50:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:50:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.05_summits.bed INFO @ Sat, 11 Dec 2021 11:50:14: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8172 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:50:19: 11000000 INFO @ Sat, 11 Dec 2021 11:50:24: 14000000 INFO @ Sat, 11 Dec 2021 11:50:27: #1 tag size is determined as 124 bps INFO @ Sat, 11 Dec 2021 11:50:27: #1 tag size = 124 INFO @ Sat, 11 Dec 2021 11:50:27: #1 total tags in treatment: 6320425 INFO @ Sat, 11 Dec 2021 11:50:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:50:27: #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 11:50:27: #1 tags after filtering in treatment: 5346051 INFO @ Sat, 11 Dec 2021 11:50:27: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 11:50:27: #1 finished! INFO @ Sat, 11 Dec 2021 11:50:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:50:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:50:28: #2 number of paired peaks: 7295 INFO @ Sat, 11 Dec 2021 11:50:28: start model_add_line... INFO @ Sat, 11 Dec 2021 11:50:28: start X-correlation... INFO @ Sat, 11 Dec 2021 11:50:28: end of X-cor INFO @ Sat, 11 Dec 2021 11:50:28: #2 finished! INFO @ Sat, 11 Dec 2021 11:50:28: #2 predicted fragment length is 232 bps INFO @ Sat, 11 Dec 2021 11:50:28: #2 alternative fragment length(s) may be 232 bps INFO @ Sat, 11 Dec 2021 11:50:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.10_model.r WARNING @ Sat, 11 Dec 2021 11:50:28: #2 Since the d (232) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:50:28: #2 You may need to consider one of the other alternative d(s): 232 WARNING @ Sat, 11 Dec 2021 11:50:28: #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 11:50:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:50:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:50:30: 12000000 INFO @ Sat, 11 Dec 2021 11:50:40: 13000000 INFO @ Sat, 11 Dec 2021 11:50:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:50:49: 14000000 INFO @ Sat, 11 Dec 2021 11:50:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:50:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:50:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.10_summits.bed INFO @ Sat, 11 Dec 2021 11:50:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6362 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:50:52: #1 tag size is determined as 124 bps INFO @ Sat, 11 Dec 2021 11:50:52: #1 tag size = 124 INFO @ Sat, 11 Dec 2021 11:50:52: #1 total tags in treatment: 6320425 INFO @ Sat, 11 Dec 2021 11:50:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:50:52: #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 11:50:52: #1 tags after filtering in treatment: 5346051 INFO @ Sat, 11 Dec 2021 11:50:52: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 11:50:52: #1 finished! INFO @ Sat, 11 Dec 2021 11:50:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:50:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:50:53: #2 number of paired peaks: 7295 INFO @ Sat, 11 Dec 2021 11:50:53: start model_add_line... INFO @ Sat, 11 Dec 2021 11:50:53: start X-correlation... INFO @ Sat, 11 Dec 2021 11:50:53: end of X-cor INFO @ Sat, 11 Dec 2021 11:50:53: #2 finished! INFO @ Sat, 11 Dec 2021 11:50:53: #2 predicted fragment length is 232 bps INFO @ Sat, 11 Dec 2021 11:50:53: #2 alternative fragment length(s) may be 232 bps INFO @ Sat, 11 Dec 2021 11:50:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.20_model.r WARNING @ Sat, 11 Dec 2021 11:50:53: #2 Since the d (232) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:50:53: #2 You may need to consider one of the other alternative d(s): 232 WARNING @ Sat, 11 Dec 2021 11:50:53: #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 11:50:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:50:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:51:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:51:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:51:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:51:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005671/SRX9005671.20_summits.bed INFO @ Sat, 11 Dec 2021 11:51:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4382 records, 4 fields): 6 millis CompletedMACS2peakCalling