Job ID = 14171344 SRX = SRX9005680 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 2140239 READS because READLEN < 1 Read 10826460 spots for SRR12515081/SRR12515081.sra Written 10826460 spots for SRR12515081/SRR12515081.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171885 ("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] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] 2 unmatched pairs [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] 1 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1115296 / 8253442 = 0.1351 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 11:46:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.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 11:46:16: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:46:16: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:46:23: 1000000 INFO @ Sat, 11 Dec 2021 11:46:30: 2000000 INFO @ Sat, 11 Dec 2021 11:46:37: 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 11:46:44: 4000000 INFO @ Sat, 11 Dec 2021 11:46:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.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 11:46:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:46:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:46:52: 5000000 INFO @ Sat, 11 Dec 2021 11:46:55: 1000000 INFO @ Sat, 11 Dec 2021 11:47:01: 6000000 INFO @ Sat, 11 Dec 2021 11:47:05: 2000000 INFO @ Sat, 11 Dec 2021 11:47:09: 7000000 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 11:47:15: 3000000 INFO @ Sat, 11 Dec 2021 11:47:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.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 11:47:16: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:47:16: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:47:18: 8000000 INFO @ Sat, 11 Dec 2021 11:47:24: 4000000 INFO @ Sat, 11 Dec 2021 11:47:24: 1000000 INFO @ Sat, 11 Dec 2021 11:47:26: 9000000 INFO @ Sat, 11 Dec 2021 11:47:33: 2000000 INFO @ Sat, 11 Dec 2021 11:47:34: 5000000 INFO @ Sat, 11 Dec 2021 11:47:35: 10000000 INFO @ Sat, 11 Dec 2021 11:47:41: 3000000 INFO @ Sat, 11 Dec 2021 11:47:43: 11000000 INFO @ Sat, 11 Dec 2021 11:47:44: 6000000 INFO @ Sat, 11 Dec 2021 11:47:50: 4000000 INFO @ Sat, 11 Dec 2021 11:47:52: 12000000 INFO @ Sat, 11 Dec 2021 11:47:54: 7000000 INFO @ Sat, 11 Dec 2021 11:47:59: 5000000 INFO @ Sat, 11 Dec 2021 11:48:00: 13000000 INFO @ Sat, 11 Dec 2021 11:48:04: 8000000 INFO @ Sat, 11 Dec 2021 11:48:07: 6000000 INFO @ Sat, 11 Dec 2021 11:48:09: 14000000 INFO @ Sat, 11 Dec 2021 11:48:14: 9000000 INFO @ Sat, 11 Dec 2021 11:48:16: 7000000 INFO @ Sat, 11 Dec 2021 11:48:17: 15000000 INFO @ Sat, 11 Dec 2021 11:48:24: 10000000 INFO @ Sat, 11 Dec 2021 11:48:24: 8000000 INFO @ Sat, 11 Dec 2021 11:48:26: 16000000 INFO @ Sat, 11 Dec 2021 11:48:27: #1 tag size is determined as 124 bps INFO @ Sat, 11 Dec 2021 11:48:27: #1 tag size = 124 INFO @ Sat, 11 Dec 2021 11:48:27: #1 total tags in treatment: 6974721 INFO @ Sat, 11 Dec 2021 11:48:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:48:27: #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 11:48:28: #1 tags after filtering in treatment: 5945929 INFO @ Sat, 11 Dec 2021 11:48:28: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 11:48:28: #1 finished! INFO @ Sat, 11 Dec 2021 11:48:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:48:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:48:28: #2 number of paired peaks: 5025 INFO @ Sat, 11 Dec 2021 11:48:28: start model_add_line... INFO @ Sat, 11 Dec 2021 11:48:28: start X-correlation... INFO @ Sat, 11 Dec 2021 11:48:28: end of X-cor INFO @ Sat, 11 Dec 2021 11:48:28: #2 finished! INFO @ Sat, 11 Dec 2021 11:48:28: #2 predicted fragment length is 310 bps INFO @ Sat, 11 Dec 2021 11:48:28: #2 alternative fragment length(s) may be 310 bps INFO @ Sat, 11 Dec 2021 11:48:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.05_model.r INFO @ Sat, 11 Dec 2021 11:48:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:48:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:48:33: 9000000 INFO @ Sat, 11 Dec 2021 11:48:34: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:48:41: 10000000 INFO @ Sat, 11 Dec 2021 11:48:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:48:44: 12000000 INFO @ Sat, 11 Dec 2021 11:48:49: 11000000 INFO @ Sat, 11 Dec 2021 11:48:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:48:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:48:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.05_summits.bed INFO @ Sat, 11 Dec 2021 11:48:51: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7561 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:48:54: 13000000 INFO @ Sat, 11 Dec 2021 11:48:58: 12000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:49:04: 14000000 INFO @ Sat, 11 Dec 2021 11:49:06: 13000000 INFO @ Sat, 11 Dec 2021 11:49:14: 15000000 INFO @ Sat, 11 Dec 2021 11:49:15: 14000000 INFO @ Sat, 11 Dec 2021 11:49:23: 16000000 INFO @ Sat, 11 Dec 2021 11:49:24: 15000000 INFO @ Sat, 11 Dec 2021 11:49:25: #1 tag size is determined as 124 bps INFO @ Sat, 11 Dec 2021 11:49:25: #1 tag size = 124 INFO @ Sat, 11 Dec 2021 11:49:25: #1 total tags in treatment: 6974721 INFO @ Sat, 11 Dec 2021 11:49:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:49:25: #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 11:49:26: #1 tags after filtering in treatment: 5945929 INFO @ Sat, 11 Dec 2021 11:49:26: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 11:49:26: #1 finished! INFO @ Sat, 11 Dec 2021 11:49:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:49:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:49:26: #2 number of paired peaks: 5025 INFO @ Sat, 11 Dec 2021 11:49:26: start model_add_line... INFO @ Sat, 11 Dec 2021 11:49:26: start X-correlation... INFO @ Sat, 11 Dec 2021 11:49:26: end of X-cor INFO @ Sat, 11 Dec 2021 11:49:26: #2 finished! INFO @ Sat, 11 Dec 2021 11:49:26: #2 predicted fragment length is 310 bps INFO @ Sat, 11 Dec 2021 11:49:26: #2 alternative fragment length(s) may be 310 bps INFO @ Sat, 11 Dec 2021 11:49:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.10_model.r INFO @ Sat, 11 Dec 2021 11:49:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:49:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:49:31: 16000000 INFO @ Sat, 11 Dec 2021 11:49:33: #1 tag size is determined as 124 bps INFO @ Sat, 11 Dec 2021 11:49:33: #1 tag size = 124 INFO @ Sat, 11 Dec 2021 11:49:33: #1 total tags in treatment: 6974721 INFO @ Sat, 11 Dec 2021 11:49:33: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:49:33: #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 11:49:33: #1 tags after filtering in treatment: 5945929 INFO @ Sat, 11 Dec 2021 11:49:33: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 11:49:33: #1 finished! INFO @ Sat, 11 Dec 2021 11:49:33: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:49:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:49:33: #2 number of paired peaks: 5025 INFO @ Sat, 11 Dec 2021 11:49:33: start model_add_line... INFO @ Sat, 11 Dec 2021 11:49:33: start X-correlation... INFO @ Sat, 11 Dec 2021 11:49:33: end of X-cor INFO @ Sat, 11 Dec 2021 11:49:33: #2 finished! INFO @ Sat, 11 Dec 2021 11:49:33: #2 predicted fragment length is 310 bps INFO @ Sat, 11 Dec 2021 11:49:33: #2 alternative fragment length(s) may be 310 bps INFO @ Sat, 11 Dec 2021 11:49:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.20_model.r INFO @ Sat, 11 Dec 2021 11:49:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:49:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:49:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:49:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:49:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:49:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:49:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.10_summits.bed INFO @ Sat, 11 Dec 2021 11:49:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5611 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:49:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:49:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:49:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005680/SRX9005680.20_summits.bed INFO @ Sat, 11 Dec 2021 11:49:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3504 records, 4 fields): 5 millis CompletedMACS2peakCalling